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@article{DBLP:journals/bioinformatics/0038NT23,
author = {Qi Wang and
Michael Nute and
Todd J. Treangen},
title = {Bakdrive: identifying a minimum set of bacterial species driving interactions
across multiple microbial communities},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {47--56},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad236},
doi = {10.1093/BIOINFORMATICS/BTAD236},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/0038NT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbbasRTC23,
author = {Zeeshan Abbas and
Mobeen Ur Rehman and
Hilal Tayara and
Kil To Chong},
title = {ORI-Explorer: a unified cell-specific tool for origin of replication
sites prediction by feature fusion},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad664},
doi = {10.1093/BIOINFORMATICS/BTAD664},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbbasRTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbdelRehimOLNK23,
author = {Abbi Abdel{-}Rehim and
Oghenejokpeme I. Orhobor and
Hang Lou and
Hao Ni and
Ross D. King},
title = {Protein-ligand binding affinity prediction exploiting sequence constituent
homology},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad502},
doi = {10.1093/BIOINFORMATICS/BTAD502},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbdelRehimOLNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbidB23,
author = {Dhoha Abid and
Michael R. Brent},
title = {NetProphet 3: a machine learning framework for transcription factor
network mapping and multi-omics integration},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad038},
doi = {10.1093/BIOINFORMATICS/BTAD038},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbidB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbrahamLBRC23,
author = {Abin Abraham and
Abigail L. Labella and
Mary Lauren Benton and
Antonis Rokas and
John A. Capra},
title = {{GSEL:} a fast, flexible python package for detecting signatures of
diverse evolutionary forces on genomic regions},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad037},
doi = {10.1093/BIOINFORMATICS/BTAD037},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbrahamLBRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AdamerRBB23,
author = {Michael F. Adamer and
Eljas Roellin and
Lucie Bourguignon and
Karsten M. Borgwardt},
title = {{SIMBSIG:} similarity search and clustering for biobank-scale data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac829},
doi = {10.1093/BIOINFORMATICS/BTAC829},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AdamerRBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AgarwalC23,
author = {Aman Agarwal and
Li Chen},
title = {DeepPHiC: predicting promoter-centered chromatin interactions using
a novel deep learning approach},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac801},
doi = {10.1093/BIOINFORMATICS/BTAC801},
timestamp = {Wed, 11 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AgarwalC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AgarwalZJC23,
author = {Aman Agarwal and
Fengdi Zhao and
Yuchao Jiang and
Li Chen},
title = {TIVAN-indel: a computational framework for annotating and predicting
non-coding regulatory small insertions and deletions},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad060},
doi = {10.1093/BIOINFORMATICS/BTAD060},
timestamp = {Wed, 11 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AgarwalZJC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AguadoPuigDMEMMM23,
author = {Quim Aguado{-}Puig and
Max Doblas and
Christos Matzoros and
Antonio Espinosa and
Juan Carlos Moure and
Santiago Marco{-}Sola and
Miquel Moret{\'{o}}},
title = {{WFA-GPU:} gap-affine pairwise read-alignment using GPUs},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad701},
doi = {10.1093/BIOINFORMATICS/BTAD701},
timestamp = {Tue, 10 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AguadoPuigDMEMMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AguileraMendozaAMCGBM23,
author = {Longendri Aguilera{-}Mendoza and
Sebasti{\'{a}}n Ayala{-}Ruano and
Felix Martinez{-}Rios and
Edgar Ch{\'{a}}vez and
C{\'{e}}sar R. Garc{\'{\i}}a{-}Jacas and
Carlos A. Brizuela and
Yovani Marrero{-}Ponce},
title = {\emph{StarPep Toolbox}: an open-source software to assist chemical
space analysis of bioactive peptides and their functions using complex
networks},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad506},
doi = {10.1093/BIOINFORMATICS/BTAD506},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AguileraMendozaAMCGBM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlamoudiSMSBGBH23,
author = {Emad Alamoudi and
Yannik Sch{\"{a}}lte and
Robert M{\"{u}}ller and
J{\"{o}}rn Starru{\ss} and
Nils Bundgaard and
Frederik Graw and
Lutz Brusch and
Jan Hasenauer},
title = {FitMultiCell: simulating and parameterizing computational models of
multi-scale and multi-cellular processes},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad674},
doi = {10.1093/BIOINFORMATICS/BTAD674},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlamoudiSMSBGBH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlankoVMP23,
author = {Jarno N. Alanko and
Jaakko Vuohtoniemi and
Tommi M{\"{a}}klin and
Simon J. Puglisi},
title = {Themisto: a scalable colored \emph{k}-mer index for sensitive pseudoalignment
against hundreds of thousands of bacterial genomes},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {260--269},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad233},
doi = {10.1093/BIOINFORMATICS/BTAD233},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlankoVMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlemanyChavarriaRM23,
author = {Merc{\`{e}} Alemany{-}Chavarria and
Jaime Rodr{\'{\i}}guez{-}Guerra and
Jean{-}Didier Mar{\'{e}}chal},
title = {{TALAIA:} a 3D visual dictionary for protein structures},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad476},
doi = {10.1093/BIOINFORMATICS/BTAD476},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlemanyChavarriaRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlmeidaSilvaZUSP23,
author = {Fabricio Almeida{-}Silva and
Tao Zhao and
Kristian K. Ullrich and
M. Eric Schranz and
Yves Van de Peer},
title = {syntenet: an R/Bioconductor package for the inference and analysis
of synteny networks},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac806},
doi = {10.1093/BIOINFORMATICS/BTAC806},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlmeidaSilvaZUSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AmarasingheASBL23,
author = {Piyumi R. Amarasinghe and
Lloyd Allison and
Peter J. Stuckey and
Maria Garcia de la Banda and
Arthur M. Lesk and
Arun Siddharth Konagurthu},
title = {Getting '{\(\phi\)}{\(\psi\)}{\(\chi\)}al' with proteins: minimum
message length inference of joint distributions of backbone and sidechain
dihedral angles},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {357--367},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad251},
doi = {10.1093/BIOINFORMATICS/BTAD251},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AmarasingheASBL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AmatriaBarralGT23,
author = {I{\~{n}}aki Amatria{-}Barral and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Juan Touri{\~{n}}o},
title = {{PATO:} genome-wide prediction of lncRNA-DNA triple helices},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad134},
doi = {10.1093/BIOINFORMATICS/BTAD134},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AmatriaBarralGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AnJPLKC23,
author = {Sugyun An and
Soyeong Jang and
Sang{-}Min Park and
Chun{-}Kyung Lee and
Hoon{-}Min Kim and
Kwang{-}Hyun Cho},
title = {Global stabilizing control of large-scale biomolecular regulatory
networks},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad045},
doi = {10.1093/BIOINFORMATICS/BTAD045},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AnJPLKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ApollonioBCFS23,
author = {Nicola Apollonio and
Daniel Blankenberg and
Fabio Cumbo and
Paolo Giulio Franciosa and
Daniele Santoni},
title = {Evaluating homophily in networks via \emph{HONTO} (HOmophily Network
TOol): a case study of chromosomal interactions in human {PPI} networks},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac763},
doi = {10.1093/BIOINFORMATICS/BTAC763},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ApollonioBCFS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AriasHK23,
author = {Pablo Millan Arias and
Kathleen A. Hill and
Lila Kari},
title = {\emph{i}DeLUCS: a deep learning interactive tool for alignment-free
clustering of {DNA} sequences},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad508},
doi = {10.1093/BIOINFORMATICS/BTAD508},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AriasHK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ArmstrongC23,
author = {Ellie E. Armstrong and
Michael G. Campana},
title = {RatesTools: a Nextflow pipeline for detecting \emph{de novo} germline
mutations in pedigree sequence data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac784},
doi = {10.1093/BIOINFORMATICS/BTAC784},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ArmstrongC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AsadaMS23,
author = {Masaki Asada and
Makoto Miwa and
Yutaka Sasaki},
title = {Integrating heterogeneous knowledge graphs into drug-drug interaction
extraction from the literature},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac754},
doi = {10.1093/BIOINFORMATICS/BTAC754},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AsadaMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AuFLMSSWSL23,
author = {Eric H. Au and
Christiana Fauci and
Yanting Luo and
Riley J. Mangan and
Daniel A Snellings and
Chelsea R. Shoben and
Seth Weaver and
Shae K. Simpson and
Craig B. Lowe},
title = {Gonomics: uniting high performance and readability for genomics with
Go},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad516},
doi = {10.1093/BIOINFORMATICS/BTAD516},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AuFLMSSWSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AusmeesN23,
author = {Kristiina Ausmees and
Carl Nettelblad},
title = {Achieving improved accuracy for imputation of ancient {DNA}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac738},
doi = {10.1093/BIOINFORMATICS/BTAC738},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AusmeesN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AwasthiCLHRA23,
author = {Swapnil Awasthi and
Chia{-}Yen Chen and
Max Lam and
Hailiang Huang and
Stephan Ripke and
C. Anthony Altar},
title = {{GWAS} quality score for evaluating associated regions in {GWAS} analyses},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad004},
doi = {10.1093/BIOINFORMATICS/BTAD004},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AwasthiCLHRA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AylwardPMHM23,
author = {Anthony J. Aylward and
Semar Petrus and
Allen Mamerto and
Nolan T. Hartwick and
Todd P. Michael},
title = {PanKmer: \emph{k}-mer-based and reference-free pangenome analysis},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad621},
doi = {10.1093/BIOINFORMATICS/BTAD621},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AylwardPMHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AytonT23,
author = {Sarah G. Ayton and
Victor Trevi{\~{n}}o},
title = {MuTATE - an {R} package for comprehensive multi-objective molecular
modeling},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad507},
doi = {10.1093/BIOINFORMATICS/BTAD507},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AytonT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BadeltLH23,
author = {Stefan Badelt and
Ronny Lorenz and
Ivo L. Hofacker},
title = {\texttt{DrTransformer}: heuristic cotranscriptional {RNA} folding
using the nearest neighbor energy model},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad034},
doi = {10.1093/BIOINFORMATICS/BTAD034},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BadeltLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BadshahC23,
author = {Irbaz I Badshah and
Pedro R. Cutillas},
title = {Systematic identification of biochemical networks in cancer cells
by functional pathway inference analysis},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac769},
doi = {10.1093/BIOINFORMATICS/BTAC769},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BadshahC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BafnaLZ23,
author = {Mihir Bafna and
Hechen Li and
Xiuwei Zhang},
title = {{CLARIFY:} cell-cell interaction and gene regulatory network refinement
from spatially resolved transcriptomics},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {484--493},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad269},
doi = {10.1093/BIOINFORMATICS/BTAD269},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BafnaLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Balci1EBKC23,
author = {Ali Tugrul Balci and
Mark Maher Ebeid and
Panayiotis V. Benos and
Dennis Kostka and
Maria Chikina},
title = {An intrinsically interpretable neural network architecture for sequence-to-function
learning},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {413--422},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad271},
doi = {10.1093/BIOINFORMATICS/BTAD271},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Balci1EBKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BanjacSD23,
author = {Jelena Banjac and
Norbert Sprenger and
Shaillay Kumar Dogra},
title = {Microbiome Toolbox: methodological approaches to derive and visualize
microbiome trajectories},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac781},
doi = {10.1093/BIOINFORMATICS/BTAC781},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BanjacSD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BarnettSRSJW23,
author = {Joshua Barnett and
Noori Sotudeh and
Poorvi Rao and
Jonah Silverman and
Tamara Jafar and
Liya Wang},
title = {AtlasXplore: a web platform for visualizing and sharing spatial epigenome
data},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad447},
doi = {10.1093/BIOINFORMATICS/BTAD447},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BarnettSRSJW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BarteriVFJMEN23,
author = {Fabio Barteri and
Alejandro Valenzuela and
Xavier Farr{\'{e}} and
David de Juan and
Gerard Muntan{\'{e}} and
Borja Esteve{-}Altava and
Arcadi Navarro},
title = {CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad623},
doi = {10.1093/BIOINFORMATICS/BTAD623},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BarteriVFJMEN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BastollaAP23,
author = {Ugo Bastolla and
David Abia and
Oscar Piette},
title = {PC{\_}ali: a tool for improved multiple alignments and evolutionary
inference based on a hybrid protein sequence and structure similarity
score},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad630},
doi = {10.1093/BIOINFORMATICS/BTAD630},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BastollaAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BeaudeVAZH23,
author = {Aur{\'{e}}lien Beaude and
Milad Rafiee Vahid and
Franck Aug{\'{e}} and
Farida Zehraoui and
Blaise Hanczar},
title = {AttOmics: attention-based architecture for diagnosis and prognosis
from omics data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {94--102},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad232},
doi = {10.1093/BIOINFORMATICS/BTAD232},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BeaudeVAZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BehbahaniLC23,
author = {Yasser Mohseni Behbahani and
Elodie Laine and
Alessandra Carbone},
title = {Deep Local Analysis deconstructs protein-protein interfaces and accurately
estimates binding affinity changes upon mutation},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {544--552},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad231},
doi = {10.1093/BIOINFORMATICS/BTAD231},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BehbahaniLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BenesBHPS23,
author = {Nikola Benes and
Lubos Brim and
Ondrej Huvar and
Samuel Pastva and
David Safr{\'{a}}nek},
title = {Boolean network sketches: a unifying framework for logical model inference},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad158},
doi = {10.1093/BIOINFORMATICS/BTAD158},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BenesBHPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BenjaminKP23,
author = {Kynon J. M. Benjamin and
Tarun Katipalli and
Apu{\~{a}} C. M. Paquola},
title = {dRFEtools: dynamic recursive feature elimination for omics},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad513},
doi = {10.1093/BIOINFORMATICS/BTAD513},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BenjaminKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BhallaSPTVCDNTRCKPNW23,
author = {Diksha Bhalla and
Marvin N. Steijaert and
Eefje S. Poppelaars and
Marc Teunis and
Monique van der Voet and
Marie Corradi and
Elisabeth D{\'{e}}vi{\`{e}}re and
Luke Noothout and
Wilco Tomassen and
Martijn Rooseboom and
Richard A. Currie and
Cyrille Krul and
Raymond H. H. Pieters and
Vera van Noort and
Marjolein Wildwater},
title = {DARTpaths, an \emph{in silico} platform to investigate molecular mechanisms
of compounds},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac767},
doi = {10.1093/BIOINFORMATICS/BTAC767},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BhallaSPTVCDNTRCKPNW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiLZW23,
author = {Xuehua Bi and
Weiyang Liang and
Qichang Zhao and
Jianxin Wang},
title = {SSLpheno: a self-supervised learning approach for gene-phenotype association
prediction using protein-protein interactions and gene ontology data},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad662},
doi = {10.1093/BIOINFORMATICS/BTAD662},
timestamp = {Mon, 26 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiLZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiancaIGLFT23,
author = {Federico Bianca and
Emilio Ispano and
Ermanno Gazzola and
Enrico Lavezzo and
Paolo Fontana and
Stefano Toppo},
title = {FunTaxIS-lite: a simple and light solution to investigate protein
functions in all living organisms},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad549},
doi = {10.1093/BIOINFORMATICS/BTAD549},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiancaIGLFT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiffignandiBPSZBBCG23,
author = {Gherard Batisti Biffignandi and
Greta Bellinzona and
Greta Petazzoni and
Davide Sassera and
Gianvincenzo Zuccotti and
Claudio Bandi and
Fausto Baldanti and
Francesco Comandatore and
Stefano Gaiarsa},
title = {P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks
using genomics},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad571},
doi = {10.1093/BIOINFORMATICS/BTAD571},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiffignandiBPSZBBCG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiharieMRM23,
author = {Kirti Biharie and
Lieke Michielsen and
Marcel J. T. Reinders and
Ahmed Mahfouz},
title = {Cell type matching across species using protein embeddings and transfer
learning},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {404--412},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad248},
doi = {10.1093/BIOINFORMATICS/BTAD248},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiharieMRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BinetAFM23,
author = {Thomas Binet and
B{\'{e}}rang{\`{e}}re Avalle and
Miraine D{\'{a}}vila Felipe and
Irene Maffucci},
title = {AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides
secondary structures},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac752},
doi = {10.1093/BIOINFORMATICS/BTAC752},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BinetAFM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BoaduCC23,
author = {Frimpong Boadu and
Hongyuan Cao and
Jianlin Cheng},
title = {Combining protein sequences and structures with transformers and equivariant
graph neural networks to predict protein function},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {318--325},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad208},
doi = {10.1093/BIOINFORMATICS/BTAD208},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BoaduCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BodinierVRFCC23,
author = {Barbara Bodinier and
Dragana Vuckovic and
Sabrina Rodrigues and
Sarah Filippi and
Julien Chiquet and
Marc Chadeau{-}Hyam},
title = {Automated calibration of consensus weighted distance-based clustering
approaches using sharp},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad635},
doi = {10.1093/BIOINFORMATICS/BTAD635},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BodinierVRFCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BonioloHRTBCRSL23,
author = {Fabio Boniolo and
Markus Hoffmann and
Norman Roggendorf and
Bahar Tercan and
Jan Baumbach and
Mauro A. A. Castro and
A. Gordon Robertson and
Dieter Saur and
Markus List},
title = {spongEffects: ceRNA modules offer patient-specific insights into the
miRNA regulatory landscape},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad276},
doi = {10.1093/BIOINFORMATICS/BTAD276},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BonioloHRTBCRSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BorelliAFDLS23,
author = {Tiago Cabral Borelli and
Gabriel Santos Arini and
Lu{\'{\i}}s G. P. Feitosa and
Pieter C. Dorrestein and
Norberto Peporine Lopes and
Ricardo Roberto da Silva},
title = {Improving annotation propagation on molecular networks through random
walks: introducing ChemWalker},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad078},
doi = {10.1093/BIOINFORMATICS/BTAD078},
timestamp = {Tue, 16 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BorelliAFDLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BorgCR23,
author = {Jean{-}Pierre Borg and
Jacques Colinge and
Patrice Ravel},
title = {Modular response analysis reformulated as a multilinear regression
problem},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad166},
doi = {10.1093/BIOINFORMATICS/BTAD166},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BorgCR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BorzouGIEG23,
author = {Pooya Borzou and
Jafar Ghaisari and
Iman Izadi and
Yasin Eshraghi and
Yousof Gheisari},
title = {A novel strategy for dynamic modeling of genome-scale interaction
networks},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad079},
doi = {10.1093/BIOINFORMATICS/BTAD079},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BorzouGIEG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BourasNHPWV23,
author = {George Bouras and
Roshan Nepal and
Ghais Houtak and
Alkis James Psaltis and
Peter{-}John Wormald and
Sarah Vreugde},
title = {Pharokka: a fast scalable bacteriophage annotation tool},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac776},
doi = {10.1093/BIOINFORMATICS/BTAC776},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BourasNHPWV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BraistedPTSNSEM23,
author = {John C. Braisted and
Andrew Patt and
Cole Tindall and
Timothy Sheils and
Jorge Neyra and
Kyle Spencer and
Tara Eicher and
Ewy A Math{\'{e}}},
title = {RaMP-DB 2.0: a renovated knowledgebase for deriving biological and
chemical insight from metabolites, proteins, and genes},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac726},
doi = {10.1093/BIOINFORMATICS/BTAC726},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BraistedPTSNSEM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuWL23,
author = {Deliang Bu and
Xiao Wang and
Qizhai Li},
title = {Summary statistics-based association test for identifying the pleiotropic
effects with set of genetic variants},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad182},
doi = {10.1093/BIOINFORMATICS/BTAD182},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuchlerOO23,
author = {Thomas B{\"{u}}chler and
Jannik Olbrich and
Enno Ohlebusch},
title = {Efficient short read mapping to a pangenome that is represented by
a graph of {ED} strings},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad320},
doi = {10.1093/BIOINFORMATICS/BTAD320},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuchlerOO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuchnerCGZ23,
author = {Bianca A. Buchner and
Tom J. Clement and
Daan H. de Groot and
J{\"{u}}rgen Zanghellini},
title = {\texttt{ecmtool}: fast and memory-efficient enumeration of elementary
conversion modes},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad095},
doi = {10.1093/BIOINFORMATICS/BTAD095},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuchnerCGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuckSFSKOZADGS23,
author = {Lena Buck and
Tobias Schmidt and
Maren Feist and
Philipp Schwarzfischer and
Dieter Kube and
Peter J. Oefner and
Helena U. Zacharias and
Michael Altenbuchinger and
Katja Dettmer and
Wolfram Gronwald and
Rainer Spang},
title = {Anomaly detection in mixed high-dimensional molecular data},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad501},
doi = {10.1093/BIOINFORMATICS/BTAD501},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuckSFSKOZADGS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BurdziakZHALP23,
author = {Cassandra Burdziak and
Chujun Julia Zhao and
Doron Haviv and
Direna Alonso{-}Curbelo and
Scott W. Lowe and
Dana Pe'er},
title = {scKINETICS: inference of regulatory velocity with single-cell transcriptomics
data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {394--403},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad267},
doi = {10.1093/BIOINFORMATICS/BTAD267},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BurdziakZHALP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BurtonCMAE23,
author = {Ross J. Burton and
Simone M. Cuff and
Matt P. Morgan and
Andreas Artemiou and
Matthias Eberl},
title = {GeoWaVe: geometric median clustering with weighted voting for ensemble
clustering of cytometry data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac751},
doi = {10.1093/BIOINFORMATICS/BTAC751},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BurtonCMAE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ButonCC23,
author = {Nicolas Buton and
Fran{\c{c}}ois Coste and
Yann Le Cunff},
title = {Predicting enzymatic function of protein sequences with attention},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad620},
doi = {10.1093/BIOINFORMATICS/BTAD620},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ButonCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CalgaroRRV23,
author = {Matteo Calgaro and
Chiara Romualdi and
Davide Risso and
Nicola Vitulo},
title = {benchdamic: benchmarking of differential abundance methods for microbiome
data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac778},
doi = {10.1093/BIOINFORMATICS/BTAC778},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CalgaroRRV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CallaghanXXCRZJYNHAPWS23,
author = {Jackson Callaghan and
Colleen H. Xu and
Jiwen Xin and
Marco Alvarado Cano and
Anders Riutta and
Eric Zhou and
Rohan Juneja and
Yao Yao and
Madhumita Narayan and
Kristina Hanspers and
Ayushi Agrawal and
Alexander R. Pico and
Chunlei Wu and
Andrew I. Su},
title = {BioThings Explorer: a query engine for a federated knowledge graph
of biomedical APIs},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad570},
doi = {10.1093/BIOINFORMATICS/BTAD570},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CallaghanXXCRZJYNHAPWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CamachoVMG23,
author = {Jos{\'{e}} Camacho and
Raffaele Vitale and
David Morales{-}Jim{\'{e}}nez and
Carolina G{\'{o}}mez{-}Llorente},
title = {Variable-selection {ANOVA} Simultaneous Component Analysis {(VASCA)}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac795},
doi = {10.1093/BIOINFORMATICS/BTAC795},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CamachoVMG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CansonDHPGKS23,
author = {Daffodil M. Canson and
Aimee L. Davidson and
Miguel de la Hoya and
Michael T. Parsons and
Dylan M. Glubb and
Olga Kondrashova and
Amanda B. Spurdle},
title = {SpliceAI-10k calculator for the prediction of pseudoexonization, intron
retention, and exon deletion},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad179},
doi = {10.1093/BIOINFORMATICS/BTAD179},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CansonDHPGKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CastorinaPSW23,
author = {Leonardo V. Castorina and
Rokas Petrenas and
Kartic Subr and
Christopher W. Wood},
title = {PDBench: evaluating computational methods for protein-sequence design},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad027},
doi = {10.1093/BIOINFORMATICS/BTAD027},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CastorinaPSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaucheteurPRGMMAOPR23,
author = {D{\'{e}}borah Caucheteur and
Zo{\"{e}} May Pendlington and
Paola Roncaglia and
Julien Gobeill and
Luc Mottin and
Nicolas Matentzoglu and
Donat Agosti and
David Osumi{-}Sutherland and
Helen E. Parkinson and
Patrick Ruch},
title = {COVoc and COVTriage: novel resources to support literature triage},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac800},
doi = {10.1093/BIOINFORMATICS/BTAC800},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaucheteurPRGMMAOPR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChanZM23,
author = {Trevor J. Chan and
Xingjian Zhang and
Michael Mak},
title = {Biophysical informatics reveals distinctive phenotypic signatures
and functional diversity of single-cell lineages},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac833},
doi = {10.1093/BIOINFORMATICS/BTAC833},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChanZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChangGHCS23,
author = {Daniel Chang and
Vinod K. Gupta and
Benjamin Hur and
Kevin Cunningham and
Jaeyun Sung},
title = {GMWI-webtool: a user-friendly browser application for assessing health
through metagenomic gut microbiome profiling},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad061},
doi = {10.1093/BIOINFORMATICS/BTAD061},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChangGHCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChatzianastasisVZ23,
author = {Michail Chatzianastasis and
Michalis Vazirgiannis and
Zijun Zhang},
title = {Explainable Multilayer Graph Neural Network for cancer gene prediction},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad643},
doi = {10.1093/BIOINFORMATICS/BTAD643},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChatzianastasisVZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChegraouiGRGGPF23,
author = {Hamza Chegraoui and
Vincent Guillemot and
Amine Rebei and
Arnaud Gloaguen and
Jacques Grill and
Cathy Philippe and
Vincent Frouin},
title = {Integrating multiomics and prior knowledge: a study of the Graphnet
penalty impact},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad454},
doi = {10.1093/BIOINFORMATICS/BTAD454},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChegraouiGRGGPF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenCMWC23,
author = {Chen Chen and
Xiao Chen and
Alex Morehead and
Tianqi Wu and
Jianlin Cheng},
title = {3D-equivariant graph neural networks for protein model quality assessment},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad030},
doi = {10.1093/BIOINFORMATICS/BTAD030},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenCMWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenLFYZHZHPW23,
author = {Wei Chen and
Zhiwei Li and
Hongyi Fang and
Qianyuan Yao and
Cheng Zhong and
Jianye Hao and
Qi Zhang and
Xuanjing Huang and
Jiajie Peng and
Zhongyu Wei},
title = {A benchmark for automatic medical consultation system: frameworks,
tasks and datasets},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac817},
doi = {10.1093/BIOINFORMATICS/BTAC817},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenLFYZHZHPW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenMLC23,
author = {Xiao Chen and
Alex Morehead and
Jian Liu and
Jianlin Cheng},
title = {A gated graph transformer for protein complex structure quality assessment
and its performance in {CASP15}},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {308--317},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad203},
doi = {10.1093/BIOINFORMATICS/BTAD203},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenMLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenSLJRJXLCN23,
author = {Qijie Chen and
Haotong Sun and
Haoyang Liu and
Yinghui Jiang and
Ting Ran and
Xurui Jin and
Xianglu Xiao and
Zhimin Lin and
Hongming Chen and
Zhangming Niu},
title = {An extensive benchmark study on biomedical text generation and mining
with ChatGPT},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad557},
doi = {10.1093/BIOINFORMATICS/BTAD557},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenSLJRJXLCN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenTSS23,
author = {Guowei Chen and
Xubo Tang and
Mang Shi and
Yanni Sun},
title = {VirBot: an {RNA} viral contig detector for metagenomic data},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad093},
doi = {10.1093/BIOINFORMATICS/BTAD093},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenTSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWL23,
author = {Can Chen and
Scott T. Weiss and
Yang{-}Yu Liu},
title = {Graph convolutional network-based feature selection for high-dimensional
and low-sample size data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad135},
doi = {10.1093/BIOINFORMATICS/BTAD135},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWLJ23,
author = {Shengquan Chen and
Rongxiang Wang and
Wenxin Long and
Rui Jiang},
title = {{ASTER:} accurately estimating the number of cell types in single-cell
chromatin accessibility data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac842},
doi = {10.1093/BIOINFORMATICS/BTAC842},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWLJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWLZY23,
author = {Peng Chen and
Jian Wang and
Hongfei Lin and
Di Zhao and
Zhihao Yang},
title = {Few-shot biomedical named entity recognition via knowledge-guided
instance generation and prompt contrastive learning},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad496},
doi = {10.1093/BIOINFORMATICS/BTAD496},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWLZY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenYG23,
author = {Lu Chen and
Liang Yu and
Lin Gao},
title = {Potent antibiotic design via guided search from antibacterial activity
evaluations},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad059},
doi = {10.1093/BIOINFORMATICS/BTAD059},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenYG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZGECJGNCM23,
author = {Ziqi Chen and
Baoyi Zhang and
Hongyu Guo and
Prashant S. Emani and
Trevor Clancy and
Chongming Jiang and
Mark Gerstein and
Xia Ning and
Chao Cheng and
Martin Renqiang Min},
title = {Binding peptide generation for {MHC} Class {I} proteins with deep
reinforcement learning},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad055},
doi = {10.1093/BIOINFORMATICS/BTAD055},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZGECJGNCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZPW23,
author = {Wei Chen and
Cheng Zhong and
Jiajie Peng and
Zhongyu Wei},
title = {DxFormer: a decoupled automatic diagnostic system based on decoder-encoder
transformer with dense symptom representations},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac744},
doi = {10.1093/BIOINFORMATICS/BTAC744},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZPW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZWLD23,
author = {Can (sam) Chen and
Jingbo Zhou and
Fan Wang and
Xue (Steve) Liu and
Dejing Dou},
title = {Structure-aware protein self-supervised learning},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad189},
doi = {10.1093/BIOINFORMATICS/BTAD189},
timestamp = {Sat, 10 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZWLD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengALLPZXLL23,
author = {Xiang Cheng and
Md Amanullah and
Weigang Liu and
Yi Liu and
Xiaoqing Pan and
Honghe Zhang and
Haiming Xu and
Pengyuan Liu and
Yan Lu},
title = {WMDS.net: a network control framework for identifying key players
in transcriptome programs},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad071},
doi = {10.1093/BIOINFORMATICS/BTAD071},
timestamp = {Tue, 26 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengALLPZXLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengMVOMJ23,
author = {Jian Cheng and
Christian Maltecca and
Paul M. Vanraden and
Jeffrey R. O'Connell and
Li Ma and
Jicai Jiang},
title = {{SLEMM:} million-scale genomic predictions with window-based {SNP}
weighting},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad127},
doi = {10.1093/BIOINFORMATICS/BTAD127},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengMVOMJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengWZZZWWLYG23,
author = {Lixin Cheng and
Haonan Wu and
Xubin Zheng and
Ning Zhang and
Pengfei Zhao and
Ran Wang and
Qiong Wu and
Tao Liu and
Xiaojun Yang and
Qingshan Geng},
title = {{GPGPS:} a robust prognostic gene pair signature of glioma ensembling
\emph{IDH} mutation and 1p/19q co-deletion},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac850},
doi = {10.1093/BIOINFORMATICS/BTAC850},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengWZZZWWLYG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengXW23,
author = {Yichen Cheng and
Yusen Xia and
Xinlei Wang},
title = {Bayesian multitask learning for medicine recommendation based on online
patient reviews},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad491},
doi = {10.1093/BIOINFORMATICS/BTAD491},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChineryWMD23,
author = {Lewis Chinery and
Newton Wahome and
Iain Moal and
Charlotte M. Deane},
title = {Paragraph - antibody paratope prediction using graph neural networks
with minimal feature vectors},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac732},
doi = {10.1093/BIOINFORMATICS/BTAC732},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChineryWMD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChoSBZZ23,
author = {Hyun Jae Cho and
Mia Shu and
Stefan Bekiranov and
Chongzhi Zang and
Aidong Zhang},
title = {Interpretable meta-learning of multi-omics data for survival analysis
and pathway enrichment},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad113},
doi = {10.1093/BIOINFORMATICS/BTAD113},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChoSBZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChoiJWZ23,
author = {Joung Min Choi and
Ming Ji and
Layne T. Watson and
Liqing Zhang},
title = {DeepMicroGen: a generative adversarial network-based method for longitudinal
microbiome data imputation},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad286},
doi = {10.1093/BIOINFORMATICS/BTAD286},
timestamp = {Tue, 13 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChoiJWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChoiMMHM23,
author = {Hyunjun Choi and
Jay Moran and
Nicholas Matsumoto and
Miguel E. Hernandez and
Jason H. Moore},
title = {Aliro: an automated machine learning tool leveraging large language
models},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad606},
doi = {10.1093/BIOINFORMATICS/BTAD606},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChoiMMHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChojnowskiZMMB23,
author = {Grzegorz Chojnowski and
Rafal Zaborowski and
Marcin Magnus and
Sunandan Mukherjee and
Janusz M. Bujnicki},
title = {{RNA} 3D structure modeling by fragment assembly with small-angle
X-ray scattering restraints},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad527},
doi = {10.1093/BIOINFORMATICS/BTAD527},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChojnowskiZMMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChuKZJZSL23,
author = {Benjamin B. Chu and
Seyoon Ko and
Jin J. Zhou and
Aubrey Jensen and
Hua Zhou and
Janet S. Sinsheimer and
Kenneth Lange},
title = {Multivariate genome-wide association analysis by iterative hard thresholding},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad193},
doi = {10.1093/BIOINFORMATICS/BTAD193},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChuKZJZSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CifelloKSVWL23,
author = {Jeffrey Cifello and
Pavel P. Kuksa and
Naveensri Saravanan and
Otto Valladares and
Li{-}San Wang and
Yuk Yee Leung},
title = {hipFG: high-throughput harmonization and integration pipeline for
functional genomics data},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad673},
doi = {10.1093/BIOINFORMATICS/BTAD673},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CifelloKSVWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ClassLBD23,
author = {Caleb A. Class and
Caiden J. Lukan and
Christopher A. Bristow and
Kim{-}Anh Do},
title = {Easy NanoString nCounter data analysis with the NanoTube},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac762},
doi = {10.1093/BIOINFORMATICS/BTAC762},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ClassLBD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Clausen23,
author = {Philip T. L. C. Clausen},
title = {Scaling neighbor joining to one million taxa with dynamic and heuristic
neighbor joining},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac774},
doi = {10.1093/BIOINFORMATICS/BTAC774},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Clausen23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CohenMRTV23,
author = {Shani Cohen and
Eden Maximof and
Shay Rokach and
Mor Tadeski and
Isana Veksler{-}Lublinsky},
title = {sInterBase: a comprehensive database of \emph{Escherichia coli} sRNA-mRNA
interactions},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad172},
doi = {10.1093/BIOINFORMATICS/BTAD172},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CohenMRTV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CokelaerC023,
author = {Thomas Cokelaer and
Sarah Cohen{-}Boulakia and
Fr{\'{e}}d{\'{e}}ric Lemoine},
title = {Reprohackathons: promoting reproducibility in bioinformatics through
training},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {11--20},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad227},
doi = {10.1093/BIOINFORMATICS/BTAD227},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CokelaerC023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ColquhounJOR23,
author = {Rachel Colquhoun and
Ben Jackson and
{\'{A}}ine Niamh O'toole and
Andrew Rambaut},
title = {{SCORPIO:} a utility for defining and classifying mutation constellations
of virus genomes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad575},
doi = {10.1093/BIOINFORMATICS/BTAD575},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ColquhounJOR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ConstantinidesHC23,
author = {Bede Constantinides and
Martin Hunt and
Derrick W. Crook},
title = {Hostile: accurate decontamination of microbial host sequences},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad728},
doi = {10.1093/BIOINFORMATICS/BTAD728},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ConstantinidesHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ConteMCCMTP23,
author = {Alessio Del Conte and
Alexander Miguel Monzon and
Damiano Clementel and
Giorgia F. Camagni and
Giovanni Minervini and
Silvio C. E. Tosatto and
Damiano Piovesan},
title = {RING-PyMOL: residue interaction networks of structural ensembles and
molecular dynamics},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad260},
doi = {10.1093/BIOINFORMATICS/BTAD260},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ConteMCCMTP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CorePWG23,
author = {Luca Del Core and
Danilo Pellin and
Ernst C. Wit and
Marco Grzegorczyk},
title = {Scalable inference of cell differentiation networks in gene therapy
clonal tracking studies of haematopoiesis},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad605},
doi = {10.1093/BIOINFORMATICS/BTAD605},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CorePWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CosterR23,
author = {Wouter De Coster and
Rosa Rademakers},
title = {NanoPack2: population-scale evaluation of long-read sequencing data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad311},
doi = {10.1093/BIOINFORMATICS/BTAD311},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CosterR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CotetAKKSMKKPMGMGHHSDDKS23,
author = {Tudor{-}Stefan Cotet and
Andreas Agrafiotis and
Victor Kreiner and
Raphael Kuhn and
Danielle Shlesinger and
Marcos Manero{-}Carranza and
Keywan Khodaverdi and
Evgenios Kladis and
Aurora Desideri Perea and
Dylan Maassen{-}Veeters and
Wiona Gl{\"{a}}nzer and
Sol{\`{e}}ne Massery and
Lorenzo Guerci and
Kai{-}Lin Hong and
Jiami Han and
Kostas Stiklioraitis and
Vittoria Martinolli D'arcy and
Raphael Dizerens and
Samuel Kilchenmann and
Lucas Stalder and
Leon Nissen and
Basil Vogelsanger and
Stine Anzb{\"{o}}ck and
Daria Laslo and
Sophie Bakker and
Melinda Kondorosy and
Marco Venerito and
Alejandro Sanz Garc{\'{\i}}a and
Isabelle Feller and
Annette Oxenius and
Sai T. Reddy and
Alexander Yermanos},
title = {ePlatypus: an ecosystem for computational analysis of immunogenomics
data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad553},
doi = {10.1093/BIOINFORMATICS/BTAD553},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CotetAKKSMKKPMGMGHHSDDKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CoudertGCPBNSRBBAAAABBNB23,
author = {Elisabeth Coudert and
Sebastien Gehant and
Edouard De Castro and
Monica Pozzato and
Delphine Baratin and
Teresa Batista Neto and
Christian J. A. Sigrist and
Nicole Redaschi and
Alan J. Bridge and
Lucila Aimo and
Ghislaine Argoud{-}Puy and
Andrea H. Auchincloss and
Kristian B. Axelsen and
Parit Bansal and
Marie{-}Claude Blatter and
Jerven T. Bolleman and
Emmanuel Boutet and
Lionel Breuza and
Blanca Cabrera Gil and
Cristina Casals{-}Casas and
Kamal Chikh Echioukh and
B{\'{e}}atrice A. Cuche and
Anne Estreicher and
Maria Livia Famiglietti and
Marc Feuermann and
Elisabeth Gasteiger and
Pascale Gaudet and
Vivienne Baillie Gerritsen and
Arnaud Gos and
Nadine Gruaz{-}Gumowski and
Chantal Hulo and
Nevila Hyka{-}Nouspikel and
Florence Jungo and
Arnaud Kerhornou and
Philippe Le Mercier and
Damien Lieberherr and
Patrick Masson and
Anne Morgat and
Venkatesh Muthukrishnan and
Salvo Paesano and
Ivo Pedruzzi and
Sandrine Pilbout and
Lucille Pourcel and
Sylvain Poux and
Manuela Pruess and
Catherine Rivoire and
Karin Sonesson and
Shyamala Sundaram and
Alex Bateman and
Maria Jesus Martin and
Sandra E. Orchard and
Michele Magrane and
Shadab Ahmad and
Emanuele Alpi and
Emily H. Bowler{-}Barnett and
Ramona Britto and
Hema Bye{-}A{-}Jee and
Austra Cukura and
Paul Denny and
Tunca Dogan and
Thankgod Ebenezer and
Jun Fan and
Penelope Garmiri and
Leonardo Jose da Costa Gonzales and
Emma Hatton{-}Ellis and
Abdulrahman Hussein and
Alexandr Ignatchenko and
Giuseppe Insana and
Rizwan Ishtiaq and
Vishal Joshi and
Dushyanth Jyothi and
Swaathi Kandasamy and
Antonia Lock and
Aurelien Luciani and
Marija Lugaric and
Jie Luo and
Yvonne Lussi and
Alistair MacDougall and
F{\'{a}}bio Madeira and
Mahdi Mahmoudy and
Alok Mishra and
Katie Moulang and
Andrew Nightingale and
Sangya Pundir and
Guoying Qi and
Shriya Raj and
Pedro Raposo and
Daniel Rice and
Rabie Saidi and
Rafael Santos and
Elena Speretta and
James D. Stephenson and
Prabhat Totoo and
Edward Turner and
Nidhi Tyagi and
Preethi Vasudev and
Kate Warner and
Xavier Watkins and
Rossana Zaru and
Hermann Zellner and
Cathy H. Wu and
Cecilia N. Arighi and
Leslie Arminski and
Chuming Chen and
Yongxing Chen and
Hongzhan Huang and
Kati Laiho and
Peter B. McGarvey and
Darren A. Natale and
Karen Ross and
C. R. Vinayaka and
Qinghua Wang and
Yuqi Wang},
title = {Annotation of biologically relevant ligands in UniProtKB using ChEBI},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac793},
doi = {10.1093/BIOINFORMATICS/BTAC793},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CoudertGCPBNSRBBAAAABBNB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CousinsHGTTCA23,
author = {Henry Cousins and
Taryn Hall and
Yinglong Guo and
Luke Tso and
Kathy T. H. Tzeng and
Le Cong and
Russ B. Altman},
title = {Gene set proximity analysis: expanding gene set enrichment analysis
through learned geometric embeddings, with drug-repurposing applications
in {COVID-19}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac735},
doi = {10.1093/BIOINFORMATICS/BTAC735},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CousinsHGTTCA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CoutoRPG23,
author = {B{\'{a}}rbara Zita Peters Couto and
Nicholas Robertson and
Ellis Patrick and
Shila Ghazanfar},
title = {\emph{MoleculeExperiment} enables consistent infrastructure for molecule-resolved
spatial omics data in bioconductor},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad550},
doi = {10.1093/BIOINFORMATICS/BTAD550},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CoutoRPG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CozziRRGKBB23,
author = {Davide Cozzi and
Massimiliano Rossi and
Simone Rubinacci and
Travis Gagie and
Dominik K{\"{o}}ppl and
Christina Boucher and
Paola Bonizzoni},
title = {{\(\mu\)}- {PBWT:} a lightweight r-indexing of the {PBWT} for storing
and querying {UK} Biobank data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad552},
doi = {10.1093/BIOINFORMATICS/BTAD552},
timestamp = {Mon, 10 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CozziRRGKBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CretinPZGG23,
author = {Gabriel Cretin and
Charlotte P{\'{e}}rin and
Nicolas Zimmermann and
Tatiana Galochkina and
Jean{-}Christophe Gelly},
title = {{ICARUS:} flexible protein structural alignment based on Protein Units},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad459},
doi = {10.1093/BIOINFORMATICS/BTAD459},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CretinPZGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CsibraS23,
author = {Eszter Csibra and
Guy{-}Bart Stan},
title = {Parsley: a web app for parsing data from plate readers},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad733},
doi = {10.1093/BIOINFORMATICS/BTAD733},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CsibraS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CunhaLFLHD23,
author = {Emanuel Cunha and
Davide Lagoa and
Jos{\'{e}} P. Faria and
Filipe Liu and
Christopher S. Henry and
Oscar D{\'{\i}}as},
title = {\emph{TranSyT}, an innovative framework for identifying transport
systems},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad466},
doi = {10.1093/BIOINFORMATICS/BTAD466},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CunhaLFLHD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DalkiranARMCADA23,
author = {Alperen Dalkiran and
Ahmet Atakan and
Ahmet S{\"{u}}reyya Rifaioglu and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Aybar C. Acar and
Tunca Dogan and
Volkan Atalay},
title = {Transfer learning for drug-target interaction prediction},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {103--110},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad234},
doi = {10.1093/BIOINFORMATICS/BTAD234},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DalkiranARMCADA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DapkunasM23,
author = {Justas Dapkunas and
Mindaugas Margelevicius},
title = {The {COMER} web server for protein analysis by homology},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac807},
doi = {10.1093/BIOINFORMATICS/BTAC807},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DapkunasM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DavidsonCGPSQWSCSPS23,
author = {Russell B. Davidson and
Mark Coletti and
Mu Gao and
Bryan Piatkowski and
Avinash Sreedasyam and
Farhan Quadir and
David J. Weston and
Jeremy Schmutz and
Jianlin Cheng and
Jeffrey Skolnick and
Jerry M. Parks and
Ada Sedova},
title = {Predicted structural proteome of \emph{Sphagnum divinum} and proteome-scale
annotation},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad511},
doi = {10.1093/BIOINFORMATICS/BTAD511},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DavidsonCGPSQWSCSPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DavisMLDLP23,
author = {Eric S. Davis and
Wancen Mu and
Stuart Lee and
Mikhail G. Dozmorov and
Michael I. Love and
Douglas H. Phanstiel},
title = {matchRanges: generating null hypothesis genomic ranges via covariate-matched
sampling},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad197},
doi = {10.1093/BIOINFORMATICS/BTAD197},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DavisMLDLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DayaoTKRDPDMB23,
author = {Monica T. Dayao and
Alexandro Trevino and
Honesty Kim and
Matthew Ruffalo and
H. Blaize D'angio and
Ryan Preska and
Umamaheswar Duvvuri and
Aaron T. Mayer and
Ziv Bar{-}Joseph},
title = {Deriving spatial features from \emph{in situ} proteomics imaging to
enhance cancer survival analysis},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {140--148},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad245},
doi = {10.1093/BIOINFORMATICS/BTAD245},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DayaoTKRDPDMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DeGroatMBAZA23,
author = {William DeGroat and
Dinesh Mendhe and
Atharva Bhusari and
Habiba Abdelhalim and
Saman Zeeshan and
Zeeshan Ahmed},
title = {\emph{IntelliGenes}: a novel machine learning pipeline for biomarker
discovery and predictive analysis using multi-genomic profiles},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad755},
doi = {10.1093/BIOINFORMATICS/BTAD755},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DeGroatMBAZA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DengTZZZF23,
author = {Yuzhong Deng and
Jianxiong Tang and
Jiyang Zhang and
Jianxiao Zou and
Que Zhu and
Shicai Fan},
title = {GraphCpG: imputation of single-cell methylomes based on locus-aware
neighboring subgraphs},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad533},
doi = {10.1093/BIOINFORMATICS/BTAD533},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DengTZZZF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DenouletBAVSATBL23,
author = {Marie Denoulet and
Mathilde Brul{\'{e}} and
Fran{\c{c}}ois Anquez and
Audrey Vincent and
Julie Schnipper and
Eric Adriaenssens and
Robert{-}Alain Toillon and
Xuefen Le Bourhis and
Chann Lagadec},
title = {{ABSP:} an automated {R} tool to efficiently analyze region-specific
CpG methylation from bisulfite sequencing {PCR}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad008},
doi = {10.1093/BIOINFORMATICS/BTAD008},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DenouletBAVSATBL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DeorowiczDL23,
author = {Sebastian Deorowicz and
Agnieszka Danek and
Heng Li},
title = {{AGC:} compact representation of assembled genomes with fast queries
and updates},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad097},
doi = {10.1093/BIOINFORMATICS/BTAD097},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DeorowiczDL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DerelleLPLAC23,
author = {Romain Derelle and
John Lees and
Jody Phelan and
Ajit Lalvani and
Nimalan Arinaminpathy and
Leonid Chindelevitch},
title = {fastlin: an ultra-fast program for \emph{Mycobacterium tuberculosis}
complex lineage typing},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad648},
doi = {10.1093/BIOINFORMATICS/BTAD648},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DerelleLPLAC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DervishiLHJVA23,
author = {Leonard Dervishi and
Wenbiao Li and
Anisa Halimi and
Xiaoqian Jiang and
Jaideep Vaidya and
Erman Ayday},
title = {Privacy preserving identification of population stratification for
collaborative genomic research},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {168--176},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad274},
doi = {10.1093/BIOINFORMATICS/BTAD274},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DervishiLHJVA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiabNAGMH23,
author = {Safaa Diab and
Amir Nassereldine and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Onur Mutlu and
Izzat El Hajj},
title = {A framework for high-throughput sequence alignment using real processing-in-memory
systems},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad155},
doi = {10.1093/BIOINFORMATICS/BTAD155},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiabNAGMH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiaoHSL23,
author = {Yanyan Diao and
Feng Hu and
Zihao Shen and
Honglin Li},
title = {MacFrag: segmenting large-scale molecules to obtain diverse fragments
with high qualities},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad012},
doi = {10.1093/BIOINFORMATICS/BTAD012},
timestamp = {Tue, 16 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiaoHSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiasCWMT23,
author = {Fernando H. C. Dias and
Manuel C{\'{a}}ceres and
Lucia Williams and
Brendan Mumey and
Alexandru I. Tomescu},
title = {A safety framework for flow decomposition problems via integer linear
programming},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad640},
doi = {10.1093/BIOINFORMATICS/BTAD640},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiasCWMT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiazGayVBWIVDNYJMSBSA23,
author = {Marcos D{\'{\i}}az{-}Gay and
Raviteja Vangara and
Mark Barnes and
Xi Wang and
S. M. Ashiqul Islam and
Ian Vermes and
Stephen Duke and
Nithish Bharadhwaj Narasimman and
Ting Yang and
Zichen Jiang and
Sarah J. Moody and
Sergey Senkin and
Paul Brennan and
Michael R. Stratton and
Ludmil B. Alexandrov},
title = {Assigning mutational signatures to individual samples and individual
somatic mutations with SigProfilerAssignment},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad756},
doi = {10.1093/BIOINFORMATICS/BTAD756},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiazGayVBWIVDNYJMSBSA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiazSeoaneRV23,
author = {Sandra D{\'{\i}}az{-}Seoane and
Xabier Rey{-}Barreiro and
Alejandro F. Villaverde},
title = {{STRIKE-GOLDD} 4.0: user-friendly, efficient analysis of structural
identifiability and observability},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac748},
doi = {10.1093/BIOINFORMATICS/BTAC748},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiazSeoaneRV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DickK23,
author = {Jeffrey M. Dick and
Xun Kang},
title = {\emph{chem16S}: community-level chemical metrics for exploring genomic
adaptation to environments},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad564},
doi = {10.1093/BIOINFORMATICS/BTAD564},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DickK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DicksonAMM23,
author = {Andrew Dickson and
Ehsaneddin Asgari and
Alice C. McHardy and
Mohammad R. K. Mofrad},
title = {{GO} Bench: shared hub for universal benchmarking of machine learning-based
protein functional annotations},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad081},
doi = {10.1093/BIOINFORMATICS/BTAD081},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DicksonAMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DidelotHKR23,
author = {Xavier Didelot and
David Helekal and
Michelle Kendall and
Paolo Ribeca},
title = {Distinguishing imported cases from locally acquired cases within a
geographically limited genomic sample of an infectious disease},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac761},
doi = {10.1093/BIOINFORMATICS/BTAC761},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DidelotHKR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DillMcFarlandMBSBJCMBBSH23,
author = {Kimberly A. Dill{-}McFarland and
Kiana Mitchell and
Sashank Batchu and
Richard Max Segnitz and
Basilin Benson and
Tomasz Janczyk and
Madison S. Cox and
Harriet Mayanja{-}Kizza and
William Henry Boom and
Penelope Benchek and
Catherine M. Stein and
Thomas R. Hawn and
Matthew C. Altman},
title = {Kimma: flexible linear mixed effects modeling with kinship covariance
for RNA-seq data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad279},
doi = {10.1093/BIOINFORMATICS/BTAD279},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DillMcFarlandMBSBJCMBBSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DimitrovaKSS23,
author = {Elena S. Dimitrova and
Adam C. Knapp and
Brandilyn Stigler and
Michael Eugene Stillman},
title = {Cyclone: open-source package for simulation and analysis of finite
dynamical systems},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad634},
doi = {10.1093/BIOINFORMATICS/BTAD634},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DimitrovaKSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Ding0L23,
author = {Kerr Ding and
Sheng Wang and
Yunan Luo},
title = {Supervised biological network alignment with graph neural networks},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {465--474},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad241},
doi = {10.1093/BIOINFORMATICS/BTAD241},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Ding0L23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DishuckRLPE23,
author = {Philip C. Dishuck and
Allison N. Rozanski and
Glennis Logsdon and
David Porubsky and
Evan E. Eichler},
title = {{GAVISUNK:} genome assembly validation via inter-SUNK distances in
Oxford Nanopore reads},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac714},
doi = {10.1093/BIOINFORMATICS/BTAC714},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DishuckRLPE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DitzRP23,
author = {Jonas C. Ditz and
Bernhard Reuter and
Nico Pfeifer},
title = {COmic: convolutional kernel networks for interpretable end-to-end
learning on (multi-)omics data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {76--85},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad204},
doi = {10.1093/BIOINFORMATICS/BTAD204},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DitzRP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DitzWMFPR23,
author = {Jonas C. Ditz and
Jacqueline Wistuba{-}Hamprecht and
Timo Maier and
Rolf Fendel and
Nico Pfeifer and
Bernhard Reuter},
title = {PlasmoFAB: a benchmark to foster machine learning for \emph{Plasmodium
falciparum} protein antigen candidate prediction},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {86--93},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad206},
doi = {10.1093/BIOINFORMATICS/BTAD206},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DitzWMFPR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DmitrenkoRZ23,
author = {Andrei Dmitrenko and
Michelle Reid and
Nicola Zamboni},
title = {Regularized adversarial learning for normalization of multi-batch
untargeted metabolomics data},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad096},
doi = {10.1093/BIOINFORMATICS/BTAD096},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DmitrenkoRZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DohertyKGBM23,
author = {Hannah M. Doherty and
George Kritikos and
Marco Galardini and
Manuel Banzhaf and
Danesh Moradigaravand},
title = {ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad171},
doi = {10.1093/BIOINFORMATICS/BTAD171},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DohertyKGBM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DongSK23,
author = {Chenyang Dong and
Siqi Shen and
S{\"{u}}nd{\"{u}}z Keles},
title = {AdaLiftOver: high-resolution identification of orthologous regulatory
elements with Adaptive liftOver},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad149},
doi = {10.1093/BIOINFORMATICS/BTAD149},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DongSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DoriaBelenguerXCMP23,
author = {Sergio Doria{-}Belenguer and
Alexandros Xenos and
Gaia Ceddia and
No{\"{e}}l Malod{-}Dognin and
Natasa Przulj},
title = {A functional analysis of omic network embedding spaces reveals key
altered functions in cancer},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad281},
doi = {10.1093/BIOINFORMATICS/BTAD281},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DoriaBelenguerXCMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DoschBTE23,
author = {Julian Dosch and
Holger Bergmann and
Vinh Tran and
Ingo Ebersberger},
title = {{FAS:} assessing the similarity between proteins using multi-layered
feature architectures},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad226},
doi = {10.1093/BIOINFORMATICS/BTAD226},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DoschBTE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DouglasKLS23,
author = {Gavin M. Douglas and
Sunu Kim and
Morgan G. I. Langille and
B. Jesse Shapiro},
title = {Efficient computation of contributional diversity metrics from microbiome
data with \emph{FuncDiv}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac809},
doi = {10.1093/BIOINFORMATICS/BTAC809},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DouglasKLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuLLWS23,
author = {Bing{-}Xue Du and
Yahui Long and
Xiaoli Li and
Min Wu and
Jian{-}Yu Shi},
title = {{CMMS-GCL:} cross-modality metabolic stability prediction with graph
contrastive learning},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad503},
doi = {10.1093/BIOINFORMATICS/BTAD503},
timestamp = {Fri, 19 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuLLWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DumitrescuJPKPL23,
author = {Alexandru Dumitrescu and
Emmi Jokinen and
Anja Paatero and
Juho Kellosalo and
Ville O. Paavilainen and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {TSignal: a transformer model for signal peptide prediction},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {347--356},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad228},
doi = {10.1093/BIOINFORMATICS/BTAD228},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DumitrescuJPKPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EdwardsDPHYUH23,
author = {Nathan Edwards and
Christian Dillard and
N. M. Prashant and
Liu Hongyu and
Mia Yang and
Evgenia Ulianova and
Anelia Horvath},
title = {SCExecute: custom cell barcode-stratified analyses of scRNA-seq data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac768},
doi = {10.1093/BIOINFORMATICS/BTAC768},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EdwardsDPHYUH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EgorovA23,
author = {Artyom A. Egorov and
Gemma Catherine Atkinson},
title = {uORF4u: a tool for annotation of conserved upstream open reading frames},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad323},
doi = {10.1093/BIOINFORMATICS/BTAD323},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EgorovA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EinarssonM23,
author = {P{\'{e}}tur Helgi Einarsson and
P{\'{a}}ll Melsted},
title = {{BUSZ:} compressed {BUS} files},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad295},
doi = {10.1093/BIOINFORMATICS/BTAD295},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EinarssonM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ElghraouiMSV23,
author = {Afif Elghraoui and
Siavash Mirarab and
Krister M. Swenson and
Faramarz Valafar},
title = {Evaluating impacts of syntenic block detection strategies on rearrangement
phylogeny using \emph{Mycobacterium tuberculosis} isolates},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad024},
doi = {10.1093/BIOINFORMATICS/BTAD024},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ElghraouiMSV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EmissahLA23,
author = {Herve Emissah and
Bengt Ljungquist and
Giorgio A. Ascoli},
title = {Bibliometric analysis of neuroscience publications quantifies the
impact of data sharing},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad746},
doi = {10.1093/BIOINFORMATICS/BTAD746},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EmissahLA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ErenCKO23,
author = {Kazim Kivan{\c{c}} Eren and
Esra {\c{C}}inar and
Hamza Umut Karakurt and
Arzucan {\"{O}}zg{\"{u}}r},
title = {Improving the filtering of false positive single nucleotide variations
by combining genomic features with quality metrics},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad694},
doi = {10.1093/BIOINFORMATICS/BTAD694},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ErenCKO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FalcoOKMS23,
author = {Alfonso De Falco and
Christophe M. Olinger and
Barbara Klink and
Michel Mittelbronn and
Daniel Stieber},
title = {Digital {PCR} cluster predictor: a universal R-package and shiny app
for the automated analysis of multiplex digital {PCR} data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad282},
doi = {10.1093/BIOINFORMATICS/BTAD282},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FalcoOKMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FalolaAAKAMSAETENRAAOIAO23,
author = {Oluwadamilare Falola and
Yagoub Adam and
Olabode Ajayi and
Judit Kumuthini and
Suraju Adewale and
Abayomi Mosaku and
Chaimae Samtal and
Glory O. Adebayo and
Jerry Emmanuel and
Milaine S. S. Tchamga and
Udochukwu Erondu and
Adebayo Nehemiah and
Suraj Rasaq and
Mary Ajayi and
Bola Akanle and
Olaleye Oladipo and
Itunuoluwa Isewon and
Marion O. Adebiyi and
Jelili Oyelade and
Ezekiel F. Adebiyi},
title = {SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational
technologies and integration of diverse omics datasets},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac791},
doi = {10.1093/BIOINFORMATICS/BTAC791},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FalolaAAKAMSAETENRAAOIAO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Fang23,
author = {Jianwen Fang},
title = {Predicting thermostability difference between cellular protein orthologs},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad504},
doi = {10.1093/BIOINFORMATICS/BTAD504},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Fang23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Fang23a,
author = {Huaying Fang},
title = {gmcoda: Graphical model for multiple compositional vectors in microbiome
studies},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad700},
doi = {10.1093/BIOINFORMATICS/BTAD700},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Fang23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangJWMRYW23,
author = {Yitian Fang and
Yi Jiang and
Leyi Wei and
Qin Ma and
Zhixiang Ren and
Qianmu Yuan and
Dong{-}Qing Wei},
title = {DeepProSite: structure-aware protein binding site prediction using
ESMFold and pretrained language model},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad718},
doi = {10.1093/BIOINFORMATICS/BTAD718},
timestamp = {Tue, 23 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangJWMRYW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangLP23,
author = {Zhuoqing Fang and
Xinyuan Liu and
Gary Peltz},
title = {GSEApy: a comprehensive package for performing gene set enrichment
analysis in Python},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac757},
doi = {10.1093/BIOINFORMATICS/BTAC757},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangPS23,
author = {Yi Fang and
Xiaoyong Pan and
Hong{-}Bin Shen},
title = {\emph{De novo}drug design by iterative multiobjective deep reinforcement
learning with graph-based molecular quality assessment},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad157},
doi = {10.1093/BIOINFORMATICS/BTAD157},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FassettiRS23,
author = {Fabio Fassetti and
Simona E. Rombo and
Cristina Serrao},
title = {Discriminative pattern discovery for the characterization of different
network populations},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad168},
doi = {10.1093/BIOINFORMATICS/BTAD168},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FassettiRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FaureSKA23,
author = {Louis Faure and
Ruslan Soldatov and
Peter V. Kharchenko and
Igor Adameyko},
title = {scFates: a scalable python package for advanced pseudotime and bifurcation
analysis from single-cell data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac746},
doi = {10.1093/BIOINFORMATICS/BTAC746},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FaureSKA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FeiziR23,
author = {Amir Feizi and
Kamalika Ray},
title = {\emph{otargen}: GraphQL-based {R} package for tidy data accessing
and processing from Open Targets Genetics},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad441},
doi = {10.1093/BIOINFORMATICS/BTAD441},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FeiziR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FeldnerBusztinNEBRGLLP23,
author = {Dylan Feldner{-}Busztin and
Panos Firbas Nisantzis and
Shelley Jane Edmunds and
Gergely Boza and
Fernando Racimo and
Shyam Gopalakrishnan and
Morten T{\o}nsberg Limborg and
Leo Lahti and
Gonzalo G. de Polavieja},
title = {Dealing with dimensionality: the application of machine learning to
multi-omics data},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad021},
doi = {10.1093/BIOINFORMATICS/BTAD021},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FeldnerBusztinNEBRGLLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FengFZFZH23,
author = {Zerong Feng and
Jiejie Feng and
Baoyi Zhang and
Yuhan Fei and
Hongsheng Zhang and
Ji Huang},
title = {PhasiHunter: a robust phased siRNA regulatory cascade mining tool
based on multiple reference sequences},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad676},
doi = {10.1093/BIOINFORMATICS/BTAD676},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FengFZFZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FengFZZ23,
author = {Zhenhuan Feng and
Peiyang Fang and
Hui Zheng and
Xiaofei Zhang},
title = {{DEP2:} an upgraded comprehensive analysis toolkit for quantitative
proteomics data},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad526},
doi = {10.1093/BIOINFORMATICS/BTAD526},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FengFZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FerchenSG23,
author = {Kyle Ferchen and
Nathan Salomonis and
H. Leighton Grimes},
title = {pyInfinityFlow: optimized imputation and analysis of high-dimensional
flow cytometry data for millions of cells},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad287},
doi = {10.1093/BIOINFORMATICS/BTAD287},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FerchenSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FernandezTorrasLBA23,
author = {Adri{\`{a}} Fern{\'{a}}ndez{-}Torras and
Martina Locatelli and
Martino Bertoni and
Patrick Aloy},
title = {BQsupports: systematic assessment of the support and novelty of new
biomedical associations},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad581},
doi = {10.1093/BIOINFORMATICS/BTAD581},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FernandezTorrasLBA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FirtinaML0CMM23,
author = {Can Firtina and
Nika Mansouri{-}Ghiasi and
Jo{\"{e}}l Lindegger and
Gagandeep Singh and
Meryem Banu Cavlak and
Haiyu Mao and
Onur Mutlu},
title = {RawHash: enabling fast and accurate real-time analysis of raw nanopore
signals for large genomes},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {297--307},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad272},
doi = {10.1093/BIOINFORMATICS/BTAD272},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FirtinaML0CMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FlemingHMVHT23,
author = {Ronan M. T. Fleming and
Hulda S. Haraldsd{\'{o}}ttir and
Le Hoai Minh and
Phan Tu Vuong and
Thomas Hankemeier and
Ines Thiele},
title = {Cardinality optimization in constraint-based modelling: application
to human metabolism},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad450},
doi = {10.1093/BIOINFORMATICS/BTAD450},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FlemingHMVHT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FoggKV23,
author = {Christiana N. Fogg and
Diane E. Kovats and
Martin Vingron},
title = {2023 Outstanding Contributions to {ISCB} Award: Shoba Ranganathan},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {3--4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad306},
doi = {10.1093/BIOINFORMATICS/BTAD306},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FoggKV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FoggKV23a,
author = {Christiana N. Fogg and
Diane E. Kovats and
Martin Vingron},
title = {2023 {ISCB} Overton Prize: Jingyi Jessica Li},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {5--6},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad307},
doi = {10.1093/BIOINFORMATICS/BTAD307},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FoggKV23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FoggKV23b,
author = {Christiana N. Fogg and
Diane E. Kovats and
Martin Vingron},
title = {2023 {ISCB} innovator award: Dana Pe'er},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {7--8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad318},
doi = {10.1093/BIOINFORMATICS/BTAD318},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FoggKV23b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FoggKV23c,
author = {Christiana N. Fogg and
Diane E. Kovats and
Martin Vingron},
title = {2023 {ISCB} accomplishments by a senior scientist award: Mark Gerstein},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {9--10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad316},
doi = {10.1093/BIOINFORMATICS/BTAD316},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FoggKV23c.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FontanesiMMP23,
author = {Michele Fontanesi and
Alessio Micheli and
Paolo Milazzo and
Marco Podda},
title = {Exploiting the structure of biochemical pathways to investigate dynamical
properties with neural networks for graphs},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad678},
doi = {10.1093/BIOINFORMATICS/BTAD678},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FontanesiMMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForrestRSP23,
author = {Joshua Forrest and
Vijay Rajagopal and
Michael P. H. Stumpf and
Michael Pan},
title = {BondGraphs.jl: composable energy-based modelling in systems biology},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad578},
doi = {10.1093/BIOINFORMATICS/BTAD578},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForrestRSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FranzLFKCSHDSB23,
author = {Max Franz and
Christian Tannus Lopes and
Dylan Fong and
Mike Kucera and
Manfred Cheung and
Metin Can Siper and
Gerardo Huck and
Yue Dong and
Sel{\c{c}}uk Onur S{\"{u}}mer and
Gary D. Bader},
title = {Cytoscape.js 2023 update: a graph theory library for visualization
and analysis},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad031},
doi = {10.1093/BIOINFORMATICS/BTAD031},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FranzLFKCSHDSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FrithSS23,
author = {Martin C. Frith and
Jim Shaw and
John L. Spouge},
title = {How to optimally sample a sequence for rapid analysis},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad057},
doi = {10.1093/BIOINFORMATICS/BTAD057},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FrithSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FrolichSSH23,
author = {Siebren Fr{\"{o}}lich and
Maarten van der Sande and
Tilman Sch{\"{a}}fers and
Simon J. van Heeringen},
title = {genomepy: genes and genomes at your fingertips},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad119},
doi = {10.1093/BIOINFORMATICS/BTAD119},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FrolichSSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FruzangoharMBT23,
author = {Mario Fruzangohar and
Paula Moolhuijzen and
Nicolette Bakaj and
Julian Taylor},
title = {CoreDetector: a flexible and efficient program for core-genome alignment
of evolutionary diverse genomes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad628},
doi = {10.1093/BIOINFORMATICS/BTAD628},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FruzangoharMBT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FuDZWQY23,
author = {Sheng Fu and
Lu Deng and
Han Zhang and
William Wheeler and
Jing Qin and
Kai Yu},
title = {Integrative analysis of individual-level data and high-dimensional
summary statistics},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad156},
doi = {10.1093/BIOINFORMATICS/BTAD156},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FuDZWQY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FukaiK23,
author = {Yohsuke T. Fukai and
Kyogo Kawaguchi},
title = {LapTrack: linear assignment particle tracking with tunable metrics},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac799},
doi = {10.1093/BIOINFORMATICS/BTAC799},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FukaiK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GadiyaZGH23,
author = {Yojana Gadiya and
Andrea Zaliani and
Philip Gribbon and
Martin Hofmann{-}Apitius},
title = {{PEMT:} a patent enrichment tool for drug discovery},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac716},
doi = {10.1093/BIOINFORMATICS/BTAC716},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GadiyaZGH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GallowaySMGSWYYOM23,
author = {Jared G. Galloway and
Kevin Sung and
Samuel Schwartz Minot and
Meghan E. Garrett and
Caitlin I Stoddard and
Alexandra C. Willcox and
Zak A. Yaffe and
Ryan Yucha and
Julie Overbaugh and
Frederick A. Matsen IV},
title = {\texttt{phippery}: a software suite for PhIP-Seq data analysis},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad583},
doi = {10.1093/BIOINFORMATICS/BTAD583},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GallowaySMGSWYYOM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GalvezMerchanMPB23,
author = {{\'{A}}ngel G{\'{a}}lvez{-}Merch{\'{a}}n and
Kyung Hoi (Joseph) Min and
Lior Pachter and
A. Sina Booeshaghi},
title = {Metadata retrieval from sequence databases with \emph{ffq}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac667},
doi = {10.1093/BIOINFORMATICS/BTAC667},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GalvezMerchanMPB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GanHGYZ23,
author = {Yanglan Gan and
Xingyu Huang and
Wenjing Guo and
Cairong Yan and
Guobing Zou},
title = {Predicting synergistic anticancer drug combination based on low-rank
global attention mechanism and bilinear predictor},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad607},
doi = {10.1093/BIOINFORMATICS/BTAD607},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GanHGYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GanL23,
author = {Dailin Gan and
Jun Li},
title = {{SCIBER:} a simple method for removing batch effects from single-cell
RNA-sequencing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac819},
doi = {10.1093/BIOINFORMATICS/BTAC819},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GanL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GaoMRM23,
author = {Jiansi Gao and
Michael R. May and
Bruce Rannala and
Brian R. Moore},
title = {PrioriTree: a utility for improving phylodynamic analyses in {BEAST}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac849},
doi = {10.1093/BIOINFORMATICS/BTAC849},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GaoMRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GardaWML23,
author = {Samuele Garda and
Leon Weber{-}Genzel and
Robert Martin and
Ulf Leser},
title = {{BELB:} a biomedical entity linking benchmark},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad698},
doi = {10.1093/BIOINFORMATICS/BTAD698},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GardaWML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GarrisonG23,
author = {Erik Garrison and
Andrea Guarracino},
title = {Unbiased pangenome graphs},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac743},
doi = {10.1093/BIOINFORMATICS/BTAC743},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GarrisonG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GasparinVCC23,
author = {Andrea Gasparin and
Federico Julian Camerota Verd{\`{u}} and
Daniele Catanzaro and
Lorenzo Castelli},
title = {An evolution strategy approach for the balanced minimum evolution
problem},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad660},
doi = {10.1093/BIOINFORMATICS/BTAD660},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GasparinVCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GautamZH23,
author = {Anupam Gautam and
Wenhuan Zeng and
Daniel H. Huson},
title = {MeganServer: facilitating interactive access to metagenomic data on
a server},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad105},
doi = {10.1093/BIOINFORMATICS/BTAD105},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GautamZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GeistlingerVLPHG23,
author = {Ludwig Geistlinger and
Roger Vargas and
Tyrone Lee and
Joshua Pan and
Edward L. Huttlin and
Robert Gentleman},
title = {BioPlexR and BioPlexPy: integrated data products for the analysis
of human protein interactions},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad091},
doi = {10.1093/BIOINFORMATICS/BTAD091},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GeistlingerVLPHG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GenzMNT23,
author = {Luca R. Genz and
Thomas Mulvaney and
Sanjana Nair and
Maya Topf},
title = {{PICKLUSTER:} a protein-interface clustering and analysis plug-in
for {UCSF} ChimeraX},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad629},
doi = {10.1093/BIOINFORMATICS/BTAD629},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GenzMNT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GhaddarD23,
author = {Bassel Ghaddar and
Subhajyoti De},
title = {Hierarchical and automated cell-type annotation and inference of cancer
cell of origin with Census},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad714},
doi = {10.1093/BIOINFORMATICS/BTAD714},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GhaddarD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GilliotG23,
author = {Pierre{-}Aur{\'{e}}lien Gilliot and
Thomas E. Gorochowski},
title = {Effective design and inference for cell sorting and sequencing based
massively parallel reporter assays},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad277},
doi = {10.1093/BIOINFORMATICS/BTAD277},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GilliotG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GimCBPLJLK23,
author = {Mogan Gim and
Junseok Choe and
Seungheun Baek and
Jueon Park and
Chaeeun Lee and
Minjae Ju and
Sumin Lee and
Jaewoo Kang},
title = {ArkDTA: attention regularization guided by non-covalent interactions
for explainable drug-target binding affinity prediction},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {448--457},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad207},
doi = {10.1093/BIOINFORMATICS/BTAD207},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GimCBPLJLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GinellFH23,
author = {Garrett M. Ginell and
Aidan J. Flynn and
Alex S. Holehouse},
title = {{SHEPHARD:} a modular and extensible software architecture for analyzing
and annotating large protein datasets},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad488},
doi = {10.1093/BIOINFORMATICS/BTAD488},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GinellFH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GjergaVD23,
author = {Enio Gjerga and
Isabel S. Naarmann{-}de Vries and
Christoph Dieterich},
title = {Characterizing alternative splicing effects on protein interaction
networks with {LINDA}},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {458--464},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad224},
doi = {10.1093/BIOINFORMATICS/BTAD224},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GjergaVD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GlenMMWWSAKPLHRDRK23,
author = {Amy Glen and
Chunyu Ma and
Luis Mendoza and
Finn Womack and
E. C. Wood and
Meghamala Sinha and
Liliana Acevedo and
Lindsey G. Kvarfordt and
Ross C. Peene and
Shaopeng Liu and
Andrew S. Hoffman and
Jared C. Roach and
Eric W. Deutsch and
Stephen A. Ramsey and
David Koslicki},
title = {{ARAX:} a graph-based modular reasoning tool for translational biomedicine},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad082},
doi = {10.1093/BIOINFORMATICS/BTAD082},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GlenMMWWSAKPLHRDRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GlocklerDM23,
author = {Manuel Gl{\"{o}}ckler and
Andreas Dr{\"{a}}ger and
Reihaneh Mostolizadeh},
title = {Hierarchical modelling of microbial communities},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad040},
doi = {10.1093/BIOINFORMATICS/BTAD040},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GlocklerDM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GohlBFPFO23,
author = {Patrick Gohl and
Jaume Bonet and
Oriol Fornes and
Joan Planas{-}Iglesias and
Narcis Fernandez{-}Fuentes and
Baldo Oliva},
title = {SBILib: a handle for protein modeling and engineering},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad613},
doi = {10.1093/BIOINFORMATICS/BTAD613},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GohlBFPFO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GomezWRKEAAY23,
author = {Javier D. Gomez and
Martha L. Wall and
Mohsin Rahim and
Shrikaar Kambhampati and
Bradley S. Evans and
Doug K. Allen and
Maciek R. Antoniewicz and
Jamey D. Young},
title = {Program for Integration and Rapid Analysis of Mass Isotopomer Distributions
{(PIRAMID)}},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad661},
doi = {10.1093/BIOINFORMATICS/BTAD661},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GomezWRKEAAY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GongJCZLMFHSRT23,
author = {Jianting Gong and
Lili Jiang and
Yongbing Chen and
Yixiang Zhang and
Xue Li and
Zhiqiang Ma and
Zhiguo Fu and
Fei He and
Pingping Sun and
Zilin Ren and
Mingyao Tian},
title = {{THPLM:} a sequence-based deep learning framework for protein stability
changes prediction upon point variations using pretrained protein
language model},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad646},
doi = {10.1093/BIOINFORMATICS/BTAD646},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GongJCZLMFHSRT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GongZDWCLLLXL23,
author = {Haifan Gong and
Yumeng Zhang and
Chenhe Dong and
Yue Wang and
Guanqi Chen and
Bilin Liang and
Haofeng Li and
Lanxuan Liu and
Jie Xu and
Guanbin Li},
title = {Unbiased curriculum learning enhanced global-local graph neural network
for protein thermodynamic stability prediction},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad589},
doi = {10.1093/BIOINFORMATICS/BTAD589},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GongZDWCLLLXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrabowskiB23,
author = {Szymon Grabowski and
Wojciech Bieniecki},
title = {copMEM2: robust and scalable maximum exact match finding},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad313},
doi = {10.1093/BIOINFORMATICS/BTAD313},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrabowskiB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrazioliMMLCPM23,
author = {Filippo Grazioli and
Pierre Machart and
Anja M{\"{o}}sch and
Kai Li and
Leonardo V. Castorina and
Nico Pfeifer and
Martin Renqiang Min},
title = {Attentive Variational Information Bottleneck for TCR-peptide interaction
prediction},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac820},
doi = {10.1093/BIOINFORMATICS/BTAC820},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrazioliMMLCPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GreenbergRS23,
author = {Grant Greenberg and
Aditya Narayan Ravi and
Ilan Shomorony},
title = {LexicHash: sequence similarity estimation via lexicographic comparison
of hashes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad652},
doi = {10.1093/BIOINFORMATICS/BTAD652},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GreenbergRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrobBCLTBLSS23,
author = {Linda Grob and
Anne Bertolini and
Matteo Carrara and
Ulrike Lischetti and
Aizhan Tastanova and
Christian Beisel and
Mitchell P. Levesque and
Daniel J. Stekhoven and
Franziska Singer},
title = {gExcite: a start-to-end framework for single-cell gene expression,
hashing, and antibody analysis},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad329},
doi = {10.1093/BIOINFORMATICS/BTAD329},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrobBCLTBLSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GroverMAE23,
author = {Siddhant Grover and
Alexey Markin and
Tavis K. Anderson and
Oliver Eulenstein},
title = {Phylogenetic diversity statistics for all clades in a phylogeny},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {177--184},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad263},
doi = {10.1093/BIOINFORMATICS/BTAD263},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GroverMAE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrozaWDDHBDLLR23,
author = {Tudor Groza and
Honghan Wu and
Marcel E. Dinger and
Daniel Danis and
Coleman Hilton and
Anita Bagley and
Jon R. Davids and
Ling Luo and
Zhiyong Lu and
Peter N. Robinson},
title = {Term-BLAST-like alignment tool for concept recognition in noisy clinical
texts},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad716},
doi = {10.1093/BIOINFORMATICS/BTAD716},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrozaWDDHBDLLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrudmanFF23,
author = {Steven Grudman and
J. Eduardo Fajardo and
Andr{\'{a}}s Fiser},
title = {Optimal selection of suitable templates in protein interface prediction},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad510},
doi = {10.1093/BIOINFORMATICS/BTAD510},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrudmanFF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuH23,
author = {Zuguang Gu and
Daniel H{\"{u}}bschmann},
title = {\emph{rGREAT}: an R/bioconductor package for functional enrichment
on genomic regions},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac745},
doi = {10.1093/BIOINFORMATICS/BTAC745},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuanLZSZ23,
author = {Xiaoyu Guan and
Zhongnian Li and
Yueying Zhou and
Wei Shao and
Daoqiang Zhang},
title = {Active learning for efficient analysis of high-throughput nanopore
data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac764},
doi = {10.1093/BIOINFORMATICS/BTAC764},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuanLZSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuangSO23,
author = {Ziyun Guang and
Matthew Smith{-}Erb and
Layla Oesper},
title = {A weighted distance-based approach for deriving consensus tumor evolutionary
trees},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {204--212},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad230},
doi = {10.1093/BIOINFORMATICS/BTAD230},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuangSO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuizardMSSKDAW23,
author = {S{\'{e}}bastien Guizard and
Katarzyna Miedzinska and
Jacqueline Smith and
Jonathan Smith and
Richard I. Kuo and
Megan Davey and
Alan L. Archibald and
Mick Watson},
title = {nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq
long-read sequencing},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad150},
doi = {10.1093/BIOINFORMATICS/BTAD150},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuizardMSSKDAW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuoFBV23,
author = {Dan Guo and
Melanie Christine F{\"{o}}ll and
Kylie A. Bemis and
Olga Vitek},
title = {A noise-robust deep clustering of biomolecular ions improves interpretability
of mass spectrometric images},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad067},
doi = {10.1093/BIOINFORMATICS/BTAD067},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuoFBV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuoFL23,
author = {Yujie Guo and
Xiaowen Feng and
Heng Li},
title = {Evaluation of haplotype-aware long-read error correction with hifieval},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad631},
doi = {10.1093/BIOINFORMATICS/BTAD631},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuoFL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuzziLV23,
author = {Pietro Hiram Guzzi and
Ugo Lomoio and
Pierangelo Veltri},
title = {GTExVisualizer: a web platform for supporting ageing studies},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad303},
doi = {10.1093/BIOINFORMATICS/BTAD303},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuzziLV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaeseHillCO23,
author = {William Haese{-}Hill and
Kathryn Crouch and
Thomas D. Otto},
title = {peaks2utr: a robust Python tool for the annotation of 3{\({'}\)}
UTRs},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad112},
doi = {10.1093/BIOINFORMATICS/BTAD112},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaeseHillCO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HagglundAG23,
author = {Emil H{\"{a}}gglund and
Siv G. E. Andersson and
Lionel Guy},
title = {{TADA:} taxonomy-aware dataset aggregator},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad742},
doi = {10.1093/BIOINFORMATICS/BTAD742},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HagglundAG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaiMYW23,
author = {Yang Hai and
Jixiang Ma and
Kaixin Yang and
Yalu Wen},
title = {Bayesian linear mixed model with multiple random effects for prediction
analysis on high-dimensional multi-omics data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad647},
doi = {10.1093/BIOINFORMATICS/BTAD647},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaiMYW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaldarODCL23,
author = {Anisha Haldar and
Vishal H. Oza and
Nathaniel S. Devoss and
Amanda D. Clark and
Brittany N. Lasseigne},
title = {CoSIA: an {R} Bioconductor package for CrOss Species Investigation
and Analysis},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad759},
doi = {10.1093/BIOINFORMATICS/BTAD759},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaldarODCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HamS23,
author = {KyungPyo Ham and
Lee Sael},
title = {Evidential meta-model for molecular property prediction},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad604},
doi = {10.1093/BIOINFORMATICS/BTAD604},
timestamp = {Tue, 28 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HamS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HamiltonF23,
author = {Nolan H. Hamilton and
Terrence S. Furey},
title = {\texttt{ROCCO}: a robust method for detection of open chromatin via
convex optimization},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad725},
doi = {10.1093/BIOINFORMATICS/BTAD725},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HamiltonF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HanWMABMAYLM23,
author = {Xu Han and
Wanli Wang and
Li{-}Hua Ma and
Ismael Ai{-}Ramahi and
Juan Botas and
Kevin Mackenzie and
Genevera I. Allen and
Damian W. Young and
Zhandong Liu and
Mirjana Maletic{-}Savatic},
title = {{SPA-STOCSY:} an automated tool for identifying annotated and non-annotated
metabolites in high-throughput {NMR} spectra},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad593},
doi = {10.1093/BIOINFORMATICS/BTAD593},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HanWMABMAYLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HanesARNHZE23,
author = {Robert Hanes and
Pilar Ayuda{-}Dur{\'{a}}n and
Leiv R{\o}nneberg and
Sigve Nakken and
Eivind Hovig and
Manuela Zucknick and
Jorrit M. Enserink},
title = {screenwerk: a modular tool for the design and analysis of drug combination
screens},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac840},
doi = {10.1093/BIOINFORMATICS/BTAC840},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HanesARNHZE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HantzeH23,
author = {Hartmut H{\"{a}}ntze and
Paul Horton},
title = {Effects of spaced k-mers on alignment-free genotyping},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {213--221},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad202},
doi = {10.1093/BIOINFORMATICS/BTAD202},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HantzeH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HardarsonPH23,
author = {Marteinn T. Hardarson and
Gunnar Palsson and
Bjarni V. Halld{\'{o}}rsson},
title = {NCOurd: modelling length distributions of {NCO} events and gene conversion
tracts},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad485},
doi = {10.1093/BIOINFORMATICS/BTAD485},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HardarsonPH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HartmannSKLK23,
author = {Till Hartmann and
Christopher Schr{\"{o}}der and
Elias Kuthe and
David Laehnemann and
Johannes K{\"{o}}ster},
title = {Insane in the vembrane: filtering and transforming {VCF/BCF} files},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac810},
doi = {10.1093/BIOINFORMATICS/BTAC810},
timestamp = {Tue, 09 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HartmannSKLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HartoutPMS23,
author = {Philip Hartout and
Bojana Pocuca and
Celia M{\'{e}}ndez{-}Garc{\'{\i}}a and
Christian Schleberger},
title = {Investigating the human and nonobese diabetic mouse {MHC} class {II}
immunopeptidome using protein language modeling},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad469},
doi = {10.1093/BIOINFORMATICS/BTAD469},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HartoutPMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HawkinsZHRMGLTDJB23,
author = {Dakota Y. Hawkins and
Daniel T. Zuch and
James Huth and
Nahomie Rodriguez{-}Sastre and
Kelley R. McCutcheon and
Abigail Glick and
Alexandra T. Lion and
Christopher F. Thomas and
Abigail E. Descoteaux and
William Evan Johnson and
Cynthia A Bradham},
title = {{ICAT:} a novel algorithm to robustly identify cell states following
perturbations in single-cell transcriptomes},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad278},
doi = {10.1093/BIOINFORMATICS/BTAD278},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HawkinsZHRMGLTDJB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeHLLCZW23,
author = {Xin He and
Xianhui Huang and
Yuexuan Long and
Zhenping Liu and
Xing Chang and
Xianlong Zhang and
Maojun Wang},
title = {Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically
associating domain in eukaryotic organisms},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad576},
doi = {10.1093/BIOINFORMATICS/BTAD576},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeHLLCZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeP23,
author = {Dongze He and
Rob Patro},
title = {\texttt{simpleaf}: a simple, flexible, and scalable framework for
single-cell data processing using alevin-fry},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad614},
doi = {10.1093/BIOINFORMATICS/BTAD614},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeQWZLL23,
author = {Xinwei He and
Kun Qian and
Ziqian Wang and
Shirou Zeng and
Hongwei Li and
Wei Vivian Li},
title = {scAce: an adaptive embedding and clustering method for single-cell
gene expression data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad546},
doi = {10.1093/BIOINFORMATICS/BTAD546},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeQWZLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeYJXYF23,
author = {Weiming He and
Jian Yang and
Yi Jing and
Lian Xu and
Kang Yu and
Xiaodong Fang},
title = {NGenomeSyn: an easy-to-use and flexible tool for publication-ready
visualization of syntenic relationships across multiple genomes},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad121},
doi = {10.1093/BIOINFORMATICS/BTAD121},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeYJXYF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeadLCE23,
author = {S. Taylor Head and
Elizabeth J. Leslie and
David J. Cutler and
Michael P. Epstein},
title = {{POIROT:} a powerful test for parent-of-origin effects in unrelated
samples leveraging multiple phenotypes},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad199},
doi = {10.1093/BIOINFORMATICS/BTAD199},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeadLCE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeckerBKGS23,
author = {Dennis Hecker and
Fatemeh Behjati{-}Ardakani and
Alexander Karollus and
Julien Gagneur and
Marcel H. Schulz},
title = {The adapted Activity-By-Contact model for enhancer-gene assignment
and its application to single-cell data},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad062},
doi = {10.1093/BIOINFORMATICS/BTAD062},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeckerBKGS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HenriksenZK23,
author = {Rasmus Amund Henriksen and
Lei Zhao and
Thorfinn Sand Korneliussen},
title = {{NGSNGS:} next-generation simulator for next-generation sequencing
data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad041},
doi = {10.1093/BIOINFORMATICS/BTAD041},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HenriksenZK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeppLDO23,
author = {Benjamin Hepp and
Florence Lorieux and
Augustin Degaugue and
Jacques Oberto},
title = {{VAPEX:} an interactive web server for the deep exploration of natural
virus and phage genomes},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad528},
doi = {10.1093/BIOINFORMATICS/BTAD528},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeppLDO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HernandezDBLC23,
author = {Iv{\'{a}}n Mart{\'{\i}}n Hern{\'{a}}ndez and
Yves Dehouck and
Ugo Bastolla and
Jos{\'{e}} Ram{\'{o}}n L{\'{o}}pez{-}Blanco and
Pablo Chac{\'{o}}n},
title = {Predicting protein stability changes upon mutation using a simple
orientational potential},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad011},
doi = {10.1093/BIOINFORMATICS/BTAD011},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HernandezDBLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeumosECMMLGN23,
author = {Lukas Heumos and
Philipp Ehmele and
Luis Kuhn Cuellar and
Kevin Menden and
Edmund Miller and
Steffen Lemke and
Gisela Gabernet and
Sven Nahnsen},
title = {mlf-core: a framework for deterministic machine learning},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad164},
doi = {10.1093/BIOINFORMATICS/BTAD164},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeumosECMMLGN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HillHO23,
author = {Christopher Hill and
Sanjarbek Hudaiberdiev and
Ivan Ovcharenko},
title = {ChromDL: a next-generation regulatory {DNA} classifier},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {377--385},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad217},
doi = {10.1093/BIOINFORMATICS/BTAD217},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HillHO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HolsteinKMM23,
author = {Tanja Holstein and
Franziska Kistner and
Lennart Martens and
Thilo Muth},
title = {PepGM: a probabilistic graphical model for taxonomic inference of
viral proteome samples with associated confidence scores},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad289},
doi = {10.1093/BIOINFORMATICS/BTAD289},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HolsteinKMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HongCCKCJK23,
author = {Hyukpyo Hong and
Mark Jayson Cortez and
Yu{-}Yu Cheng and
Hang Joon Kim and
Boseung Choi and
Kresimir Josic and
Jae Kyoung Kim},
title = {Inferring delays in partially observed gene regulation processes},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad670},
doi = {10.1093/BIOINFORMATICS/BTAD670},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HongCCKCJK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HongLLZLZC23,
author = {Xiaokun Hong and
Ningshan Li and
Jiyang Lv and
Yan Zhang and
Jing Li and
Jian Zhang and
Hai{-}Feng Chen},
title = {PTMint database of experimentally verified {PTM} regulation on protein-protein
interaction},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac823},
doi = {10.1093/BIOINFORMATICS/BTAC823},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HongLLZLZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoopsK23,
author = {Susan L. Hoops and
Dan Knights},
title = {LMdist: Local Manifold distance accurately measures beta diversity
in ecological gradients},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad727},
doi = {10.1093/BIOINFORMATICS/BTAD727},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoopsK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HosseiniPMGPBOC23,
author = {Marjan Hosseini and
Aaron Palmer and
William Manka and
Patrick G. S. Grady and
Venkata Patchigolla and
Jinbo Bi and
Rachel J. O'Neill and
Zhiyi Chi and
Derek Aguiar},
title = {Deep statistical modelling of nanopore sequencing translocation times
reveals latent non-B {DNA} structures},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {242--251},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad220},
doi = {10.1093/BIOINFORMATICS/BTAD220},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HosseiniPMGPBOC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouWBWS23,
author = {Xiaoyang Hou and
Yu Wang and
Dongbo Bu and
Yaojun Wang and
Shiwei Sun},
title = {EMNGly: predicting N-linked glycosylation sites using the language
models for feature extraction},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad650},
doi = {10.1093/BIOINFORMATICS/BTAD650},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouWBWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoytHG23,
author = {Charles Tapley Hoyt and
Amelia L. Hoyt and
Benjamin M. Gyori},
title = {Prediction and curation of missing biomedical identifier mappings
with Biomappings},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad130},
doi = {10.1093/BIOINFORMATICS/BTAD130},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoytHG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HsiehLZSGK23,
author = {Ping{-}Han Hsieh and
Camila Miranda Lopes{-}Ramos and
Manuela Zucknick and
Geir Kjetil Sandve and
Kimberly Glass and
Marieke L. Kuijjer},
title = {Adjustment of spurious correlations in co-expression measurements
from RNA-Sequencing data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad610},
doi = {10.1093/BIOINFORMATICS/BTAD610},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HsiehLZSGK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuKRCX23,
author = {Yan Hu and
Vipina Kuttichi Keloth and
Kalpana Raja and
Yong Chen and
Hua Xu},
title = {Towards precise {PICO} extraction from abstracts of randomized controlled
trials using a section-specific learning approach},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad542},
doi = {10.1093/BIOINFORMATICS/BTAD542},
timestamp = {Fri, 26 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuKRCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuS23,
author = {Yi{-}Juan Hu and
Glen A. Satten},
title = {Compositional analysis of microbiome data using the linear decomposition
model {(LDM)}},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad668},
doi = {10.1093/BIOINFORMATICS/BTAD668},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuYZLR23,
author = {Peihong Hu and
Qi Ye and
Weiyan Zhang and
Jingping Liu and
Tong Ruan},
title = {Integration of multiple terminology bases: a multi-view alignment
method using the hierarchical structure},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad689},
doi = {10.1093/BIOINFORMATICS/BTAD689},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuYZLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuaSFW23,
author = {Yang Hua and
Xiaoning Song and
Zhen{-}Hua Feng and
Xiaojun Wu},
title = {{MFR-DTA:} a multi-functional and robust model for predicting drug-target
binding affinity and region},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad056},
doi = {10.1093/BIOINFORMATICS/BTAD056},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuaSFW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangFWZYNQZHFSYYB23,
author = {Bin Huang and
Tingwen Fan and
Kaiyue Wang and
Haicang Zhang and
Chungong Yu and
Shuyu Nie and
Yangshuo Qi and
Wei{-}Mou Zheng and
Jian Han and
Zheng Fan and
Shiwei Sun and
Sheng Ye and
Huaiyi Yang and
Dongbo Bu},
title = {Accurate and efficient protein sequence design through learning concise
local environment of residues},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad122},
doi = {10.1093/BIOINFORMATICS/BTAD122},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangFWZYNQZHFSYYB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangHCLLLG23,
author = {Kaibin Huang and
Shengyun Huang and
Guojing Chen and
Xue Li and
Shawn Li and
Ying Liang and
Yi Gao},
title = {An end-to-end multi-task system of automatic lesion detection and
anatomical localization in whole-body bone scintigraphy by deep learning},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac753},
doi = {10.1093/BIOINFORMATICS/BTAC753},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangHCLLLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangJZWLLFWZGRYL23,
author = {Daoyi Huang and
Jianping Jiang and
Tingting Zhao and
Shengnan Wu and
Pin Li and
Yongfen Lyu and
Jincai Feng and
Mingyue Wei and
Zhixing Zhu and
Jianlei Gu and
Yongyong Ren and
Guangjun Yu and
Hui Lu},
title = {diseaseGPS: auxiliary diagnostic system for genetic disorders based
on genotype and phenotype},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad517},
doi = {10.1093/BIOINFORMATICS/BTAD517},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangJZWLLFWZGRYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangL23,
author = {Neng Huang and
Heng Li},
title = {compleasm: a faster and more accurate reimplementation of {BUSCO}},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad595},
doi = {10.1093/BIOINFORMATICS/BTAD595},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangLIDDH23,
author = {Licai Huang and
James P. Long and
Ehsan Irajizad and
James D. Doecke and
Kim{-}Anh Do and
Min Jin Ha},
title = {A unified mediation analysis framework for integrative cancer proteogenomics
with clinical outcomes},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad023},
doi = {10.1093/BIOINFORMATICS/BTAD023},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangLIDDH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangXNNXLW23,
author = {Neng Huang and
Minghua Xu and
Fan Nie and
Peng Ni and
Chuan{-}Le Xiao and
Feng Luo and
Jianxin Wang},
title = {NanoSNP: a progressive and haplotype-aware {SNP} caller on low-coverage
nanopore sequencing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac824},
doi = {10.1093/BIOINFORMATICS/BTAC824},
timestamp = {Tue, 06 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangXNNXLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangZ023,
author = {Zhijian Huang and
Pan Zhang and
Lei Deng},
title = {DeepCoVDR: deep transfer learning with graph transformer and cross-attention
for predicting {COVID-19} drug response},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {475--483},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad244},
doi = {10.1093/BIOINFORMATICS/BTAD244},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangZ023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuoLWDS23,
author = {Yu Huo and
Hongpei Li and
Xiao Wang and
Xiaochen Du and
Peter S. Swain},
title = {Nunchaku: optimally partitioning data into piece-wise contiguous segments},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad688},
doi = {10.1093/BIOINFORMATICS/BTAD688},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuoLWDS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuthAGCTH23,
author = {Manuel Huth and
Jonas Arruda and
Roy Gusinow and
Lorenzo Contento and
Evelina Tacconelli and
Jan Hasenauer},
title = {Accessibility of covariance information creates vulnerability in Federated
Learning frameworks},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad531},
doi = {10.1093/BIOINFORMATICS/BTAD531},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuthAGCTH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JablonskiB23,
author = {Kim Philipp Jablonski and
Niko Beerenwinkel},
title = {Coherent pathway enrichment estimation by modeling inter-pathway dependencies
using regularized regression},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad522},
doi = {10.1093/BIOINFORMATICS/BTAD522},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JablonskiB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Jain23,
author = {Chirag Jain},
title = {Coverage-preserving sparsification of overlap graphs for long-read
assembly},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad124},
doi = {10.1093/BIOINFORMATICS/BTAD124},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Jain23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JainSK23,
author = {Aakriti Jain and
Neelja Singhal and
Manish Kumar},
title = {AFRbase: a database of protein mutations responsible for antifungal
resistance},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad677},
doi = {10.1093/BIOINFORMATICS/BTAD677},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JainSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JavkarRSP23,
author = {Kiran Javkar and
Hugh Rand and
Errol Strain and
Mihai Pop},
title = {{PRAWNS:} compact pan-genomic features for whole-genome population
genomics},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac844},
doi = {10.1093/BIOINFORMATICS/BTAC844},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JavkarRSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JeanmouginBPVL23,
author = {Marine Jeanmougin and
Hans Petter Brodal and
Heidi Dietrichson Pharo and
Hege Marie Vedeld and
Guro Elisabeth Lind},
title = {PoDCall: positive droplet calling and normalization of droplet digital
{PCR} {DNA} methylation data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac766},
doi = {10.1093/BIOINFORMATICS/BTAC766},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JeanmouginBPVL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JeonLNN23,
author = {Hyeongseon Jeon and
Kyu{-}Sang Lim and
Yet Nguyen and
Dan Nettleton},
title = {Adjusting for gene-specific covariates to improve RNA-seq analysis},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad498},
doi = {10.1093/BIOINFORMATICS/BTAD498},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JeonLNN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JeongKOKK23,
author = {Dabin Jeong and
Bonil Koo and
Minsik Oh and
Tae{-}Bum Kim and
Sun Kim},
title = {{GOAT:} Gene-level biomarker discovery from multi-Omics data using
graph ATtention neural network for eosinophilic asthma subtype},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad582},
doi = {10.1093/BIOINFORMATICS/BTAD582},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JeongKOKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiSTS23,
author = {Yongxin Ji and
Jiayu Shang and
Xubo Tang and
Yanni Sun},
title = {{HOTSPOT:} hierarchical host prediction for assembled plasmid contigs
with transformer},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad283},
doi = {10.1093/BIOINFORMATICS/BTAD283},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiSTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiangYTG23,
author = {Limin Jiang and
Hui Yu and
Jijun Tang and
Yan Guo},
title = {CoMutDB: the landscape of somatic mutation co-occurrence in cancers},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac725},
doi = {10.1093/BIOINFORMATICS/BTAC725},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiangYTG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaoGJWY23,
author = {Yang Jiao and
Lingkun Gu and
Yingtao Jiang and
Mo Weng and
Mei Yang},
title = {Digitally predicting protein localization and manipulating protein
activity in fluorescence images using 4D reslicing {GAN}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac719},
doi = {10.1093/BIOINFORMATICS/BTAC719},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaoGJWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaoWWLWL23,
author = {Peishun Jiao and
Beibei Wang and
Xuan Wang and
Bo Liu and
Yadong Wang and
Junyi Li},
title = {Struct2GO: protein function prediction based on graph pooling algorithm
and AlphaFold2 structure information},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad637},
doi = {10.1093/BIOINFORMATICS/BTAD637},
timestamp = {Wed, 15 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaoWWLWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaoYASZX23,
author = {Shihu Jiao and
Xiucai Ye and
Chunyan Ao and
Tetsuya Sakurai and
Quan Zou and
Lei Xu},
title = {Adaptive learning embedding features to improve the predictive performance
of SARS-CoV-2 phosphorylation sites},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad627},
doi = {10.1093/BIOINFORMATICS/BTAD627},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaoYASZX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinKCCYWL23,
author = {Qiao Jin and
Won Kim and
Qingyu Chen and
Donald C. Comeau and
Lana Yeganova and
W. John Wilbur and
Zhiyong Lu},
title = {MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed
search logs for zero-shot biomedical information retrieval},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad651},
doi = {10.1093/BIOINFORMATICS/BTAD651},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinKCCYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinWCPWXQL23,
author = {Zhi Jin and
Tingfang Wu and
Taoning Chen and
Deng Pan and
Xuejiao Wang and
Jingxin Xie and
Lijun Quan and
Qiang Lyu},
title = {{CAPLA:} improved prediction of protein-ligand binding affinity by
a deep learning approach based on a cross-attention mechanism},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad049},
doi = {10.1093/BIOINFORMATICS/BTAD049},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinWCPWXQL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JohnsonSSC23,
author = {Brian Johnson and
Yubo Shuai and
Jason Schweinsberg and
Kit Curtius},
title = {cloneRate: fast estimation of single-cell clonal dynamics using coalescent
theory},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad561},
doi = {10.1093/BIOINFORMATICS/BTAD561},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JohnsonSSC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JohnsonTLS23,
author = {Nicholas A. G. Johnson and
Liezel Tamon and
Xin Liu and
Aleksandr B. Sahakyan},
title = {ROptimus: a parallel general-purpose adaptive optimization engine},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad292},
doi = {10.1093/BIOINFORMATICS/BTAD292},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JohnsonTLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JokinenDHGMBHL23,
author = {Emmi Jokinen and
Alexandru Dumitrescu and
Jani Huuhtanen and
Vladimir Gligorijevic and
Satu Mustjoki and
Richard Bonneau and
Markus Heinonen and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {TCRconv: predicting recognition between {T} cell receptors and epitopes
using contextualized motifs},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac788},
doi = {10.1093/BIOINFORMATICS/BTAC788},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JokinenDHGMBHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JoshiBHKF23,
author = {Parnal Joshi and
Sagnik Banerjee and
Xiao Hu and
Pranav M. Khade and
Iddo Friedberg},
title = {GOThresher: a program to remove annotation biases from protein function
annotation datasets},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad048},
doi = {10.1093/BIOINFORMATICS/BTAD048},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JoshiBHKF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JoshiDCK23,
author = {Dhaivat Joshi and
Suhas N. Diggavi and
Mark J. P. Chaisson and
Sreeram Kannan},
title = {HQAlign: aligning nanopore reads for {SV} detection using current-level
modeling},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad580},
doi = {10.1093/BIOINFORMATICS/BTAD580},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JoshiDCK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JuigneDMGB23,
author = {Camille Juign{\'{e}} and
Olivier Dameron and
Fran{\c{c}}ois Moreews and
Florence Gondret and
Emmanuelle Becker},
title = {Fixing molecular complexes in BioPAX standards to enrich interactions
and detect redundancies using semantic web technologies},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad257},
doi = {10.1093/BIOINFORMATICS/BTAD257},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JuigneDMGB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KabirBRSUBA23,
author = {Anowarul Kabir and
Manish Bhattarai and
Kim {\O}. Rasmussen and
Amarda Shehu and
Anny Usheva and
Alan R. Bishop and
Boian S. Alexandrov},
title = {Examining {DNA} breathing with pyDNA-EPBD},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad699},
doi = {10.1093/BIOINFORMATICS/BTAD699},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KabirBRSUBA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaliaKH23,
author = {Apurva Kalia and
Dilip Krishnan and
Soha Hassoun},
title = {{CSI:} Contrastive data Stratification for Interaction prediction
and its application to compound-protein interaction prediction},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad456},
doi = {10.1093/BIOINFORMATICS/BTAD456},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaliaKH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaminskiLPAD23,
author = {Kamil Kaminski and
Jan Ludwiczak and
Kamil Pawlicki and
Vikram Alva and
Stanislaw Dunin{-}Horkawicz},
title = {pLM-BLAST: distant homology detection based on direct comparison of
sequence representations from protein language models},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad579},
doi = {10.1093/BIOINFORMATICS/BTAD579},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaminskiLPAD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KampK23,
author = {Axel von Kamp and
Steffen Klamt},
title = {Balancing biomass reaction stoichiometry and measured fluxes in flux
balance analysis},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad600},
doi = {10.1093/BIOINFORMATICS/BTAD600},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KampK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KangEJHYL23,
author = {Yanlei Kang and
Arne Elofsson and
Yunliang Jiang and
Weihong Huang and
Minzhe Yu and
Zhong Li},
title = {{AFTGAN:} prediction of multi-type {PPI} based on attention free transformer
and graph attention network},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad052},
doi = {10.1093/BIOINFORMATICS/BTAD052},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KangEJHYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaratzasBAKSSBP23,
author = {Evangelos Karatzas and
Fotis A. Baltoumas and
Eleni Aplakidou and
Panagiota I. Kontou and
Panos Stathopoulos and
Leonidas Stefanis and
Pantelis G. Bagos and
Georgios A. Pavlopoulos},
title = {Flame (v2.0): advanced integration and interpretation of functional
enrichment results from multiple sources},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad490},
doi = {10.1093/BIOINFORMATICS/BTAD490},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaratzasBAKSSBP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarlebachCSCHRMVR23,
author = {Guy Karlebach and
Leigh Carmody and
Jagadish Chandrabose Sundaramurthi and
Elena Casiraghi and
Peter Hansen and
Justin T. Reese and
Christopher J. Mungall and
Giorgio Valentini and
Peter N. Robinson},
title = {An expectation-maximization framework for comprehensive prediction
of isoform-specific functions},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad132},
doi = {10.1093/BIOINFORMATICS/BTAD132},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarlebachCSCHRMVR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KasteS23,
author = {Joshua A. M. Kaste and
Yair Shachar{-}Hill},
title = {Accurate flux predictions using tissue-specific gene expression in
plant metabolic modeling},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad186},
doi = {10.1093/BIOINFORMATICS/BTAD186},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KasteS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KayaN23,
author = {Hikmet Emre Kaya and
Kevin J. Naidoo},
title = {CytoCopasi: a chemical systems biology target and drug discovery visual
data analytics platform},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad745},
doi = {10.1093/BIOINFORMATICS/BTAD745},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KayaN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaynarCBTNC23,
author = {Gun Kaynar and
Doruk Cakmakci and
Caroline Bund and
Julien Todeschi and
Izzie{-}Jacques Namer and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek},
title = {PiDeeL: metabolic pathway-informed deep learning model for survival
analysis and pathological classification of gliomas},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad684},
doi = {10.1093/BIOINFORMATICS/BTAD684},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaynarCBTNC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KernJSS23,
author = {Martin Kern and
Sabrina Jaeger{-}Honz and
Falk Schreiber and
Bj{\"{o}}rn Sommer},
title = {APL@voro - interactive visualization and analysis of cell membrane
simulations},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad083},
doi = {10.1093/BIOINFORMATICS/BTAD083},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KernJSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KerseviciuteG23,
author = {Ieva Kerseviciute and
Juozas Gordevicius},
title = {\emph{aPEAR}: an {R} package for autonomous visualization of pathway
enrichment networks},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad672},
doi = {10.1093/BIOINFORMATICS/BTAD672},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KerseviciuteG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanOGRWC23,
author = {Saifur R. Khan and
Andreea Obersterescu and
Erica P. Gunderson and
Babak Razani and
Michael B. Wheeler and
Brian J. Cox},
title = {metGWAS 1.0: an {R} workflow for network-driven over-representation
analysis between independent metabolomic and meta-genome-wide association
studies},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad523},
doi = {10.1093/BIOINFORMATICS/BTAD523},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanOGRWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanRK23,
author = {Abdul Rehman Khan and
Marcel J. T. Reinders and
Indu Khatri},
title = {Determining epitope specificity of T-cell receptors with transformers},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad632},
doi = {10.1093/BIOINFORMATICS/BTAD632},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanWSBPM23,
author = {Md. Abdullah{-}Al{-}Kamran Khan and
Jian Wu and
Yuhan Sun and
Alexander D. Barrow and
Anthony T. Papenfuss and
Stefano Mangiola},
title = {cellsig plug-in enhances CIBERSORTx signature selection for multidataset
transcriptomes with sparse multilevel modelling},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad685},
doi = {10.1093/BIOINFORMATICS/BTAD685},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanWSBPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhareMZ23,
author = {Harshavardhan Khare and
Nathaly Dongo Mendoza and
Chiara Zurzolo},
title = {CellWalker: a user-friendly and modular computational pipeline for
morphological analysis of microscopy images},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad710},
doi = {10.1093/BIOINFORMATICS/BTAD710},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhareMZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhatooniTW23,
author = {Zahed Khatooni and
Navid Teymourian and
Heather L. Wilson},
title = {Using a novel structure/function approach to select diverse swine
major histocompatibility complex 1 alleles to predict epitopes for
vaccine development},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad590},
doi = {10.1093/BIOINFORMATICS/BTAD590},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhatooniTW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhiliME23,
author = {Mohamed Reda El Khili and
Safyan Aman Memon and
Amin Emad},
title = {{MARSY:} a multitask deep-learning framework for prediction of drug
combination synergy scores},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad177},
doi = {10.1093/BIOINFORMATICS/BTAD177},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhiliME23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhoroshevskyiLRS23,
author = {Oleksandr Khoroshevskyi and
Nathan Leroy and
Vincent P. Reuter and
Nathan C. Sheffield},
title = {GEOfetch: a command-line tool for downloading data and standardized
metadata from {GEO} and {SRA}},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad069},
doi = {10.1093/BIOINFORMATICS/BTAD069},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhoroshevskyiLRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KilleGTP23,
author = {Bryce Kille and
Erik Garrison and
Todd J. Treangen and
Adam M. Phillippy},
title = {Minmers are a generalization of minimizers that enable unbiased local
Jaccard estimation},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad512},
doi = {10.1093/BIOINFORMATICS/BTAD512},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KilleGTP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimCSZ23,
author = {Yeonil Kim and
Yueh{-}Yun Chi and
Judong Shen and
Fei Zou},
title = {Robust genetic model-based SNP-set association test using CauchyGM},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac728},
doi = {10.1093/BIOINFORMATICS/BTAC728},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimCSZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimMS23,
author = {Hyunbin Kim and
Milot Mirdita and
Martin Steinegger},
title = {Foldcomp: a library and format for compressing and indexing large
protein structure sets},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad153},
doi = {10.1093/BIOINFORMATICS/BTAD153},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimPLBLKMSK23,
author = {Kijin Kim and
Kyungmin Park and
Seonghyeon Lee and
Seung{-}Hwan Baek and
Tae{-}Hun Lim and
Jongwoo Kim and
Balachandran Manavalan and
Jin{-}Won Song and
Won{-}Keun Kim},
title = {VirPipe: an easy-to-use and customizable pipeline for detecting viral
genomes from Nanopore sequencing},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad293},
doi = {10.1093/BIOINFORMATICS/BTAD293},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimPLBLKMSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimVKJG23,
author = {Minsoo Kim and
Daniel D. Vo and
Michi E. Kumagai and
Connor T. Jops and
Michael J. Gandal},
title = {GeneticsMakie.jl: a versatile and scalable toolkit for visualizing
locus-level genetic and genomic data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac786},
doi = {10.1093/BIOINFORMATICS/BTAC786},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimVKJG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Klein23,
author = {Hans{-}Ulrich Klein},
title = {demuxmix: demultiplexing oligonucleotide-barcoded single-cell {RNA}
sequencing data with regression mixture models},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad481},
doi = {10.1093/BIOINFORMATICS/BTAD481},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Klein23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlonizakisNG23,
author = {Antonios Klonizakis and
Christoforos Nikolaou and
Thomas Graf},
title = {{SEGCOND} predicts putative transcriptional condensate-associated
genomic regions by integrating multi-omics data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac742},
doi = {10.1093/BIOINFORMATICS/BTAC742},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KlonizakisNG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlonowskiLALK23,
author = {Jonathan Klonowski and
Qianqian Liang and
Zeynep H. Coban Akdemir and
Cecilia Lo and
Dennis Kostka},
title = {aenmd: annotating escape from nonsense-mediated decay for transcripts
with protein-truncating variants},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad556},
doi = {10.1093/BIOINFORMATICS/BTAD556},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KlonowskiLALK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlukowskiRG23,
author = {Piotr Klukowski and
Roland Riek and
Peter G{\"{u}}ntert},
title = {NMRtist: an online platform for automated biomolecular {NMR} spectra
analysis},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad066},
doi = {10.1093/BIOINFORMATICS/BTAD066},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KlukowskiRG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KonanovBBMBGBFMKLGI23,
author = {Dmitry Konanov and
Vladislav V. Babenko and
Aleksandra M. Belova and
Arina G. Madan and
Daria I Boldyreva and
Oksana E. Glushenko and
Ivan Butenko and
Dmitry E. Fedorov and
Alexander I Manolov and
Danil V. Krivonos and
Vassili N. Lazarev and
Vadim M. Govorun and
Elena N. Ilina},
title = {Snapper: high-sensitive detection of methylation motifs based on Oxford
Nanopore reads},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad702},
doi = {10.1093/BIOINFORMATICS/BTAD702},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KonanovBBMBGBFMKLGI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KorpelaJDHML23,
author = {Dani Korpela and
Emmi Jokinen and
Alexandru Dumitrescu and
Jani Huuhtanen and
Satu Mustjoki and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {{EPIC-TRACE:} predicting {TCR} binding to unseen epitopes using attention
and contextualized embeddings},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad743},
doi = {10.1093/BIOINFORMATICS/BTAD743},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KorpelaJDHML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KramerSC23,
author = {Alexander Kramer and
Theo Sanderson and
Russell Corbett{-}Detig},
title = {Treenome Browser: co-visualization of enormous phylogenies and millions
of genomes},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac772},
doi = {10.1093/BIOINFORMATICS/BTAC772},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KramerSC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KreflCB23,
author = {Daniel Krefl and
Alessandro Brandulas Cammarata and
Sven Bergmann},
title = {PascalX: a Python library for {GWAS} gene and pathway enrichment tests},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad296},
doi = {10.1093/BIOINFORMATICS/BTAD296},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KreflCB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KrismerBSM23,
author = {Elena Krismer and
Isabell Bludau and
Maximilian T. Strauss and
Matthias Mann},
title = {AlphaPeptStats: an open-source Python package for automated and scalable
statistical analysis of mass spectrometry-based proteomics},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad461},
doi = {10.1093/BIOINFORMATICS/BTAD461},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KrismerBSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KudoHYSH23,
author = {Genki Kudo and
Takumi Hirao and
Ryunosuke Yoshino and
Yasuteru Shigeta and
Takatsugu Hirokawa},
title = {Pocket to concavity: a tool for the refinement of protein-ligand binding
site shape from alpha spheres},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad212},
doi = {10.1093/BIOINFORMATICS/BTAD212},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KudoHYSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KulkarniZCD23,
author = {Roshan Kulkarni and
Yudi Zhang and
Steven B. Cannon and
Karin S. Dorman},
title = {{CAPG:} comprehensive allopolyploid genotyper},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac729},
doi = {10.1093/BIOINFORMATICS/BTAC729},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KulkarniZCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KumarKDDJ23,
author = {Ambuj Kumar and
Burak T. Kaynak and
Karin S. Dorman and
Pemra Doruker and
Robert L. Jernigan},
title = {Predicting allosteric pockets in protein biological assemblages},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad275},
doi = {10.1093/BIOINFORMATICS/BTAD275},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KumarKDDJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KumarLBPWLVA23,
author = {Ajay Anand Kumar and
Bart Loeys and
Gerarda Van De Beek and
Nils Peeters and
Wim Wuyts and
Lut Van Laer and
Geert Vandeweyer and
Maaike Alaerts},
title = {varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted
{NGS} data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac756},
doi = {10.1093/BIOINFORMATICS/BTAC756},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KumarLBPWLVA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KumarSAC23,
author = {Shivam Kumar and
Dipanka Sarmah and
Shailendra Asthana and
Samrat Chatterjee},
title = {konnect2prot: a web application to explore the protein properties
in a functional protein-protein interaction network},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac815},
doi = {10.1093/BIOINFORMATICS/BTAC815},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KumarSAC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KyawCKGCMP23,
author = {Wunna Kyaw and
Ryan C. Chai and
Weng Hua Khoo and
Leonard D. Goldstein and
Peter I Croucher and
John M. Murray and
Tri Giang Phan},
title = {{ENTRAIN:} integrating trajectory inference and gene regulatory networks
with spatial data to co-localize the receptor-ligand interactions
that specify cell fate},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad765},
doi = {10.1093/BIOINFORMATICS/BTAD765},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KyawCKGCMP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LYiKDTCBMG23,
author = {Sehi L'Yi and
Mark S. Keller and
Ariaki Dandawate and
Len Taing and
Chen{-}Hao Chen and
Myles Brown and
Clifford A. Meyer and
Nils Gehlenborg},
title = {Cistrome Explorer: an interactive visual analysis tool for large-scale
epigenomic data},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad018},
doi = {10.1093/BIOINFORMATICS/BTAD018},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LYiKDTCBMG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LacanSH23,
author = {Alice Lacan and
Mich{\`{e}}le Sebag and
Blaise Hanczar},
title = {GAN-based data augmentation for transcriptomics: survey and comparative
assessment},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {111--120},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad239},
doi = {10.1093/BIOINFORMATICS/BTAD239},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LacanSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaiH23,
author = {En{-}Yu Lai and
Yen{-}Tsung Huang},
title = {Genome-wide multimediator analyses using the generalized Berk-Jones
statistics with the composite test},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad544},
doi = {10.1093/BIOINFORMATICS/BTAD544},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaiH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LakiotakiPLFCTT23,
author = {Kleanthi Lakiotaki and
Zacharias Papadovasilakis and
Vincenzo Lagani and
Stefanos Fafalios and
Paulos Charonyktakis and
Michail Tsagris and
Ioannis Tsamardinos},
title = {Automated machine learning for genome wide association studies},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad545},
doi = {10.1093/BIOINFORMATICS/BTAD545},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LakiotakiPLFCTT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LarraldeZ23,
author = {Martin Larralde and
Georg Zeller},
title = {PyHMMER: a Python library binding to {HMMER} for efficient sequence
analysis},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad214},
doi = {10.1093/BIOINFORMATICS/BTAD214},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LarraldeZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LarssonFSL23,
author = {Ludvig Larsson and
Lovisa Franz{\'{e}}n and
Patrik L. St{\aa}hl and
Joakim Lundeberg},
title = {\emph{Semla:} a versatile toolkit for spatially resolved transcriptomics
analysis and visualization},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad626},
doi = {10.1093/BIOINFORMATICS/BTAD626},
timestamp = {Tue, 28 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LarssonFSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Lassmann23,
author = {Timo Lassmann},
title = {SAMStat 2: quality control for next generation sequencing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad019},
doi = {10.1093/BIOINFORMATICS/BTAD019},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Lassmann23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LauECYLMWGL23,
author = {Bayo Lau and
Prashant S. Emani and
Jackson Chapman and
Lijing Yao and
Tarsus Lam and
Paul Merrill and
Jonathan Warrell and
Mark B. Gerstein and
Hugo Y. K. Lam},
title = {Insights from incorporating quantum computing into drug design workflows},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac789},
doi = {10.1093/BIOINFORMATICS/BTAC789},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LauECYLMWGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LavegliaBAR23,
author = {Vincenzo Laveglia and
Milana Bazayeva and
Claudia Andreini and
Antonio Rosato},
title = {Hunting down zinc(II)-binding sites in proteins with distance matrices},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad653},
doi = {10.1093/BIOINFORMATICS/BTAD653},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LavegliaBAR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaveryBCMSW23,
author = {Jessica A. Lavery and
Samantha Brown and
Michael Curry and
Axel Martin and
Daniel D. Sjoberg and
Karissa Whiting},
title = {A data processing pipeline for the {AACR} project {GENIE} biopharma
collaborative data with the \{genieBPC\} {R} package},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac796},
doi = {10.1093/BIOINFORMATICS/BTAC796},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaveryBCMSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LearyXMJSKSRYP23,
author = {Jack R. Leary and
Yi Xu and
Ashley B. Morrison and
Chong Jin and
Emily C. Shen and
Peyton C. Kuhlers and
Ye Su and
Naim U. Rashid and
Jen Jen Yeh and
Xianlu Laura Peng},
title = {Sub-Cluster Identification through Semi-Supervised Optimization of
Rare-Cell Silhouettes {(SCISSORS)} in single-cell RNA-sequencing},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad449},
doi = {10.1093/BIOINFORMATICS/BTAD449},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LearyXMJSKSRYP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeCNWHGBWR23,
author = {Eric Lee and
Kevin Chern and
Michael Nissen and
Xuehai Wang and
Chris Huang and
Anita K. Gandhi and
Alexandre Bouchard{-}C{\^{o}}t{\'{e}} and
Andrew P. Weng and
Andrew Roth},
title = {SpatialSort: a Bayesian model for clustering and cell population annotation
of spatial proteomics data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {131--139},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad242},
doi = {10.1093/BIOINFORMATICS/BTAD242},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeCNWHGBWR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeWJCYOKKJJLKJSKYPNJ23,
author = {Jae{-}Won Lee and
Jong{-}Hyun Won and
Seonggwang Jeon and
Yujin Choo and
Yubin Yeon and
Jin{-}Seon Oh and
Minsoo Kim and
Seonhwa Kim and
InSuk Joung and
Cheongjae Jang and
Sung Jong Lee and
Tae Hyun Kim and
Kyong Hwan Jin and
Giltae Song and
Eun{-}Sol Kim and
Jejoong Yoo and
Eunok Paek and
Yung{-}Kyun Noh and
Keehyoung Joo},
title = {DeepFold: enhancing protein structure prediction through optimized
loss functions, improved template features, and re-optimized energy
function},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad712},
doi = {10.1093/BIOINFORMATICS/BTAD712},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeWJCYOKKJJLKJSKYPNJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeiCHZL23,
author = {Jimeng Lei and
Zongheng Cai and
Xinyi He and
Wanting Zheng and
Jianxiao Liu},
title = {An approach of gene regulatory network construction using mixed entropy
optimizing context-related likelihood mutual information},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac717},
doi = {10.1093/BIOINFORMATICS/BTAC717},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeiCHZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Leonard23,
author = {Conrad Leonard},
title = {\emph{streammd}: fast low-memory duplicate marking using a Bloom filter},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad181},
doi = {10.1093/BIOINFORMATICS/BTAD181},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Leonard23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Li23,
author = {Heng Li},
title = {Protein-to-genome alignment with miniprot},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad014},
doi = {10.1093/BIOINFORMATICS/BTAD014},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Li23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiCCJZ23,
author = {Chen Li and
Xiaoyang Chen and
Shengquan Chen and
Rui Jiang and
Xuegong Zhang},
title = {simCAS: an embedding-based method for simulating single-cell chromatin
accessibility sequencing data},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad453},
doi = {10.1093/BIOINFORMATICS/BTAD453},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiCCJZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiCYL23,
author = {Chen Li and
Ting{-}Fung Chan and
Can Yang and
Zhixiang Lin},
title = {stVAE deconvolves cell-type composition in large-scale cellular resolution
spatial transcriptomics},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad642},
doi = {10.1093/BIOINFORMATICS/BTAD642},
timestamp = {Tue, 26 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiCYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiDZHSY23,
author = {Lechuan Li and
Ruth Dannenfelser and
Yu Zhu and
Nathaniel Hejduk and
Santiago Segarra and
Vicky Yao},
title = {Joint embedding of biological networks for cross-species functional
alignment},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad529},
doi = {10.1093/BIOINFORMATICS/BTAD529},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiDZHSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiGGW23,
author = {Yang Li and
Zihou Guo and
Xin Gao and
Guohua Wang},
title = {{MMCL-CDR:} enhancing cancer drug response prediction with multi-omics
and morphology images contrastive representation learning},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad734},
doi = {10.1093/BIOINFORMATICS/BTAD734},
timestamp = {Tue, 09 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiGGW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiJWLDHW23,
author = {Zhongshen Li and
Junru Jin and
Yu Wang and
Wentao Long and
Yuanhao Ding and
Haiyan Hu and
Leyi Wei},
title = {ExamPle: explainable deep learning framework for the prediction of
plant small secreted peptides},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad108},
doi = {10.1093/BIOINFORMATICS/BTAD108},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiJWLDHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLJJWZLLL23,
author = {Yuxin Li and
Xuhua Liu and
Xueyan Jia and
Tao Jiang and
Jianghao Wu and
Qianlong Zhang and
Junhuai Li and
Xiangning Li and
Anan Li},
title = {A high-performance deep-learning-based pipeline for whole-brain vasculature
segmentation at the capillary resolution},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad145},
doi = {10.1093/BIOINFORMATICS/BTAD145},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLJJWZLLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiS23,
author = {Mengbo Li and
Gordon K. Smyth},
title = {Neither random nor censored: estimating intensity-dependent probabilities
for missing values in label-free proteomics},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad200},
doi = {10.1093/BIOINFORMATICS/BTAD200},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiSCS23,
author = {Xiang Li and
Qian Shi and
Ke Chen and
Mingfu Shao},
title = {Seeding with minimized subsequence},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {232--241},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad218},
doi = {10.1093/BIOINFORMATICS/BTAD218},
timestamp = {Fri, 09 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiSCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiSCWCL23,
author = {Lingyu Li and
Liangjie Sun and
Guangyi Chen and
Chi{-}Wing Wong and
Wai{-}Ki Ching and
Zhi{-}Ping Liu},
title = {LogBTF: gene regulatory network inference using Boolean threshold
network model from single-cell gene expression data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad256},
doi = {10.1093/BIOINFORMATICS/BTAD256},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiSCWCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiSRZYZCX23,
author = {Heng Li and
Mijuan Shi and
Keyi Ren and
Lei Zhang and
Weidong Ye and
Wanting Zhang and
Yingyin Cheng and
Xiaoqin Xia},
title = {Visual Omics: a web-based platform for omics data analysis and visualization
with rich graph-tuning capabilities},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac777},
doi = {10.1093/BIOINFORMATICS/BTAC777},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiSRZYZCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiWXTZWWCHL23,
author = {Yunxiang Li and
Yumeng Wei and
Sheng Xu and
Qingxiong Tan and
Licheng Zong and
Jiuming Wang and
Yixuan Wang and
Jiayang Chen and
Liang Hong and
Yu Li},
title = {AcrNET: predicting anti-CRISPR with deep learning},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad259},
doi = {10.1093/BIOINFORMATICS/BTAD259},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiWXTZWWCHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiYZWS23,
author = {Jia{-}Ning Li and
Guang Yang and
Peng{-}Cheng Zhao and
Xue{-}Xin Wei and
Jian{-}Yu Shi},
title = {CProMG: controllable protein-oriented molecule generation with desired
binding affinity and drug-like properties},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {326--336},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad222},
doi = {10.1093/BIOINFORMATICS/BTAD222},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiYZWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZFXZMCZP23,
author = {Zutan Li and
Yuan Zhang and
Jingya Fang and
Zhihui Xu and
Hao Zhang and
Minfang Mao and
Yuanyuan Chen and
Liangyun Zhang and
Cong Pian},
title = {NcPath: a novel platform for visualization and enrichment analysis
of human non-coding {RNA} and {KEGG} signaling pathways},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac812},
doi = {10.1093/BIOINFORMATICS/BTAC812},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZFXZMCZP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZLZ23,
author = {Limin Li and
Yameng Zhao and
Huiran Li and
Shuqin Zhang},
title = {{BLTSA:} pseudotime prediction for single cells by branched local
tangent space alignment},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad054},
doi = {10.1093/BIOINFORMATICS/BTAD054},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZXWLWLLGC23,
author = {Qizhi Li and
Xubin Zheng and
Jize Xie and
Ran Wang and
Mengyao Li and
Man Hon Wong and
Kwong{-}Sak Leung and
Shuai Li and
Qingshan Geng and
Lixin Cheng},
title = {bvnGPS: a generalizable diagnostic model for acute bacterial and viral
infection using integrative host transcriptomics and pretrained neural
networks},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad109},
doi = {10.1093/BIOINFORMATICS/BTAD109},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZXWLWLLGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZZWL23,
author = {Yiming Li and
Min Zeng and
Fuhao Zhang and
Fang{-}Xiang Wu and
Min Li},
title = {DeepCellEss: cell line-specific essential protein prediction with
attention-based interpretable deep learning},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac779},
doi = {10.1093/BIOINFORMATICS/BTAC779},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiangDCWRZ23,
author = {Jiangshan Liang and
Luchen Deng and
Shize Chen and
Yimin Wang and
Zongcai Ruan and
Lingli Zhang},
title = {Vaa3D-x for cross-platform teravoxel-scale immersive exploration of
multidimensional image data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac794},
doi = {10.1093/BIOINFORMATICS/BTAC794},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiangDCWRZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiangFQZC23,
author = {Xujun Liang and
Ying Fu and
Lingzhi Qu and
Pengfei Zhang and
Yongheng Chen},
title = {Prediction of drug side effects with transductive matrix co-completion},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad006},
doi = {10.1093/BIOINFORMATICS/BTAD006},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiangFQZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiaoOSKJLTAUMZ23,
author = {Xinmeng Liao and
Mehmet Ozcan and
Mengnan Shi and
Woonghee Kim and
Han Jin and
Xiangyu Li and
Hasan Turkez and
Adnane Achour and
Mathias Uhl{\'{e}}n and
Adil Mardinoglu and
Cheng Zhang},
title = {Open MoA: revealing the mechanism of action (MoA) based on network
topology and hierarchy},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad666},
doi = {10.1093/BIOINFORMATICS/BTAD666},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiaoOSKJLTAUMZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiaoSS23,
author = {Herui Liao and
Jiayu Shang and
Yanni Sun},
title = {GDmicro: classifying host disease status with {GCN} and deep adaptation
network based on the human gut microbiome data},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad747},
doi = {10.1093/BIOINFORMATICS/BTAD747},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiaoSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiaoXMZ23,
author = {Zhirui Liao and
Lei Xie and
Hiroshi Mamitsuka and
Shanfeng Zhu},
title = {Sc2Mol: a scaffold-based two-step molecule generator with variational
autoencoder and transformer},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac814},
doi = {10.1093/BIOINFORMATICS/BTAC814},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiaoXMZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiaoZ23,
author = {Weiheng Liao and
Xuelian Zhang},
title = {Patpat: a public proteomics dataset search framework},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad076},
doi = {10.1093/BIOINFORMATICS/BTAD076},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiaoZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinKHBN23,
author = {Andy Lin and
Brooke L. Deatherage Kaiser and
Janine R. Hutchison and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {MS1Connect: a mass spectrometry run similarity measure},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad058},
doi = {10.1093/BIOINFORMATICS/BTAD058},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinKHBN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LindeggerCAGMM23,
author = {Jo{\"{e}}l Lindegger and
Damla Senol Cali and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Nika Mansouri{-}Ghiasi and
Onur Mutlu},
title = {Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs,
GPUs, and ASICs},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad151},
doi = {10.1093/BIOINFORMATICS/BTAD151},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LindeggerCAGMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LioGLFBKLT23,
author = {Chit Tong Lio and
Gordon Grabert and
Zakaria Louadi and
Amit Fenn and
Jan Baumbach and
Tim Kacprowski and
Markus List and
Olga Tsoy},
title = {Systematic analysis of alternative splicing in time course data using
Spycone},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac846},
doi = {10.1093/BIOINFORMATICS/BTAC846},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LioGLFBKLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiouHR23,
author = {Lathan Liou and
Milena Hornburg and
David S. Robertson},
title = {Global {FDR} control across multiple RNAseq experiments},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac718},
doi = {10.1093/BIOINFORMATICS/BTAC718},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiouHR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuEG23,
author = {Yi Liu and
Benjamin L. Elsworth and
Tom R. Gaunt},
title = {Using language models and ontology topology to perform semantic mapping
of traits between biomedical datasets},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad169},
doi = {10.1093/BIOINFORMATICS/BTAD169},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuEG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuHK23,
author = {Renming Liu and
Matthew J. Hirn and
Arjun Krishnan},
title = {Accurately modeling biased random walks on weighted networks using
\emph{node2vec+}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad047},
doi = {10.1093/BIOINFORMATICS/BTAD047},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuHK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuLZ23,
author = {Jun Liu and
Dong Liu and
Gui{-}Jun Zhang},
title = {DeepUMQA3: a web server for accurate assessment of interface residue
accuracy in protein complexes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad591},
doi = {10.1093/BIOINFORMATICS/BTAD591},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuM23,
author = {Huiling Liu and
Wenxiu Ma},
title = {scHiCDiff: detecting differential chromatin interactions in single-cell
Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad625},
doi = {10.1093/BIOINFORMATICS/BTAD625},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuMZZKMCGWZ23,
author = {Jian Liu and
Fubin Ma and
Yongdi Zhu and
Naiqian Zhang and
Lingming Kong and
Jia Mi and
Haiyan Cong and
Rui Gao and
Mingyi Wang and
Yusen Zhang},
title = {MaxCLK: discovery of cancer driver genes via maximal clique and information
entropy of modules},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad737},
doi = {10.1093/BIOINFORMATICS/BTAD737},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuMZZKMCGWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuS23,
author = {Daniel Liu and
Martin Steinegger},
title = {Block Aligner: an adaptive SIMD-accelerated aligner for sequences
and position-specific scoring matrices},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad487},
doi = {10.1093/BIOINFORMATICS/BTAD487},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuTZTLGHF23,
author = {Zi Hao Liu and
Jo{\~{a}}o M. C. Teixeira and
Oufan Zhang and
Thomas E. Tsangaris and
Jie Li and
Claudiu C. Gradinaru and
Teresa Head{-}Gordon and
Julie D. Forman{-}Kay},
title = {Local Disordered Region Sampling {(LDRS)} for ensemble modeling of
proteins with experimentally undetermined or low confidence prediction
segments},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad739},
doi = {10.1093/BIOINFORMATICS/BTAD739},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuTZTLGHF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuYLW23,
author = {Yiwei Liu and
Changhuo Yang and
Hong{-}Dong Li and
Jianxin Wang},
title = {IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based
method for predicting isoform functions},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad530},
doi = {10.1093/BIOINFORMATICS/BTAD530},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuYLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuYZWXWZ23,
author = {Yuhang Liu and
Hao Yuan and
Qiang Zhang and
Zixuan Wang and
Shuwen Xiong and
Naifeng Wen and
Yongqing Zhang},
title = {Multiple sequence alignment based on deep reinforcement learning with
self-attention and positional encoding},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad636},
doi = {10.1093/BIOINFORMATICS/BTAD636},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuYZWXWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZSZZGSD23,
author = {Jinding Liu and
Yaru Zhang and
Yapin Shi and
Yiqing Zheng and
Yali Zhu and
Zhuoran Guan and
Danyu Shen and
Daolong Dou},
title = {FungiExp: a user-friendly database and analysis platform for exploring
fungal gene expression and alternative splicing},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad042},
doi = {10.1093/BIOINFORMATICS/BTAD042},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZSZZGSD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZZLDP23,
author = {Yufeng Liu and
Ye Zhong and
Xuan Zhao and
Lijuan Liu and
Liya Ding and
Hanchuan Peng},
title = {Tracing weak neuron fibers},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac816},
doi = {10.1093/BIOINFORMATICS/BTAC816},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZZLDP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LoukachevitchMBRBIBT23,
author = {Natalia V. Loukachevitch and
Suresh Manandhar and
Elina Baral and
Igor Rozhkov and
Pavel Braslavski and
Vladimir Ivanov and
Tatiana Batura and
Elena Tutubalina},
title = {{NEREL-BIO:} a dataset of biomedical abstracts annotated with nested
named entities},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad161},
doi = {10.1093/BIOINFORMATICS/BTAD161},
timestamp = {Thu, 06 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LoukachevitchMBRBIBT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuebbertP23,
author = {Laura Luebbert and
Lior Pachter},
title = {Efficient querying of genomic reference databases with \emph{gget}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac836},
doi = {10.1093/BIOINFORMATICS/BTAC836},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuebbertP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoWLLCL23,
author = {Ling Luo and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Robert Leaman and
Qingyu Chen and
Zhiyong Lu},
title = {{AIONER:} all-in-one scheme-based biomedical named entity recognition
using deep learning},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad310},
doi = {10.1093/BIOINFORMATICS/BTAD310},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoWLLCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LyTrongBM23,
author = {Nhan Ly{-}Trong and
Giuseppe M. J. Barca and
Bui Quang Minh},
title = {AliSim-HPC: parallel sequence simulator for phylogenetics},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad540},
doi = {10.1093/BIOINFORMATICS/BTAD540},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LyTrongBM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LyuZLQ23,
author = {Pin Lyu and
Yijie Zhai and
Taibo Li and
Jiang Qian},
title = {CellAnn: a comprehensive, super-fast, and user-friendly single-cell
annotation web server},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad521},
doi = {10.1093/BIOINFORMATICS/BTAD521},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LyuZLQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaCSMT23,
author = {Jun Ma and
Manuel C{\'{a}}ceres and
Leena Salmela and
Veli M{\"{a}}kinen and
Alexandru I. Tomescu},
title = {Chaining for accurate alignment of erroneous long reads to acyclic
variation graphs},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad460},
doi = {10.1093/BIOINFORMATICS/BTAD460},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaCSMT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaFKLGSHS23,
author = {Steve Ma and
Longxuan Fan and
Sai Anish Konanki and
Eva Liu and
John H. Gennari and
Lucian P. Smith and
Joseph L. Hellerstein and
Herbert M. Sauro},
title = {VSCode-Antimony: a source editor for building, analyzing, and translating
antimony models},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad753},
doi = {10.1093/BIOINFORMATICS/BTAD753},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaFKLGSHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaLZWLGZLGS23,
author = {Jiani Ma and
Chen Li and
Yiwen Zhang and
Zhikang Wang and
Shanshan Li and
Yuming Guo and
Lin Zhang and
Hui Liu and
Xin Gao and
Jiangning Song},
title = {MULGA, a unified multi-view graph autoencoder-based approach for identifying
drug-protein interaction and drug repositioning},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad524},
doi = {10.1093/BIOINFORMATICS/BTAD524},
timestamp = {Fri, 19 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaLZWLGZLGS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MacneePBKPSMBRCTBMLNML23,
author = {Marie Macnee and
Eduardo P{\'{e}}rez{-}Palma and
Tobias Br{\"{u}}nger and
Chiara Kl{\"{o}}ckner and
Konrad Platzer and
Arthur Stefanski and
Ludovica Montanucci and
Allan Bayat and
Maximilian Radtke and
Ryan L. Collins and
Michael E. Talkowski and
Daniel Blankenberg and
Rikke S. M{\o}ller and
Johannes R. Lemke and
Michael Nothnagel and
Patrick May and
Dennis Lal},
title = {CNV-ClinViewer: enhancing the clinical interpretation of large copy-number
variants online},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad290},
doi = {10.1093/BIOINFORMATICS/BTAD290},
timestamp = {Sat, 06 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MacneePBKPSMBRCTBMLNML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MadeoSMMC23,
author = {Giovanni Madeo and
Castrense Savojardo and
Matteo Manfredi and
Pier Luigi Martelli and
Rita Casadio},
title = {CoCoNat: a novel method based on deep learning for coiled-coil prediction},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad495},
doi = {10.1093/BIOINFORMATICS/BTAD495},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MadeoSMMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MahadeshwarTWPP23,
author = {Gandhar Mahadeshwar and
Rafael de Cesaris Araujo Tavares and
Han Wan and
Zion R. Perry and
Anna Marie Pyle},
title = {RSCanner: rapid assessment and visualization of {RNA} structure content},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad111},
doi = {10.1093/BIOINFORMATICS/BTAD111},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MahadeshwarTWPP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MailhotMN23,
author = {Olivier Mailhot and
Fran{\c{c}}ois Major and
Rafael Najmanovich},
title = {The DynaSig-ML Python package: automated learning of biomolecular
dynamics-function relationships},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad180},
doi = {10.1093/BIOINFORMATICS/BTAD180},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MailhotMN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalekpourSAS23,
author = {Seyed Amir Malekpour and
Maryam Shahdoust and
Rosa Aghdam and
Mehdi Sadeghi},
title = {wpLogicNet: logic gate and structure inference in gene regulatory
networks},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad072},
doi = {10.1093/BIOINFORMATICS/BTAD072},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalekpourSAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalinverniCGB23,
author = {Roberto Malinverni and
David Corujo and
Bernat Gel and
Marcus Buschbeck},
title = {regioneReloaded: evaluating the association of multiple genomic region
sets},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad704},
doi = {10.1093/BIOINFORMATICS/BTAD704},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalinverniCGB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MallawaarachchiRDPGGBHIH23,
author = {Vijini Mallawaarachchi and
Michael J. Roach and
Przemyslaw Decewicz and
Bhavya Nalagampalli Papudeshi and
Sarah K. Giles and
Susanna R. Grigson and
George Bouras and
Ryan D. Hesse and
Laura K. Inglis and
Abbey L. K. Hutton and
Elizabeth A. Dinsdale and
Robert A. Edwards},
title = {Phables: from fragmented assemblies to high-quality bacteriophage
genomes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad586},
doi = {10.1093/BIOINFORMATICS/BTAD586},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MallawaarachchiRDPGGBHIH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MancusoLK23,
author = {Christopher A. Mancuso and
Renming Liu and
Arjun Krishnan},
title = {PyGenePlexus: a Python package for gene discovery using network-based
machine learning},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad064},
doi = {10.1093/BIOINFORMATICS/BTAD064},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MancusoLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManeFVBC23,
author = {Aniket C. Mane and
Mahsa Faizrahnemoon and
Tom{\'{a}}s Vinar and
Brona Brejov{\'{a}} and
C{\'{e}}dric Chauve},
title = {PlasBin-flow: a flow-based {MILP} algorithm for plasmid contigs binning},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {288--296},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad250},
doi = {10.1093/BIOINFORMATICS/BTAD250},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ManeFVBC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManzLG23,
author = {Trevor Manz and
Sehi L'Yi and
Nils Gehlenborg},
title = {Gos: a declarative library for interactive genomics visualization
in Python},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad050},
doi = {10.1093/BIOINFORMATICS/BTAD050},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ManzLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarchetL23,
author = {Camille Marchet and
Antoine Limasset},
title = {Scalable sequence database search using partitioned aggregated Bloom
comb trees},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {252--259},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad225},
doi = {10.1093/BIOINFORMATICS/BTAD225},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarchetL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarcoSolaEGPGM23,
author = {Santiago Marco{-}Sola and
Jordan M. Eizenga and
Andrea Guarracino and
Benedict Paten and
Erik Garrison and
Miquel Moret{\'{o}}},
title = {Optimal gap-affine alignment in \emph{O}(\emph{s}) space},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad074},
doi = {10.1093/BIOINFORMATICS/BTAD074},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarcoSolaEGPGM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarriottKKDAI23,
author = {Heather Marriott and
Renata Kabiljo and
Ahmad Al Khleifat and
Richard J. B. Dobson and
Ammar Al{-}Chalabi and
Alfredo Iacoangeli},
title = {DNAscan2: a versatile, scalable, and user-friendly analysis pipeline
for human next-generation sequencing data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad152},
doi = {10.1093/BIOINFORMATICS/BTAD152},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarriottKKDAI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarshPJBFABE23,
author = {Jacob I Marsh and
Jakob Petereit and
Brady A Johnston and
Philipp E. Bayer and
Cassandria G. Tay Fernandez and
Hawlader A Al{-}Mamun and
Jacqueline Batley and
David Edwards},
title = {crosshap: {R} package for local haplotype visualization for trait
association analysis},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad518},
doi = {10.1093/BIOINFORMATICS/BTAD518},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarshPJBFABE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MartensBMSCY23,
author = {Kaspar M{\"{a}}rtens and
Michele Bortolomeazzi and
Lucia Montorsi and
Jo Spencer and
Francesca D. Ciccarelli and
Christopher Yau},
title = {Rarity: discovering rare cell populations from single-cell imaging
data},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad750},
doi = {10.1093/BIOINFORMATICS/BTAD750},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MartensBMSCY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MartinAPCML23,
author = {Samuel Martin and
Martin Ayling and
Livia Patrono and
Mario C{\'{a}}ccamo and
Pablo Murcia and
Richard M. Leggett},
title = {Capturing variation in metagenomic assembly graphs with MetaCortex},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad020},
doi = {10.1093/BIOINFORMATICS/BTAD020},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MartinAPCML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MartinNLH23,
author = {Roman Martin and
Minh Kien Nguyen and
Nick Lowack and
Dominik Heider},
title = {{ODNA:} identification of organellar {DNA} by machine learning},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad326},
doi = {10.1093/BIOINFORMATICS/BTAD326},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MartinNLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MartinezHGSDXBCHBSH23,
author = {Teresa De Jesus Martinez and
Elliot A. Hershberg and
Emma Guo and
Garrett Stevens and
Colin M. Diesh and
Peter Xie and
Caroline Bridge and
Scott Cain and
Robin Haw and
Robert M. Buels and
Lincoln D. Stein and
Ian H. Holmes},
title = {JBrowse Jupyter: a Python interface to JBrowse 2},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad032},
doi = {10.1093/BIOINFORMATICS/BTAD032},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MartinezHGSDXBCHBSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MassaratLRWDG23,
author = {Arya R. Massarat and
Michael Lamkin and
Ciara Reeve and
Amy L. Williams and
Matteo D'Antonio and
Melissa Gymrek},
title = {Haptools: a toolkit for admixture and haplotype analysis},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad104},
doi = {10.1093/BIOINFORMATICS/BTAD104},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MassaratLRWDG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MassonisVB23,
author = {Gemma Massonis and
Alejandro F. Villaverde and
Julio R. Banga},
title = {Improving dynamic predictions with ensembles of observable models},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac755},
doi = {10.1093/BIOINFORMATICS/BTAC755},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MassonisVB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MastropietroCA23,
author = {Andrea Mastropietro and
Gianluca De Carlo and
Aris Anagnostopoulos},
title = {{XGDAG:} explainable gene-disease associations via graph neural networks},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad482},
doi = {10.1093/BIOINFORMATICS/BTAD482},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MastropietroCA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MasutaniKM23,
author = {Bansho Masutani and
Riki Kawahara and
Shinichi Morishita},
title = {Decomposing mosaic tandem repeats accurately from long reads},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad185},
doi = {10.1093/BIOINFORMATICS/BTAD185},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MasutaniKM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MattockMCRW23,
author = {Jennifer Mattock and
Marina Mart{\'{\i}}nez{-}{\'{A}}lvaro and
Matthew A Cleveland and
Rainer Roehe and
Mick Watson},
title = {KOunt: a reproducible {KEGG} orthologue abundance workflow},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad483},
doi = {10.1093/BIOINFORMATICS/BTAD483},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MattockMCRW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MazuzSKRS23,
author = {Eyal Mazuz and
Guy Shtar and
Nir Kutsky and
Lior Rokach and
Bracha Shapira},
title = {Pretrained transformer models for predicting the withdrawal of drugs
from the market},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad519},
doi = {10.1093/BIOINFORMATICS/BTAD519},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MazuzSKRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/McConnellP23,
author = {Brendan S. McConnell and
Matthew W. Parker},
title = {Protein intrinsically disordered regions have a non-random, modular
architecture},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad732},
doi = {10.1093/BIOINFORMATICS/BTAD732},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/McConnellP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MeirellesKKFST23,
author = {Andr{\'{e}} L. S. Meirelles and
Tahsin M. Kur{\c{c}} and
Jun Kong and
Renato Ferreira and
Joel H. Saltz and
George Teodoro},
title = {Effective and efficient active learning for deep learning-based tissue
image analysis},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad138},
doi = {10.1093/BIOINFORMATICS/BTAD138},
timestamp = {Thu, 08 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MeirellesKKFST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MendelevichGPTM23,
author = {Asia Mendelevich and
Saumya Gupta and
Aleksei Pakharev and
Athanasios Teodosiadis and
Andrey A. Mironov and
Alexander A. Gimelbrant},
title = {Foreign {RNA} spike-ins enable accurate allele-specific expression
analysis at scale},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {431--439},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad254},
doi = {10.1093/BIOINFORMATICS/BTAD254},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MendelevichGPTM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MidlikNADSVV23,
author = {Adam Midlik and
Sreenath Nair and
Stephen Anyango and
Mandar S. Deshpande and
David Sehnal and
Mihaly Varadi and
Sameer Velankar},
title = {PDBImages: a command-line tool for automated macromolecular structure
visualization},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad744},
doi = {10.1093/BIOINFORMATICS/BTAD744},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MidlikNADSVV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MikalsenZ23,
author = {Andrew J. Mikalsen and
Jaroslaw Zola},
title = {Coriolis: enabling metagenomic classification on lightweight mobile
devices},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {66--75},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad243},
doi = {10.1093/BIOINFORMATICS/BTAD243},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MikalsenZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MilleRCR23,
author = {Marie Mille and
Julie Ripoll and
Bastien Cazaux and
Eric Rivals},
title = {dipwmsearch: a Python package for searching di-PWM motifs},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad141},
doi = {10.1093/BIOINFORMATICS/BTAD141},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MilleRCR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Misirli23,
author = {G{\"{o}}ksel Misirli},
title = {libSBOLj3: a graph-based library for design and data exchange in synthetic
biology},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad525},
doi = {10.1093/BIOINFORMATICS/BTAD525},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Misirli23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoLHM23,
author = {Yu K. Mo and
Robert Lanfear and
Matthew W. Hahn and
Bui Quang Minh},
title = {Updated site concordance factors minimize effects of homoplasy and
taxon sampling},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac741},
doi = {10.1093/BIOINFORMATICS/BTAC741},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoLHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoXYCL23,
author = {Qing Mo and
Zexin Xu and
Hui Yan and
Pin Chen and
Yutong Lu},
title = {{VSTH:} a user-friendly web server for structure-based virtual screening
on Tianhe-2},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac740},
doi = {10.1093/BIOINFORMATICS/BTAC740},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoXYCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoenJ23,
author = {Marcus T. Moen and
Iain G. Johnston},
title = {HyperHMM: efficient inference of evolutionary and progressive dynamics
on hypercubic transition graphs},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac803},
doi = {10.1093/BIOINFORMATICS/BTAC803},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoenJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MondalRPFB23,
author = {Abhijit Mondal and
Luiz Thib{\'{e}}rio Rangel and
Jack G. Payette and
Gregory Fournier and
Mukul S. Bansal},
title = {DaTeR: error-correcting phylogenetic chronograms using relative time
constraints},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad084},
doi = {10.1093/BIOINFORMATICS/BTAD084},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MondalRPFB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MongiaBAYLBKBM23,
author = {Mihir Mongia and
Romel Baral and
Abhinav Adduri and
Donghui Yan and
Yudong Liu and
Yuying Bian and
Paul Kim and
Bahar Behsaz and
Hosein Mohimani},
title = {AdenPredictor: accurate prediction of the adenylation domain specificity
of nonribosomal peptide biosynthetic gene clusters in microbial genomes},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {40--46},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad235},
doi = {10.1093/BIOINFORMATICS/BTAD235},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MongiaBAYLBKBM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MontiSSANBC23,
author = {Francesco Monti and
David Stewart and
Anuradha Surendra and
Irina Alecu and
Thao Nguyen{-}Tran and
Steffany A. L. Bennett and
Miroslava Cuperlovic{-}Culf},
title = {Signed Distance Correlation (SiDCo): an online implementation of distance
correlation and partial distance correlation for data-driven network
analysis},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad210},
doi = {10.1093/BIOINFORMATICS/BTAD210},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MontiSSANBC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Moreau23,
author = {Erwan Moreau},
title = {Literature-based discovery: addressing the issue of the subpar evaluation
methodology},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad090},
doi = {10.1093/BIOINFORMATICS/BTAD090},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Moreau23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorelWS23,
author = {Benoit Morel and
Tom A. Williams and
Alexandros Stamatakis},
title = {Asteroid: a new algorithm to infer species trees from gene trees under
high proportions of missing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac832},
doi = {10.1093/BIOINFORMATICS/BTAC832},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorelWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorenoMQ23,
author = {Thaidy Moreno and
Joaquin Magana and
David A. Quigley},
title = {{AARDVARK:} an automated reversion detector for variants affecting
resistance kinetics},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad509},
doi = {10.1093/BIOINFORMATICS/BTAD509},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorenoMQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorrisSAZSMHCSRHSCBCPMKT23,
author = {John H. Morris and
Karthik Soman and
Rabia E. Akbas and
Xiaoyuan Zhou and
Brett Smith and
Elaine C. Meng and
Conrad C. Huang and
Gabriel Cerono and
Gundolf Schenk and
Angela Rizk{-}Jackson and
Adil Harroud and
Lauren M. Sanders and
Sylvain V. Costes and
Krish Bharat and
Arjun Chakraborty and
Alexander R. Pico and
Taline Mardirossian and
Michael J. Keiser and
Alice Tang and
Josef Hardi and
Yongmei Shi and
Mark A. Musen and
Sharat Israni and
Sui Huang and
Peter W. Rose and
Charlotte A. Nelson and
Sergio E. Baranzini},
title = {The scalable precision medicine open knowledge engine {(SPOKE):} a
massive knowledge graph of biomedical information},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad080},
doi = {10.1093/BIOINFORMATICS/BTAD080},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorrisSAZSMHCSRHSCBCPMKT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorrisonZJS23,
author = {Jacob Morrison and
Wanding Zhou and
Benjamin K. Johnson and
Hui Shen},
title = {Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite
sequencing},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad729},
doi = {10.1093/BIOINFORMATICS/BTAD729},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorrisonZJS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Moshiri23,
author = {Niema Moshiri},
title = {ViralConsensus: a fast and memory-efficient tool for calling viral
consensus genome sequences directly from read alignment data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad317},
doi = {10.1093/BIOINFORMATICS/BTAD317},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Moshiri23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MovassaghSP23,
author = {Mercedeh Movassagh and
Steven J. Schiff and
Joseph N. Paulson},
title = {mbQTL: an R/Bioconductor package for microbial quantitative trait
loci {(QTL)} estimation},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad565},
doi = {10.1093/BIOINFORMATICS/BTAD565},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MovassaghSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuDLDPL23,
author = {Wancen Mu and
Eric S. Davis and
Stuart Lee and
Mikhail G. Dozmorov and
Douglas H. Phanstiel and
Michael I. Love},
title = {bootRanges: flexible generation of null sets of genomic ranges for
hypothesis testing},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad190},
doi = {10.1093/BIOINFORMATICS/BTAD190},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuDLDPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MunteFPTGMRRACM23,
author = {Elisabet Munt{\'{e}} and
Lidia Feliubadal{\'{o}} and
Marta Pineda and
Eva Tornero and
Maribel Gonz{\'{a}}lez and
Jos{\'{e}} Marcos Moreno{-}Cabrera and
Carla Roca and
Joan Bales Rubio and
Laura Arnaldo and
Gabriel Capell{\'{a}} and
Jose Luis Mosquera and
Conxi L{\'{a}}zaro},
title = {vaRHC: an {R} package for semi-automation of variant classification
in hereditary cancer genes according to {ACMG/AMP} and gene-specific
ClinGen guidelines},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad128},
doi = {10.1093/BIOINFORMATICS/BTAD128},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MunteFPTGMRRACM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuntoniP23,
author = {Anna Paola Muntoni and
Andrea Pagnani},
title = {DCAlign v1.0: aligning biological sequences using co-evolution models
and informed priors},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad537},
doi = {10.1093/BIOINFORMATICS/BTAD537},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuntoniP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuzellecTCA23,
author = {Boris Muzellec and
Maria Telenczuk and
Vincent Cabeli and
Mathieu Andreux},
title = {PyDESeq2: a python package for bulk RNA-seq differential expression
analysis},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad547},
doi = {10.1093/BIOINFORMATICS/BTAD547},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuzellecTCA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MyronovMKP23,
author = {Alexander Myronov and
Giovanni Mazzocco and
Paulina Kr{\'{o}}l and
Dariusz Plewczynski},
title = {BERTrand - peptide:TCR binding prediction using Bidirectional Encoder
Representations from Transformers augmented with random {TCR} pairing},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad468},
doi = {10.1093/BIOINFORMATICS/BTAD468},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MyronovMKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NaakeRH23,
author = {Thomas Naake and
Johannes Rainer and
Wolfgang Huber},
title = {MsQuality: an interoperable open-source package for the calculation
of standardized quality metrics of mass spectrometry data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad618},
doi = {10.1093/BIOINFORMATICS/BTAD618},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NaakeRH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NabiDAT23,
author = {Afshan Nabi and
Berke Dilekoglu and
Ogun Adebali and
{\"{O}}znur Tastan},
title = {Discovering misannotated lncRNAs using deep learning training dynamics},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac821},
doi = {10.1093/BIOINFORMATICS/BTAC821},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NabiDAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NadtochiyLFT23,
author = {Anna Nadtochiy and
Peter Luu and
Scott E. Fraser and
Thai V. Truong},
title = {VoDEx: a Python library for time annotation and management of volumetric
functional imaging data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad568},
doi = {10.1093/BIOINFORMATICS/BTAD568},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NadtochiyLFT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NallapareddyBSHLWSRO23,
author = {Vamsi Nallapareddy and
Nicola Bordin and
Ian Sillitoe and
Michael Heinzinger and
Maria Littmann and
Vaishali P. Waman and
Neeladri Sen and
Burkhard Rost and
Christine A. Orengo},
title = {CATHe: detection of remote homologues for {CATH} superfamilies using
embeddings from protein language models},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad029},
doi = {10.1093/BIOINFORMATICS/BTAD029},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NallapareddyBSHLWSRO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NamJYSSBVSPWK23,
author = {Yonghyun Nam and
Sang{-}Hyuk Jung and
Jae{-}Seung Yun and
Vivek Sriram and
Pankhuri Singhal and
Marta Byrska{-}Bishop and
Anurag Verma and
Hyunjung Shin and
Woong{-}Yang Park and
Hong{-}Hee Won and
Dokyoon Kim},
title = {Discovering comorbid diseases using an inter-disease interactivity
network based on biobank-scale PheWAS data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac822},
doi = {10.1093/BIOINFORMATICS/BTAC822},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NamJYSSBVSPWK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NeuenschwanderDAMBRDRM23,
author = {Samuel Neuenschwander and
Diana I Cruz D{\'{a}}valos and
Lucas Anchieri and
B{\'{a}}rbara Sousa da Mota and
Davide Bozzi and
Simone Rubinacci and
Olivier Delaneau and
Simon Rasmussen and
Anna{-}Sapfo Malaspinas},
title = {Mapache: a flexible pipeline to map ancient {DNA}},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad028},
doi = {10.1093/BIOINFORMATICS/BTAD028},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NeuenschwanderDAMBRDRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NgocODOSG23,
author = {Laura D. T. Vo Ngoc and
Randy Osei and
Katrin Dohr and
Catharina Olsen and
Sara Seneca and
Alexander Gheldof},
title = {{EDIR:} exome database of interspersed repeats},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac771},
doi = {10.1093/BIOINFORMATICS/BTAC771},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NgocODOSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Nguyen23,
author = {Dat Thanh Nguyen},
title = {An integrative pipeline for circular {RNA} quantitative trait locus
discovery with application in human {T} cells},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad667},
doi = {10.1093/BIOINFORMATICS/BTAD667},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Nguyen23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NguyenJKK23,
author = {Ngoc{-}Quang Nguyen and
Gwanghoon Jang and
Hajung Kim and
Jaewoo Kang},
title = {Perceiver {CPI:} a nested cross-attention network for compound-protein
interaction prediction},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac731},
doi = {10.1093/BIOINFORMATICS/BTAC731},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NguyenJKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NoginBHZEYWS23,
author = {Yevgeni Nogin and
Daniella Bar{-}Lev and
Dganit Hanania and
Tahir Detinis Zur and
Yuval Ebenstein and
Eitan Yaakobi and
Nir Weinberger and
Yoav Shechtman},
title = {Design of optimal labeling patterns for optical genome mapping via
information theory},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad601},
doi = {10.1093/BIOINFORMATICS/BTAD601},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NoginBHZEYWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NoginZMBAES23,
author = {Yevgeni Nogin and
Tahir Detinis Zur and
Sapir Margalit and
Ilana Barzilai and
Onit Alalouf and
Yuval Ebenstein and
Yoav Shechtman},
title = {DeepOM: single-molecule optical genome mapping via deep learning},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad137},
doi = {10.1093/BIOINFORMATICS/BTAD137},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NoginZMBAES23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NooriLTZ23,
author = {Ayush Noori and
Michelle M. Li and
Amelia L. M. Tan and
Marinka Zitnik},
title = {\texttt{Metapaths}: similarity search in heterogeneous knowledge graphs
via meta-paths},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad297},
doi = {10.1093/BIOINFORMATICS/BTAD297},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NooriLTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NouriKGRS23,
author = {Nima Nouri and
Andre H. Kurlovs and
Giorgio Gaglia and
Emanuele de Rinaldis and
Virginia Savova},
title = {Scaling up single-cell RNA-seq data analysis with CellBridge workflow},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad760},
doi = {10.1093/BIOINFORMATICS/BTAD760},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NouriKGRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OargaBJ23,
author = {Alexandru Oarga and
Bridget Bannerman and
Jorge J{\'{u}}lvez},
title = {{CONTRABASS:} exploiting flux constraints in genome-scale models for
the detection of vulnerabilities},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad053},
doi = {10.1093/BIOINFORMATICS/BTAD053},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OargaBJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OgataMDXHSPLD23,
author = {Jonathan D. Ogata and
Wancen Mu and
Eric S. Davis and
Bingjie Xue and
J. Chuck Harrell and
Nathan C. Sheffield and
Douglas H. Phanstiel and
Michael I. Love and
Mikhail G. Dozmorov},
title = {excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome
assemblies},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad198},
doi = {10.1093/BIOINFORMATICS/BTAD198},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OgataMDXHSPLD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OlaimatMSB23,
author = {Mohammad Al Olaimat and
Jared Martinez and
Fahad Saeed and
Serdar Bozdag},
title = {{PPAD:} a deep learning architecture to predict progression of Alzheimer's
disease},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {149--157},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad249},
doi = {10.1093/BIOINFORMATICS/BTAD249},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OlaimatMSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OlouladeGCAW23,
author = {Babatounde Moctard Oloulade and
Jianliang Gao and
Jiamin Chen and
Raeed Al{-}Sabri and
Zhenpeng Wu},
title = {Cancer drug response prediction with surrogate modeling-based graph
neural architecture search},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad478},
doi = {10.1093/BIOINFORMATICS/BTAD478},
timestamp = {Mon, 17 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OlouladeGCAW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OrsolicS23,
author = {Davor Orsolic and
Tomislav Smuc},
title = {Dynamic applicability domain (dAD): compound-target binding affinity
estimates with local conformal prediction},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad465},
doi = {10.1093/BIOINFORMATICS/BTAD465},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OrsolicS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OubounytAPWMHBE23,
author = {Mhaned Oubounyt and
Lorenz Adlung and
Fabio Patroni and
Nina Kerstin Wenke and
Andreas Maier and
Michael Hartung and
Jan Baumbach and
Maria L. Elkjaer},
title = {Inference of differential key regulatory networks and mechanistic
drug repurposing candidates from scRNA-seq data with SCANet},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad644},
doi = {10.1093/BIOINFORMATICS/BTAD644},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OubounytAPWMHBE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PackerWHESFPGEHMRBWDT23,
author = {Richard J. Packer and
Alex T. Williams and
William Hennah and
Micaela T. Eisenberg and
Nick Shrine and
Katherine A Fawcett and
Willow Pearson and
Anna L. Guyatt and
Ahmed Edris and
Edward J. Hollox and
Mikko Marttila and
Balasubramanya S. Rao and
John Raymond Bratty and
Louise V. Wain and
Frank Dudbridge and
Martin D. Tobin},
title = {DeepPheWAS: an {R} package for phenotype generation and association
analysis for phenome-wide association studies},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad073},
doi = {10.1093/BIOINFORMATICS/BTAD073},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PackerWHESFPGEHMRBWDT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PadronManriqueVELNSGR23,
author = {Cristian Padron{-}Manrique and
Aar{\'{o}}n V{\'{a}}zquez{-}Jim{\'{e}}nez and
Diego Armando Esquivel{-}Hernandez and
Yoscelina Estrella Martinez Lopez and
Daniel Neri{-}Rosario and
Jean Paul S{\'{a}}nchez{-}Casta{\~{n}}eda and
David Giron{-}Villalobos and
Osbaldo Resendis{-}Antonio},
title = {mb-PHENIX: diffusion and supervised uniform manifold approximation
for denoizing microbiota data},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad706},
doi = {10.1093/BIOINFORMATICS/BTAD706},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PadronManriqueVELNSGR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanLBWGPAWIS23,
author = {Tong Pan and
Chen Li and
Yue Bi and
Zhikang Wang and
Robin B. Gasser and
Anthony W. Purcell and
Tatsuya Akutsu and
Geoffrey I. Webb and
Seiya Imoto and
Jiangning Song},
title = {PFresGO: an attention mechanism-based deep-learning approach for protein
annotation by integrating gene ontology inter-relationships},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad094},
doi = {10.1093/BIOINFORMATICS/BTAD094},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanLBWGPAWIS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanLZLZWWWCLWG23,
author = {Junhang Pan and
Xiangchen Li and
Mingwu Zhang and
Yewei Lu and
Yelei Zhu and
Kunyang Wu and
Yiwen Wu and
Weixin Wang and
Bin Chen and
Zhengwei Liu and
Xiaomeng Wang and
Junshun Gao},
title = {TransFlow: a Snakemake workflow for transmission analysis of\emph{Mycobacterium
tuberculosis}whole-genome sequencing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac785},
doi = {10.1093/BIOINFORMATICS/BTAC785},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanLZLZWWWCLWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanWGZ23,
author = {Yuliang Pan and
Yang Wang and
Jihong Guan and
Shuigeng Zhou},
title = {{PCGAN:} a generative approach for protein complex identification
from protein interaction networks},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad473},
doi = {10.1093/BIOINFORMATICS/BTAD473},
timestamp = {Mon, 19 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanWGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanZC23,
author = {Shaojun Pan and
Xing{-}Ming Zhao and
Lu{\'{\i}}s Pedro Coelho},
title = {SemiBin2: self-supervised contrastive learning leads to better MAGs
for short- and long-read sequencing},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {21--29},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad209},
doi = {10.1093/BIOINFORMATICS/BTAD209},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkICSW23,
author = {Minhyuk Park and
Stefan Ivanovic and
Gillian Chu and
Chengze Shen and
Tandy J. Warnow},
title = {{UPP2:} fast and accurate alignment of datasets with fragmentary sequences},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad007},
doi = {10.1093/BIOINFORMATICS/BTAD007},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkICSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkKJNNP23,
author = {Seong{-}Joon Park and
Sunghwan Kim and
Jaeho Jeong and
Albert No and
Jong{-}Seon No and
Hosung Park},
title = {Reducing cost in DNA-based data storage by sequence analysis-aided
soft information decoding of variable-length reads},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad548},
doi = {10.1093/BIOINFORMATICS/BTAD548},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkKJNNP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkLKJL23,
author = {Jaesub Park and
Sangyeon Lee and
Kwansoo Kim and
Jaegyun Jung and
Doheon Lee},
title = {Large-scale prediction of adverse drug reactions-related proteins
with network embedding},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac843},
doi = {10.1093/BIOINFORMATICS/BTAC843},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkLKJL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkLLLGFLW23,
author = {Jun Young Park and
Jang Jae Lee and
Younghwa Lee and
Dongsoo Lee and
Jungsoo Gim and
Lindsay A. Farrer and
Kun Ho Lee and
Sungho Won},
title = {Machine learning-based quantification for disease uncertainty increases
the statistical power of genetic association studies},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad534},
doi = {10.1093/BIOINFORMATICS/BTAD534},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkLLLGFLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkRUTC23,
author = {Sehi Park and
Mobeen Ur Rehman and
Farman Ullah and
Hilal Tayara and
Kil To Chong},
title = {iCpG-Pos: an accurate computational approach for identification of
CpG sites using positional features on single-cell whole genome sequence
data},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad474},
doi = {10.1093/BIOINFORMATICS/BTAD474},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkRUTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaulWRSPMAZ23,
author = {Robin Paul and
Jian Wang and
Colleen Reilly and
Edgar Sioson and
Jaimin Patel and
Gavriel Matt and
Aleksandar Acic and
Xin Zhou},
title = {ppBAM: ProteinPaint {BAM} track for read alignment visualization and
variant genotyping},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad300},
doi = {10.1093/BIOINFORMATICS/BTAD300},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaulWRSPMAZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PeiGYNK23,
author = {Dong Pei and
Rachel Griffard and
Nanda Kumar Yellapu and
Emily Nissen and
Devin C. Koestler},
title = {optima: an open-source {R} package for the Tapestri platform for integrative
single cell multiomics data analysis},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad611},
doi = {10.1093/BIOINFORMATICS/BTAD611},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PeiGYNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PellizzoniMB23,
author = {Paolo Pellizzoni and
Giulia Muzio and
Karsten M. Borgwardt},
title = {Higher-order genetic interaction discovery with network-based biological
priors},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {523--533},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad273},
doi = {10.1093/BIOINFORMATICS/BTAD273},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PellizzoniMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PengD23,
author = {Xiyu Peng and
Karin S. Dorman},
title = {Accurate estimation of molecular counts from amplicon sequence data
with unique molecular identifiers},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad002},
doi = {10.1093/BIOINFORMATICS/BTAD002},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PengD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PenzarNNZMLRBK23,
author = {Dmitry Penzar and
Daria Nogina and
Elizaveta Noskova and
Arsenii Zinkevich and
Georgy Meshcheryakov and
Andrey Lando and
Abdul Muntakim Rafi and
Carl G. de Boer and
Ivan V. Kulakovskiy},
title = {LegNet: a best-in-class deep learning model for short {DNA} regulatory
regions},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad457},
doi = {10.1093/BIOINFORMATICS/BTAD457},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PenzarNNZMLRBK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PerniceSGVFSATCTBBOC23,
author = {Simone Pernice and
Roberta Sirovich and
Elena Grassi and
Marco Viviani and
Martina Ferri and
Francesco Sassi and
Luca Alessandr{\`{\i}} and
Dora Tortarolo and
Raffaele A. Calogero and
Livio Trusolino and
Andrea Bertotti and
Marco Beccuti and
Martina Olivero and
Francesca Cordero},
title = {CONNECTOR, fitting and clustering of longitudinal data to reveal a
new risk stratification system},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad201},
doi = {10.1093/BIOINFORMATICS/BTAD201},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PerniceSGVFSATCTBBOC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PetriS23,
author = {Alexander J. Petri and
Kristoffer Sahlin},
title = {isONform: reference-free transcriptome reconstruction from Oxford
Nanopore data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {222--231},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad264},
doi = {10.1093/BIOINFORMATICS/BTAD264},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PetriS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PettiBRDTZRKO23,
author = {Samantha Petti and
Nicholas Bhattacharya and
Roshan Rao and
Justas Dauparas and
Neil Thomas and
Juannan Zhou and
Alexander M. Rush and
Peter K. Koo and
Sergey Ovchinnikov},
title = {End-to-end learning of multiple sequence alignments with differentiable
Smith-Waterman},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac724},
doi = {10.1093/BIOINFORMATICS/BTAC724},
timestamp = {Thu, 18 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PettiBRDTZRKO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PfeiferCMSCHBHH23,
author = {Bastian Pfeifer and
Hryhorii Chereda and
Roman Martin and
Anna Saranti and
Sandra Clemens and
Anne{-}Christin Hauschild and
Tim Bei{\ss}barth and
Andreas Holzinger and
Dominik Heider},
title = {Ensemble-GNN: federated ensemble learning with graph neural networks
for disease module discovery and classification},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad703},
doi = {10.1093/BIOINFORMATICS/BTAD703},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PfeiferCMSCHBHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PhamNTNNPNGPN23,
author = {My{-}Diem Nguyen Pham and
Thanh{-}Nhan Nguyen and
Le Son Tran and
Que{-}Tran Bui Nguyen and
Thien{-}Phuc Hoang Nguyen and
Thi Mong Quynh Pham and
Hoai{-}Nghia Nguyen and
Hoa Giang and
Minh{-}Duy Phan and
Vy Nguyen},
title = {epiTCR: a highly sensitive predictor for TCR-peptide binding},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad284},
doi = {10.1093/BIOINFORMATICS/BTAD284},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PhamNTNNPNGPN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PhamWPCSIVBCGDPMMC23,
author = {Duy T. Pham and
Kenneth E. Westerman and
Cong Pan and
Ling Chen and
Shylaja Srinivasan and
Elvira Isganaitis and
Mary Ellen Vajravelu and
Fida Bacha and
Steve Chernausek and
Rose Gubitosi{-}Klug and
Jasmin Divers and
Catherine Pihoker and
Santica M. Marcovina and
Alisa K. Manning and
Han Chen},
title = {Re-analysis and meta-analysis of summary statistics from gene-environment
interaction studies},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad730},
doi = {10.1093/BIOINFORMATICS/BTAD730},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PhamWPCSIVBCGDPMMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PhilippBGSB23,
author = {Niklas Philipp and
Cedric K. Brinkmann and
Jens Georg and
Daniel Schindler and
Bork A Berghoff},
title = {DIGGER-Bac: prediction of seed regions for high-fidelity construction
of synthetic small RNAs in bacteria},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad285},
doi = {10.1093/BIOINFORMATICS/BTAD285},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PhilippBGSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PibiriSL23,
author = {Giulio Ermanno Pibiri and
Yoshihiro Shibuya and
Antoine Limasset},
title = {Locality-preserving minimal perfect hashing of \emph{k}-mers},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {534--543},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad219},
doi = {10.1093/BIOINFORMATICS/BTAD219},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PibiriSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PillichCCFGIKLOPP23,
author = {Rudolf T. Pillich and
Jing Chen and
Christopher Churas and
Dylan Fong and
Benjamin M. Gyori and
Trey Ideker and
Klas Karis and
Sophie N. Liu and
Keiichiro Ono and
Alexander R. Pico and
Dexter Pratt},
title = {NDEx IQuery: a multi-method network gene set analysis leveraging the
Network Data Exchange},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad118},
doi = {10.1093/BIOINFORMATICS/BTAD118},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PillichCCFGIKLOPP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PintoCARO23,
author = {Jos{\'{e}} Pinto and
Rafael S. Costa and
Leonardo Alexandre and
Jo{\~{a}}o Ramos and
Rui Oliveira},
title = {{SBML2HYB:} a Python interface for {SBML} compatible hybrid modeling},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad044},
doi = {10.1093/BIOINFORMATICS/BTAD044},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PintoCARO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PiochiPM23,
author = {Luiz Felipe Piochi and
Ant{\'{o}}nio J. Preto and
Irina S. Moreira},
title = {{DELFOS} - drug efficacy leveraging forked and specialized networks
- benchmarking scRNA-seq data in multi-omics-based prediction of cancer
sensitivity},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad645},
doi = {10.1093/BIOINFORMATICS/BTAD645},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PiochiPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Pirinen23,
author = {Matti Pirinen},
title = {linemodels: clustering effects based on linear relationships},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad115},
doi = {10.1093/BIOINFORMATICS/BTAD115},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Pirinen23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PitmanHMQ23,
author = {Anders Pitman and
Xiaomeng Huang and
Gabor T. Marth and
Yi Qiao},
title = {quickBAM: a parallelized {BAM} file access {API} for high-throughput
sequence analysis informatics},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad463},
doi = {10.1093/BIOINFORMATICS/BTAD463},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PitmanHMQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PlateauHollevilleGBJLMMM23,
author = {Cyprien Plateau{-}Holleville and
Simon Guionni{\`{e}}re and
Benjamin Boyer and
Brian Jim{\'{e}}nez{-}Garc{\'{\i}}a and
Guillaume Levieux and
St{\'{e}}phane M{\'{e}}rillou and
Maxime Maria and
Matthieu Mont{\`{e}}s},
title = {\emph{UDock2}: interactive real-time multi-body protein-protein docking
software},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad609},
doi = {10.1093/BIOINFORMATICS/BTAD609},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PlateauHollevilleGBJLMMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PlattLOB23,
author = {Adam Platt and
E. Josiah Lutton and
Edward Offord and
Till Bretschneider},
title = {MiCellAnnGELo: annotate microscopy time series of complex cell surfaces
with 3D virtual reality},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad013},
doi = {10.1093/BIOINFORMATICS/BTAD013},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PlattLOB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PontyR23,
author = {Yann Ponty and
Sushmita Roy},
title = {{ISMB/ECCB} 2023 proceedings},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {1--2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad319},
doi = {10.1093/BIOINFORMATICS/BTAD319},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PontyR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PorokhinLH23,
author = {Vladimir Porokhin and
Li{-}Ping Liu and
Soha Hassoun},
title = {Using graph neural networks for site-of-metabolism prediction and
its applications to ranking promiscuous enzymatic products},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad089},
doi = {10.1093/BIOINFORMATICS/BTAD089},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PorokhinLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PratesLHL23,
author = {Lucas Prates and
Renan B. Lemes and
T{\'{a}}bita H{\"{u}}nemeier and
Florencia G. Leonardi},
title = {Population-based change-point detection for the identification of
homozygosity islands},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad170},
doi = {10.1093/BIOINFORMATICS/BTAD170},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PratesLHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ProdanovB23,
author = {Timofey Prodanov and
Vikas Bansal},
title = {A multilocus approach for accurate variant calling in low-copy repeats
using whole-genome sequencing},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {279--287},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad268},
doi = {10.1093/BIOINFORMATICS/BTAD268},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ProdanovB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PuniyaD23,
author = {Bhanwar Lal Puniya and
Andreas Dr{\"{a}}ger},
title = {Advancements in computational modelling of biological systems: seventh
annual SysMod meeting},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad539},
doi = {10.1093/BIOINFORMATICS/BTAD539},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PuniyaD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QiaoBTSL23,
author = {Zhili Qiao and
Elle Barnes and
Susannah Tringe and
Daniel P. Schachtman and
Peng Liu},
title = {Poisson hurdle model-based method for clustering microbiome features},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac782},
doi = {10.1093/BIOINFORMATICS/BTAC782},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QiaoBTSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QuYMZ23,
author = {Wei Qu and
Ronghui You and
Hiroshi Mamitsuka and
Shanfeng Zhu},
title = {DeepMHCI: an anchor position-aware deep interaction model for accurate
{MHC-I} peptide binding affinity prediction},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad551},
doi = {10.1093/BIOINFORMATICS/BTAD551},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QuYMZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RademakerGX23,
author = {Daniel{-}T. Rademaker and
Kevin J. van Geemen and
Li C. Xue},
title = {GradPose: a very fast and memory-efficient gradient descent-based
tool for superimposing millions of protein structures from computational
simulations},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad444},
doi = {10.1093/BIOINFORMATICS/BTAD444},
timestamp = {Mon, 12 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RademakerGX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RafieiZAGPM23,
author = {Fatemeh Rafiei and
Hojjat Zeraati and
Karim Abbasi and
Jahan B. Ghasemi and
Mahboubeh Parsaeian and
Ali Masoudi{-}Nejad},
title = {DeepTraSynergy: drug combinations using multimodal deep learning with
transformers},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad438},
doi = {10.1093/BIOINFORMATICS/BTAD438},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RafieiZAGPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RahamanKZ23,
author = {Md. Mahfuzur Rahaman and
Nabila Shahnaz Khan and
Shaojie Zhang},
title = {RNAMotifComp: a comprehensive method to analyze and identify structurally
similar {RNA} motif families},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {337--346},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad223},
doi = {10.1093/BIOINFORMATICS/BTAD223},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RahamanKZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RahmanNTASR23,
author = {Mohammad Nuwaisir Rahman and
Abdullah Al Noman and
Abir Mohammad Turza and
Mohammed Abid Abrar and
Md. Abul Hassan Samee and
M. Saifur Rahman},
title = {ScribbleDom: using scribble-annotated histology images to identify
domains in spatial transcriptomics data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad594},
doi = {10.1093/BIOINFORMATICS/BTAD594},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RahmanNTASR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RahmanTSB23,
author = {Md Ashiqur Rahman and
Abdullah Aman Tutul and
Mahfuza Sharmin and
Md. Shamsuzzoha Bayzid},
title = {{BEENE:} deep learning-based nonlinear embedding improves batch effect
estimation},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad479},
doi = {10.1093/BIOINFORMATICS/BTAD479},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RahmanTSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RakeshVLFBR23,
author = {Mohan Rakesh and
H{\'{e}}l{\`{e}}ne V{\'{e}}zina and
Catherine Laprise and
Ellen E. Freeman and
Kelly M. Burkett and
Marie{-}H{\'{e}}l{\`{e}}ne Roy{-}Gagnon},
title = {{GENLIB:} new function to simulate haplotype transmission in large
complex genealogies},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad136},
doi = {10.1093/BIOINFORMATICS/BTAD136},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RakeshVLFBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RanaSMS23,
author = {Priyanka Rana and
Arcot Sowmya and
Erik Meijering and
Yang Song},
title = {Imbalanced classification for protein subcellular localization with
multilabel oversampling},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac841},
doi = {10.1093/BIOINFORMATICS/BTAC841},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RanaSMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RapakouliaVOLUV23,
author = {Trisevgeni Rapakoulia and
Sara Lopez Ruiz De Vargas and
Persia Akbari Omgba and
Verena Laupert and
Igor Ulitsky and
Martin Vingron},
title = {{CENTRE:} a gradient boosting algorithm for Cell-type-specific ENhancer-Target
pREdiction},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad687},
doi = {10.1093/BIOINFORMATICS/BTAD687},
timestamp = {Sat, 06 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RapakouliaVOLUV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaredonYKLKNK23,
author = {Micha Sam Brickman Raredon and
Junchen Yang and
Neeharika Kothapalli and
Wesley Lewis and
Naftali Kaminski and
Laura E. Niklason and
Yuval Kluger},
title = {Comprehensive visualization of cell-cell interactions in single-cell
and spatial transcriptomics with {NICHES}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac775},
doi = {10.1093/BIOINFORMATICS/BTAC775},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RaredonYKLKNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RauschenbergerLWG23,
author = {Armin Rauschenberger and
Zied Landoulsi and
Mark A. van de Wiel and
Enrico Glaab},
title = {Penalized regression with multiple sources of prior effects},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad680},
doi = {10.1093/BIOINFORMATICS/BTAD680},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RauschenbergerLWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReauRXB23,
author = {Manon R{\'{e}}au and
Nicolas Renaud and
Li C. Xue and
Alexandre M. J. J. Bonvin},
title = {DeepRank-GNN: a graph neural network framework to learn patterns in
protein-protein interfaces},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac759},
doi = {10.1093/BIOINFORMATICS/BTAC759},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReauRXB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenFZM23,
author = {Rui Ren and
Kuangnan Fang and
Qingzhao Zhang and
Shuangge Ma},
title = {FunctanSNP: an {R} package for functional analysis of dense {SNP}
data (with interactions)},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad741},
doi = {10.1093/BIOINFORMATICS/BTAD741},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenFZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenSZNBL23,
author = {Xiaoliang Ren and
Yanwen Shao and
Yiwen Zhang and
Ying Ni and
Yu Bi and
Runsheng Li},
title = {Primerdiffer: a python command-line module for large-scale primer
design in haplotype genotyping},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad188},
doi = {10.1093/BIOINFORMATICS/BTAD188},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenSZNBL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenWLLY23,
author = {Liangrui Ren and
Jun Wang and
Zhao Li and
Qingzhong Li and
Guoxian Yu},
title = {scMCs: a framework for single-cell multi-omics data integration and
multiple clusterings},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad133},
doi = {10.1093/BIOINFORMATICS/BTAD133},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenWLLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReyBarreiroV23,
author = {Xabier Rey{-}Barreiro and
Alejandro F. Villaverde},
title = {Benchmarking tools for a priori identifiability analysis},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad065},
doi = {10.1093/BIOINFORMATICS/BTAD065},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReyBarreiroV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RiahiLSWJOZPWMQ23,
author = {Saleh Riahi and
Jae Hyeon Lee and
Taylor Sorenson and
Shuai Wei and
Sven Jager and
Reza Olfati{-}Saber and
Yanfeng Zhou and
Anna Park and
Maria Wendt and
Herv{\'{e}} Minoux and
Yu Qiu},
title = {Surface {ID:} a geometry-aware system for protein molecular surface
comparison},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad196},
doi = {10.1093/BIOINFORMATICS/BTAD196},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RiahiLSWJOZPWMQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RibeiroG23,
author = {Rui P. Ribeiro and
Alejandro Giorgetti},
title = {pyGOMoDo: GPCRs modeling and docking with python},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad294},
doi = {10.1093/BIOINFORMATICS/BTAD294},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RibeiroG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RobidouP23,
author = {Lucas Robidou and
Pierre Peterlongo},
title = {\texttt{fimpera}: drastic improvement of Approximate Membership Query
data-structures with counts},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad305},
doi = {10.1093/BIOINFORMATICS/BTAD305},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RobidouP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RobinsonTTM23,
author = {James T. Robinson and
Helga Thorvaldsd{\'{o}}ttir and
Douglass Turner and
Jill P. Mesirov},
title = {igv.js: an embeddable JavaScript implementation of the Integrative
Genomics Viewer {(IGV)}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac830},
doi = {10.1093/BIOINFORMATICS/BTAC830},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RobinsonTTM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoblesJSSBWOQ23,
author = {Edgar E. Robles and
Ye Jin and
Padhraic Smyth and
Richard H. Scheuermann and
Jack D. Bui and
Huan{-}You Wang and
Jean Oak and
Yu Qian},
title = {A cell-level discriminative neural network model for diagnosis of
blood cancers},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad585},
doi = {10.1093/BIOINFORMATICS/BTAD585},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoblesJSSBWOQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RohanianNKC23,
author = {Omid Rohanian and
Mohammadmahdi Nouriborji and
Samaneh Kouchaki and
David A. Clifton},
title = {On the effectiveness of compact biomedical transformers},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad103},
doi = {10.1093/BIOINFORMATICS/BTAD103},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RohanianNKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RohdeSS23,
author = {Palle Duun Rohde and
Izel Fourie S{\o}rensen and
Peter S{\o}rensen},
title = {Expanded utility of the {R} package, qgg, with applications within
genomic medicine},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad656},
doi = {10.1093/BIOINFORMATICS/BTAD656},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RohdeSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RomainL23,
author = {Sandra Romain and
Claire Lemaitre},
title = {SVJedi-graph: improving the genotyping of close and overlapping structural
variants with long reads using a variation graph},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {270--278},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad237},
doi = {10.1093/BIOINFORMATICS/BTAD237},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RomainL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RomashchenkoLPR23,
author = {Nikolai Romashchenko and
Benjamin Linard and
Fabio Pardi and
Eric Rivals},
title = {{EPIK:} precise and scalable evolutionary placement with informative
\emph{k}-mers},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad692},
doi = {10.1093/BIOINFORMATICS/BTAD692},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RomashchenkoLPR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RosignoliPP23,
author = {Serena Rosignoli and
Luisa di Paola and
Alessandro Paiardini},
title = {PyPCN: protein contact networks in PyMOL},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad675},
doi = {10.1093/BIOINFORMATICS/BTAD675},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RosignoliPP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RougnyBLM23,
author = {Adrien Rougny and
Irina Balaur and
Augustin Luna and
Alexander Mazein},
title = {StonPy: a tool to parse and query collections of {SBGN} maps in a
graph database},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad100},
doi = {10.1093/BIOINFORMATICS/BTAD100},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RougnyBLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoyCZ23,
author = {Asmita Roy and
Jun Chen and
Xianyang Zhang},
title = {A general framework for powerful confounder adjustment in omics association
studies},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad563},
doi = {10.1093/BIOINFORMATICS/BTAD563},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoyCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuZL23,
author = {Xiaoqing Ru and
Quan Zou and
Chen Lin},
title = {Optimization of drug-target affinity prediction methods through feature
processing schemes},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad615},
doi = {10.1093/BIOINFORMATICS/BTAD615},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SahadevanSAFHHS23,
author = {Sudeep Sahadevan and
Thileepan Sekaran and
Nadia Ashaf and
Marko Fritz and
Matthias W. Hentze and
Wolfgang Huber and
Thomas Schwarzl},
title = {htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac747},
doi = {10.1093/BIOINFORMATICS/BTAC747},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SahadevanSAFHHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SahayAHC23,
author = {Shabnam Sahay and
Shishir Adhikari and
Sahand Hormoz and
Shaon Chakrabarti},
title = {An improved rhythmicity analysis method using Gaussian Processes detects
cell-density dependent circadian oscillations in stem cells},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad602},
doi = {10.1093/BIOINFORMATICS/BTAD602},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SahayAHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SalkovicSBSB23,
author = {Edin Salkovic and
Mohammad Amin Sadeghi and
Abdelkader Baggag and
Ahmed Gamal Rashed Salem and
Halima Bensmail},
title = {OutSingle: a novel method of detecting and injecting outliers in RNA-Seq
count data using the optimal hard threshold for singular values},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad142},
doi = {10.1093/BIOINFORMATICS/BTAD142},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SalkovicSBSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SanchezBCJNBV23,
author = {Luis Francisco Hern{\'{a}}ndez S{\'{a}}nchez and
Bram Burger and
Rodrigo Alexander Castro Campos and
Stefan Johansson and
P{\aa}l R. Nj{\o}lstad and
Harald Barsnes and
Marc Vaudel},
title = {Extending protein interaction networks using proteoforms and small
molecules},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad598},
doi = {10.1093/BIOINFORMATICS/BTAD598},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SanchezBCJNBV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SanchezBJGLCCJ23,
author = {Th{\'{e}}ophile Sanchez and
Erik Madison Bray and
Pierre Jobic and
J{\'{e}}r{\'{e}}my Guez and
Anne{-}Catherine Letournel and
Guillaume Charpiat and
Jean Cury and
Flora Jay},
title = {\texttt{dnadna}: a deep learning framework for population genetics
inference},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac765},
doi = {10.1093/BIOINFORMATICS/BTAC765},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SanchezBJGLCCJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SantJKS23,
author = {Jaromir Sant and
Paul A. Jenkins and
Jere Koskela and
Dario Span{\`{o}}},
title = {{EWF:} simulating exact paths of the Wright-Fisher diffusion},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad017},
doi = {10.1093/BIOINFORMATICS/BTAD017},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SantJKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SapciLYATK23,
author = {Ali Osman Berk Sapci and
Shan Lu and
Shuchen Yan and
Ferhat Ay and
{\"{O}}znur Tastan and
S{\"{u}}nd{\"{u}}z Keles},
title = {MuDCoD: multi-subject community detection in personalized dynamic
gene networks from single-cell {RNA} sequencing},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad592},
doi = {10.1093/BIOINFORMATICS/BTAD592},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SapciLYATK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SaralaPS23,
author = {Olli Sarala and
Tanja Pyh{\"{a}}j{\"{a}}rvi and
Mikko J. Sillanp{\"{a}}{\"{a}}},
title = {{BELMM:} Bayesian model selection and random walk smoothing in time-series
clustering},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad686},
doi = {10.1093/BIOINFORMATICS/BTAD686},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SaralaPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SatoUFUI23,
author = {Noriaki Sato and
Miho Uematsu and
Kosuke Fujimoto and
Satoshi Uematsu and
Seiya Imoto},
title = {\emph{ggkegg}: analysis and visualization of {KEGG} data utilizing
the grammar of graphics},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad622},
doi = {10.1093/BIOINFORMATICS/BTAD622},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SatoUFUI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ScandinoCR23,
author = {Riccardo Scandino and
Federico Calabrese and
Alessandro Romanel},
title = {Synggen: fast and data-driven generation of synthetic heterogeneous
{NGS} cancer data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac792},
doi = {10.1093/BIOINFORMATICS/BTAC792},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ScandinoCR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchaferGY23,
author = {Richard A Sch{\"{a}}fer and
Qingxiang Guo and
Rendong Yang},
title = {ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity
prediction from diverse genomic and transcriptomic alterations},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad659},
doi = {10.1093/BIOINFORMATICS/BTAD659},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchaferGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchaferRSSHBFV23,
author = {Richard A. Sch{\"{a}}fer and
Dominik Rabsch and
Guillaume E. Scholz and
Peter F. Stadler and
Wolfgang R. Hess and
Rolf Backofen and
J{\"{o}}rg Fallmann and
Bj{\"{o}}rn Vo{\ss}},
title = {{RNA} interaction format: a general data format for {RNA} interactions},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad665},
doi = {10.1093/BIOINFORMATICS/BTAD665},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchaferRSSHBFV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchalteFJVPSLWRMSSGDDWH23,
author = {Yannik Sch{\"{a}}lte and
Fabian Fr{\"{o}}hlich and
Paul J. Jost and
Jakob Vanhoefer and
Dilan Pathirana and
Paul Stapor and
Polina A. Lakrisenko and
Dantong Wang and
Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
Simon Merkt and
Leonard Schmiester and
Philipp St{\"{a}}dter and
Stephan Grein and
Erika Dudkin and
Domagoj Doresic and
Daniel Weindl and
Jan Hasenauer},
title = {pyPESTO: a modular and scalable tool for parameter estimation for
dynamic models},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad711},
doi = {10.1093/BIOINFORMATICS/BTAD711},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchalteFJVPSLWRMSSGDDWH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchmidtRMKKL23,
author = {Axel Schmidt and
Sebastian R{\"{o}}ner and
Karola Mai and
Hannah Klinkhammer and
Martin Kircher and
Kerstin U. Ludwig},
title = {Predicting the pathogenicity of missense variants using features derived
from AlphaFold2},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad280},
doi = {10.1093/BIOINFORMATICS/BTAD280},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchmidtRMKKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchrieverK23,
author = {Hannah Schriever and
Dennis Kostka},
title = {Vaeda computationally annotates doublets in single-cell {RNA} sequencing
data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac720},
doi = {10.1093/BIOINFORMATICS/BTAC720},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchrieverK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchusterK23,
author = {Viktoria Schuster and
Anders Krogh},
title = {The Deep Generative Decoder: {MAP} estimation of representations improves
modelling of single-cell {RNA} data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad497},
doi = {10.1093/BIOINFORMATICS/BTAD497},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchusterK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SciaccaASFLPPL23,
author = {Elisabetta C. Sciacca and
Salvatore Alaimo and
Gianmarco Silluzio and
Alfredo Ferro and
Vito Latora and
Costantino Pitzalis and
Alfredo Pulvirenti and
Myles J. Lewis},
title = {DEGGs: an {R} package with shiny app for the identification of differentially
expressed gene-gene interactions in high-throughput sequencing data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad192},
doi = {10.1093/BIOINFORMATICS/BTAD192},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SciaccaASFLPPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SequeirosPVBO23,
author = {Carlos Sequeiros and
Manuel P{\'{a}}jaro and
Carlos V{\'{a}}zquez and
Julio R. Banga and
Irene Otero{-}Muras},
title = {{IDESS:} a toolbox for identification and automated design of stochastic
gene circuits},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad682},
doi = {10.1093/BIOINFORMATICS/BTAD682},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SequeirosPVBO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShafferBBFFGEWMCSHW23,
author = {Michael Shaffer and
Mikayla A. Borton and
Ben Bolduc and
Jos{\'{e}} P. Faria and
Rory M. Flynn and
Parsa Ghadermazi and
Janaka N. Edirisinghe and
Elisha M. Wood{-}Charlson and
Christopher S. Miller and
Siu Hung Joshua Chan and
Matthew B. Sullivan and
Christopher S. Henry and
Kelly C. Wrighton},
title = {kb{\_}DRAM: annotation and metabolic profiling of genomes with {DRAM}
in KBase},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad110},
doi = {10.1093/BIOINFORMATICS/BTAD110},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShafferBBFFGEWMCSHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShakerLLYLLKOKN23,
author = {Bilal Shaker and
Jingyu Lee and
Yunhyeok Lee and
Myeong{-}Sang Yu and
Hyang{-}Mi Lee and
Eunee Lee and
Hoon{-}Chul Kang and
Kwang{-}Seok Oh and
Hyung Wook Kim and
Dokyun Na},
title = {A machine learning-based quantitative model (LogBB{\_}Pred) to predict
the blood-brain barrier permeability (logBB value) of drug compounds},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad577},
doi = {10.1093/BIOINFORMATICS/BTAD577},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShakerLLYLLKOKN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShangPTS23,
author = {Jiayu Shang and
Cheng Peng and
Xubo Tang and
Yanni Sun},
title = {PhaVIP: Phage VIrion Protein classification based on chaos game representation
and Vision Transformer},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {30--39},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad229},
doi = {10.1093/BIOINFORMATICS/BTAD229},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShangPTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SharmaX23,
author = {Divya Sharma and
Wei Xu},
title = {ReGeNNe: genetic pathway-based deep neural network using canonical
correlation regularizer for disease prediction},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad679},
doi = {10.1093/BIOINFORMATICS/BTAD679},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SharmaX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShaveDANKC23,
author = {Steven R. Shave and
John C. Dawson and
Abdullah M. Athar and
Cuong Q. Nguyen and
Richard Kasprowicz and
Neil O. Carragher},
title = {Phenonaut: multiomics data integration for phenotypic space exploration},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad143},
doi = {10.1093/BIOINFORMATICS/BTAD143},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShaveDANKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenXHTPCHR23,
author = {Wei Shen and
Hongyan Xiang and
Tianquan Huang and
Hui Tang and
Mingli Peng and
Dachuan Cai and
Peng Hu and
Hong Ren},
title = {{KMCP:} accurate metagenomic profiling of both prokaryotic and viral
populations by pseudo-mapping},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac845},
doi = {10.1093/BIOINFORMATICS/BTAC845},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenXHTPCHR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShengBN23,
author = {Yueqi Sheng and
Boaz Barak and
Mor Nitzan},
title = {Robust reconstruction of single-cell RNA-seq data with iterative gene
weight updates},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {423--430},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad253},
doi = {10.1093/BIOINFORMATICS/BTAD253},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShengBN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShiBDMFDJH23,
author = {Ruohua Shi and
Keyan Bi and
Kai Du and
Lei Ma and
Fang Fang and
Lingyu Duan and
Tingting Jiang and
Tie{-}Jun Huang},
title = {PS-Net: human perception-guided segmentation network for {EM} cell
membrane},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad464},
doi = {10.1093/BIOINFORMATICS/BTAD464},
timestamp = {Wed, 14 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShiBDMFDJH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShinGHS23,
author = {Woosub Shin and
John H. Gennari and
Joseph L. Hellerstein and
Herbert M. Sauro},
title = {An automated model annotation system {(AMAS)} for {SBML} models},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad658},
doi = {10.1093/BIOINFORMATICS/BTAD658},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShinGHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShokranehAL23,
author = {Neda Shokraneh and
Mariam Arab and
Maxwell W. Libbrecht},
title = {Integrative chromatin domain annotation through graph embedding of
Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac813},
doi = {10.1093/BIOINFORMATICS/BTAC813},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShokranehAL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShueySABBBCCGLMMOPRRSSST23,
author = {Megan M. Shuey and
William W. Stead and
Ida Aka and
April L. Barnado and
Lisa Bastarache and
Elly Brokamp and
Meredith Campbell and
Robert J. Carroll and
Jeffrey A. Goldstein and
Adam Lewis and
Beth A. Malow and
Jonathan D. Mosley and
Travis Osterman and
Dolly A Padovani{-}Claudio and
Andrea Ramirez and
Dan M. Roden and
Bryce A Schuler and
Edward Siew and
Jennifer Sucre and
Isaac Thomsen and
Rory J. Tinker and
Sara Van Driest and
Colin Walsh and
Jeremy L. Warner and
Quinn Stanton Wells and
Lee E. Wheless},
title = {Next-generation phenotyping: introducing phecodeX for enhanced discovery
research in medical phenomics},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad655},
doi = {10.1093/BIOINFORMATICS/BTAD655},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShueySABBBCCGLMMOPRRSSST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShulginaE23,
author = {Yekaterina Shulgina and
Sean R. Eddy},
title = {Codetta: predicting the genetic code from nucleotide sequence},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac802},
doi = {10.1093/BIOINFORMATICS/BTAC802},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShulginaE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SilvaQRMS23,
author = {Anjali Silva and
Xiaoke Qin and
Steven J. Rothstein and
Paul D. McNicholas and
Sanjeena Subedi},
title = {Finite mixtures of matrix variate Poisson-log normal distributions
for three-way count data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad167},
doi = {10.1093/BIOINFORMATICS/BTAD167},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SilvaQRMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghPP23,
author = {Jaskaran Singh and
Yingzhou Edward Pan and
Shunmoogum A Patten},
title = {{NMJ} Analyser: a novel method to quantify neuromuscular junction
morphology in zebrafish},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad720},
doi = {10.1093/BIOINFORMATICS/BTAD720},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghPP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SkogOKON23,
author = {Signe Skog and
Lovisa {\"{O}}rkenby and
Unn Kugelberg and
Anita {\"{O}}st and
Daniel N{\"{a}}tt},
title = {Seqpac: a framework for sRNA-seq analysis in {R} using sequence-based
counts},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad144},
doi = {10.1093/BIOINFORMATICS/BTAD144},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SkogOKON23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SledzieskiDSCB23,
author = {Samuel Sledzieski and
Kapil Devkota and
Rohit Singh and
Lenore Cowen and
Bonnie Berger},
title = {{TT3D:} Leveraging precomputed protein 3D sequence models to predict
protein-protein interactions},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad663},
doi = {10.1093/BIOINFORMATICS/BTAD663},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SledzieskiDSCB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmithCMT23,
author = {Matthew D. Smith and
Marshall A Case and
Emily K. Makowski and
Peter M. Tessier},
title = {Position-Specific Enrichment Ratio Matrix scores predict antibody
variant properties from deep sequencing data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad446},
doi = {10.1093/BIOINFORMATICS/BTAD446},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmithCMT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmithH23,
author = {Megan L. Smith and
Matthew W. Hahn},
title = {Phylogenetic inference using generative adversarial networks},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad543},
doi = {10.1093/BIOINFORMATICS/BTAD543},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmithH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmithYT23,
author = {Kyle Smith and
Cheng Ye and
Yatish Turakhia},
title = {Tracking and curating putative SARS-CoV-2 recombinants with {RIVET}},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad538},
doi = {10.1093/BIOINFORMATICS/BTAD538},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmithYT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmolanderJE23,
author = {Johannes Smolander and
Sini Junttila and
Laura L. Elo},
title = {Cell-connectivity-guided trajectory inference from single-cell data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad515},
doi = {10.1093/BIOINFORMATICS/BTAD515},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmolanderJE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SouliosSBHS23,
author = {Kyriakos Soulios and
Patrick Scheibe and
Matthias Bernt and
J{\"{o}}rg Hackerm{\"{u}}ller and
Jana Schor},
title = {\texttt{deepFPlearn} +: enhancing toxicity prediction across the chemical
universe using graph neural networks},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad713},
doi = {10.1093/BIOINFORMATICS/BTAD713},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SouliosSBHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SousaC23,
author = {Diana F. Sousa and
Francisco M. Couto},
title = {{K-RET:} knowledgeable biomedical relation extraction system},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad174},
doi = {10.1093/BIOINFORMATICS/BTAD174},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SousaC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SpytekKLBWB23,
author = {Mikolaj Spytek and
Mateusz Krzyzinski and
Sophie Hanna Langbein and
Hubert Baniecki and
Marvin N. Wright and
Przemyslaw Biecek},
title = {survex: an {R} package for explaining machine learning survival models},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad723},
doi = {10.1093/BIOINFORMATICS/BTAD723},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SpytekKLBWB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SrikakulamKDBK23,
author = {Sanjay Kumar Srikakulam and
Sebastian Keller and
Fawaz Dabbaghie and
Robert Bals and
Olga V. Kalinina},
title = {MetaProFi: an ultrafast chunked Bloom filter for storing and querying
protein and nucleotide sequence data for accurate identification of
functionally relevant genetic variants},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad101},
doi = {10.1093/BIOINFORMATICS/BTAD101},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SrikakulamKDBK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StPierreOB23,
author = {Julien St{-}Pierre and
Karim Oualkacha and
Sahir Rai Bhatnagar},
title = {Efficient penalized generalized linear mixed models for variable selection
and genetic risk prediction in high-dimensional data},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad063},
doi = {10.1093/BIOINFORMATICS/BTAD063},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StPierreOB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StanojevicAKHCHKO23,
author = {Marija Stanojevic and
Jovan Andjelkovic and
Adrienne Kasprowicz and
Louise A. Huuki and
Jennifer Chao and
S. Blair Hedges and
Sudhir Kumar and
Zoran Obradovic},
title = {Discovering research articles containing evolutionary timetrees by
machine learning},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad035},
doi = {10.1093/BIOINFORMATICS/BTAD035},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StanojevicAKHCHKO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StaritzbichlerRSH23,
author = {Ren{\'{e}} Staritzbichler and
Nikola Ristic and
T{\"{u}}lin Stapke and
Peter W. Hildebrand},
title = {SmoothT - a server constructing low-energy pathways from conformational
ensembles for interactive visualization and enhanced sampling},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad176},
doi = {10.1093/BIOINFORMATICS/BTAD176},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StaritzbichlerRSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StolfiMPTV23,
author = {Paola Stolfi and
Andrea Mastropietro and
Giuseppe Pasculli and
Paolo Tieri and
Davide Vergni},
title = {{NIAPU:} network-informed adaptive positive-unlabeled learning for
disease gene identification},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac848},
doi = {10.1093/BIOINFORMATICS/BTAC848},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StolfiMPTV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StrayerZYVBHSBJPBEEPWSCR23,
author = {Nick Strayer and
Siwei Zhang and
Lydia Yao and
Tess Vessels and
Cosmin Adrian Bejan and
Ryan S. Hsi and
Jana K. Shirey{-}Rice and
Justin M. Balko and
Douglas B. Johnson and
Elizabeth J. Phillips and
Alex Bick and
Todd L. Edwards and
Digna R. Velez Edwards and
Jill M. Pulley and
Quinn Stanton Wells and
Michael R. Savona and
Nancy J. Cox and
Dan M. Roden and
Douglas M. Ruderfer and
Yaomin Xu},
title = {Interactive network-based clustering and investigation of multimorbidity
association matrices with associationSubgraphs},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac780},
doi = {10.1093/BIOINFORMATICS/BTAC780},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StrayerZYVBHSBJPBEEPWSCR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StreckKS23,
author = {Adam Streck and
Tom L. Kaufmann and
Roland F. Schwarz},
title = {{SMITH:} spatially constrained stochastic model for simulation of
intra-tumour heterogeneity},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad102},
doi = {10.1093/BIOINFORMATICS/BTAD102},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StreckKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StriblingGR23,
author = {Daniel Stribling and
Lauren A. Gay and
Rolf Renne},
title = {Hybkit: a Python {API} and command-line toolkit for hybrid sequence
data from chimeric {RNA} methods},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad721},
doi = {10.1093/BIOINFORMATICS/BTAD721},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StriblingGR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SuGZSYYX23,
author = {Changqing Su and
Yuhan Gao and
You Zhou and
Yaoqi Sun and
Chenggang Yan and
Haibing Yin and
Bo Xiong},
title = {AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution
with optimal iteration numbers predicting},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac760},
doi = {10.1093/BIOINFORMATICS/BTAC760},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SuGZSYYX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SubramaniyaTK23,
author = {Sai Raghavendra Maddhuri Venkata Subramaniya and
Genki Terashi and
Daisuke Kihara},
title = {Enhancing cryo-EM maps with 3D deep generative networks for assisting
protein structure modeling},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad494},
doi = {10.1093/BIOINFORMATICS/BTAD494},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SubramaniyaTK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunFLZLWL23,
author = {Pingping Sun and
Shijie Fan and
Shaochuan Li and
Yingwei Zhao and
Chang Lu and
Ka{-}Chun Wong and
Xiangtao Li},
title = {Automated exploitation of deep learning for cancer patient stratification
across multiple types},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad654},
doi = {10.1093/BIOINFORMATICS/BTAD654},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunFLZLWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SyrlybaevaS23,
author = {Raulia Syrlybaeva and
Eva{-}Maria Strauch},
title = {Deep learning of protein sequence design of protein-protein interactions},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac733},
doi = {10.1093/BIOINFORMATICS/BTAC733},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SyrlybaevaS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TabatabaeeZWM23,
author = {Yasamin Tabatabaee and
Chao Zhang and
Tandy J. Warnow and
Siavash Mirarab},
title = {Phylogenomic branch length estimation using quartets},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {185--193},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad221},
doi = {10.1093/BIOINFORMATICS/BTAD221},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TabatabaeeZWM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Tagashira23,
author = {Masaki Tagashira},
title = {ConsAlign: simultaneous {RNA} structural aligner based on rich transfer
learning and thermodynamic ensemble model of alignment scoring},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad255},
doi = {10.1093/BIOINFORMATICS/BTAD255},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Tagashira23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TaheriTKRSHZV23,
author = {Sara Mohammad Taheri and
Vartika Tewari and
Rohan Kapre and
Ehsan Rahiminasab and
Karen Sachs and
Charles Tapley Hoyt and
Jeremy Zucker and
Olga Vitek},
title = {Optimal adjustment sets for causal query estimation in partially observed
biomolecular networks},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {494--503},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad270},
doi = {10.1093/BIOINFORMATICS/BTAD270},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TaheriTKRSHZV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TanS23,
author = {Wuwei Tan and
Yang Shen},
title = {Multimodal learning of noncoding variant effects using genome sequence
and chromatin structure},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad541},
doi = {10.1093/BIOINFORMATICS/BTAD541},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TanS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TanasieKHB23,
author = {Anda Ramona Tanasie and
Peter Kerpedjiev and
Stefan Hammer and
Stefan Badelt},
title = {DrForna: visualization of cotranscriptional folding},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad555},
doi = {10.1093/BIOINFORMATICS/BTAD555},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TanasieKHB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangHW23,
author = {Ruoyu Tang and
Xinyu He and
Ruiqi Wang},
title = {Constructing maps between distinct cell fates and parametric conditions
by systematic perturbations},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad624},
doi = {10.1093/BIOINFORMATICS/BTAD624},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TeixeiraPUA23,
author = {Marco Teixeira and
Stephanie Pillay and
Aysun Urhan and
Thomas Abeel},
title = {{SHIP:} identifying antimicrobial resistance gene transfer between
plasmids},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad612},
doi = {10.1093/BIOINFORMATICS/BTAD612},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TeixeiraPUA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TeruelBN23,
author = {Nat{\'{a}}lia Teruel and
Vinicius Magalh{\~{a}}es Borges and
Rafael Najmanovich},
title = {Surfaces: a software to quantify and visualize interactions within
and between proteins and ligands},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad608},
doi = {10.1093/BIOINFORMATICS/BTAD608},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TeruelBN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TeschnerGDLABDMMTH23,
author = {David Teschner and
David Gomez{-}Zepeda and
Arthur Declercq and
Mateusz K. Lacki and
Seymen Avci and
Konstantin Bob and
Ute Distler and
Thomas Michna and
Lennart Martens and
Stefan Tenzer and
Andreas Hildebrandt},
title = {Ionmob: a Python package for prediction of peptide collisional cross-section
values},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad486},
doi = {10.1093/BIOINFORMATICS/BTAD486},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TeschnerGDLABDMMTH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TeufelRMSGWM23,
author = {Felix Teufel and
Jan C. Refsgaard and
Christian T. Madsen and
Carsten Stahlhut and
Mads Gr{\o}nborg and
Ole Winther and
Dennis Madsen},
title = {DeepPeptide predicts cleaved peptides in proteins using conditional
random fields},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad616},
doi = {10.1093/BIOINFORMATICS/BTAD616},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TeufelRMSGWM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TheissHRHSREBU23,
author = {Maria Theiss and
Jean{-}Karim H{\'{e}}rich{\'{e}} and
Craig Russell and
David Helekal and
Alisdair Soppitt and
Jonas Ries and
Jan Ellenberg and
Alvis Brazma and
Virginie Uhlmann},
title = {Simulating structurally variable nuclear pore complexes for microscopy},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad587},
doi = {10.1093/BIOINFORMATICS/BTAD587},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TheissHRHSREBU23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TongTHZZXHCWFCWZ23,
author = {Yuantao Tong and
Fanglin Tan and
Honglian Huang and
Zeyu Zhang and
Hui Zong and
Yujia Xie and
Danqi Huang and
Shiyang Cheng and
Ziyi Wei and
Meng Fang and
M. James C. Crabbe and
Ying Wang and
Xiaoyan Zhang},
title = {ViMRT: a text-mining tool and search engine for automated virus mutation
recognition},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac721},
doi = {10.1093/BIOINFORMATICS/BTAC721},
timestamp = {Tue, 09 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TongTHZZXHCWFCWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TrinhBHP23,
author = {Van{-}Giang Trinh and
Belaid Benhamou and
Thomas A. Henzinger and
Samuel Pastva},
title = {Trap spaces of multi-valued networks: definition, computation, and
applications},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {513--522},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad262},
doi = {10.1093/BIOINFORMATICS/BTAD262},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TrinhBHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TriskaAEB23,
author = {Petr Triska and
Fabian Amman and
Lukas Endler and
Andreas Bergthaler},
title = {{WAVES} (Web-based tool for Analysis and Visualization of Environmental
Samples) - a web application for visualization of wastewater pathogen
sequencing results},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad160},
doi = {10.1093/BIOINFORMATICS/BTAD160},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TriskaAEB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TuLYZ23,
author = {Jia{-}Juan Tu and
Hui{-}Sheng Li and
Hong Yan and
Xiao{-}Fei Zhang},
title = {EnDecon: cell type deconvolution of spatially resolved transcriptomics
data via ensemble learning},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac825},
doi = {10.1093/BIOINFORMATICS/BTAC825},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TuLYZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UlgenOS23,
author = {Ege {\"{U}}lgen and
Ozan Ozisik and
Osman Ugur Sezerman},
title = {{PANACEA:} network-based methods for pharmacotherapy prioritization
in personalized oncology},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad022},
doi = {10.1093/BIOINFORMATICS/BTAD022},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UlgenOS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UllahHSY23,
author = {Matee Ullah and
Fazal Hadi and
Jiangning Song and
Dong{-}Jun Yu},
title = {PScL-2LSAESM: bioimage-based prediction of protein subcellular localization
by integrating heterogeneous features with the two-level {SAE-SM}
and mean ensemble method},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac727},
doi = {10.1093/BIOINFORMATICS/BTAC727},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UllahHSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UllrichG23,
author = {Kristian K. Ullrich and
Nikoleta E. Glynatsi},
title = {oggmap: a Python package to extract gene ages per orthogroup and link
them with single-cell {RNA} data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad657},
doi = {10.1093/BIOINFORMATICS/BTAD657},
timestamp = {Thu, 16 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UllrichG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UlrichPJ23,
author = {Elias Ulrich and
Stefan M. Pfister and
Natalie J{\"{a}}ger},
title = {Revana: a comprehensive tool for regulatory variant analysis and visualization
of cancer genomes},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac831},
doi = {10.1093/BIOINFORMATICS/BTAC831},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UlrichPJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UmerenkovNSSSSIK23,
author = {Dmitriy Umerenkov and
Fedor Nikolaev and
Tatiana I Shashkova and
Pavel V. Strashnov and
Maria Sindeeva and
Andrey Shevtsov and
Nikita V. Ivanisenko and
Olga L. Kardymon},
title = {{PROSTATA:} a framework for protein stability assessment using transformers},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad671},
doi = {10.1093/BIOINFORMATICS/BTAD671},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UmerenkovNSSSSIK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23,
author = {Sean Upchurch and
Emilio Palumbo and
Jeremy Adams and
David Bujold and
Guillaume Bourque and
Jared Nedzel and
Keenan Graham and
Meenakshi S. Kagda and
Pedro Assis and
Benjamin C. Hitz and
Emilio Righi and
Roderic Guig{\'{o}} and
Barbara J. Wold and
Alvis Brazma and
Julia Burchard and
Joe Capka and
Michael Cherry and
Laura Clarke and
Brian Craft and
Manolis Dermitzakis and
Mark Diekhans and
John Dursi and
Michael Sean Fitzsimons and
Zac Flaming and
Romina Garrido and
Alfred Gil and
Paul Godden and
Matt Green and
Mitch Guttman and
Brian Haas and
Max Haeussler and
Bo Li and
Sten Linnarsson and
Adam Lipski and
David Liu and
Simonne Longerich and
David Lougheed and
Jonathan Manning and
John C. Marioni and
Christopher Meyer and
Stephen B. Montgomery and
Alyssa Morrow and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Jared L. Nedzel and
David Nguyen and
Kevin Osborn and
Francis Ouellette and
Irene Papatheodorou and
Dmitri D. Pervouchine and
Arun K. Ramani and
Jordi Rambla and
Bashir Sadjad and
David Steinberg and
Jeremiah Talkar and
Timothy Tickle and
Kathy Tzeng and
Saman Vaisipour and
Sean Watford and
Barbara Wold and
Zhenyu Zhang and
Jing Zhu},
title = {RNAget: an {API} to securely retrieve {RNA} quantifications},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad126},
doi = {10.1093/BIOINFORMATICS/BTAD126},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ValleInclanC23,
author = {Jose Espejo Valle{-}Incl{\'{a}}n and
Isidro Cort{\'{e}}s{-}Ciriano},
title = {ReConPlot: an {R} package for the visualization and interpretation
of genomic rearrangements},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad719},
doi = {10.1093/BIOINFORMATICS/BTAD719},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ValleInclanC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VandelliSMFBCGBAT23,
author = {Andrea Vandelli and
Magdalena Arnal Segura and
Michele Monti and
Jonathan Fiorentino and
Laura Broglia and
Alessio Colantoni and
Natalia Sanchez de Groot and
Marc Torrent Burgas and
Alexandros Armaos and
Gian Gaetano Tartaglia},
title = {The {PRALINE} database: protein and Rna humAn singLe nucleotIde variaNts
in condEnsates},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac847},
doi = {10.1093/BIOINFORMATICS/BTAC847},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VandelliSMFBCGBAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VarenykSHL23,
author = {Yuliia Varenyk and
Thomas Spicher and
Ivo L. Hofacker and
Ronny Lorenz},
title = {Modified RNAs and predictions with the ViennaRNA Package},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad696},
doi = {10.1093/BIOINFORMATICS/BTAD696},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VarenykSHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VaroquauxNV23,
author = {Nelle Varoquaux and
William S. Noble and
Jean{-}Philippe Vert},
title = {Inference of 3D genome architecture by modeling overdispersion of
Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac838},
doi = {10.1093/BIOINFORMATICS/BTAC838},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VaroquauxNV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VavraBSSFDMB23,
author = {Ondrej Vavra and
Jakub Ber{\'{a}}nek and
Jan Stourac and
Martin Surkovsk{\'{y}} and
Jiri Filipovic and
Jir{\'{\i}} Damborsk{\'{y}} and
Jan Martinovic and
David Bednar},
title = {pyCaverDock: Python implementation of the popular tool for analysis
of ligand transport with advanced caching and batch calculation support},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad443},
doi = {10.1093/BIOINFORMATICS/BTAD443},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VavraBSSFDMB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VillarrealKPGCSR23,
author = {Jaime Mart{\'{\i}}nez de Villarreal and
Mark Kalisz and
Gabriel Piedrafita and
Osvaldo Gra{\~{n}}a{-}Castro and
Dafni Chondronasiou and
Manuel Serrano and
Francisco X. Real},
title = {Pseudoalignment tools as an efficient alternative to detect repeated
transposable elements in scRNAseq data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac737},
doi = {10.1093/BIOINFORMATICS/BTAC737},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VillarrealKPGCSR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VillegasMorcilloRFB23,
author = {Amelia Villegas{-}Morcillo and
Louis Robinson and
Arthur Flajolet and
Thomas D. Barrett},
title = {ManyFold: an efficient and flexible library for training and validating
protein folding models},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac773},
doi = {10.1093/BIOINFORMATICS/BTAC773},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VillegasMorcilloRFB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VilovH23,
author = {Sergey Vilov and
Matthias Heinig},
title = {DeepSom: a CNN-based approach to somatic variant calling in {WGS}
samples without a matched normal},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac828},
doi = {10.1093/BIOINFORMATICS/BTAC828},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VilovH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VincetiTPRI23,
author = {Alessandro Vinceti and
Lucia Trastulla and
Umberto Perron and
Andrea Raiconi and
Francesco Iorio},
title = {A heuristic algorithm solving the mutual-exclusivity-sorting problem},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad016},
doi = {10.1093/BIOINFORMATICS/BTAD016},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VincetiTPRI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VisSKL23,
author = {Jonathan K. Vis and
Mark A. Santcroos and
Walter A. Kosters and
Jeroen F. J. Laros},
title = {A Boolean algebra for genetic variants},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad001},
doi = {10.1093/BIOINFORMATICS/BTAD001},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VisSKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VisonaDMSLBO23,
author = {Giovanni Vison{\`{a}} and
Diane Duroux and
Lucas Miranda and
Emese S{\"{u}}kei and
Yiran Li and
Karsten M. Borgwardt and
Carlos G. Oliver},
title = {Multimodal learning in clinical proteomics: enhancing antimicrobial
resistance prediction models with chemical information},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad717},
doi = {10.1093/BIOINFORMATICS/BTAD717},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VisonaDMSLBO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VogesJS23,
author = {Lucas F. Voges and
Lukas C. Jarren and
Stephan Seifert},
title = {Exploitation of surrogate variables in random forests for unbiased
analysis of mutual impact and importance of features},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad471},
doi = {10.1093/BIOINFORMATICS/BTAD471},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VogesJS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VolkelLHTKT23,
author = {Kevin Volkel and
Kevin N. Lin and
Paul W. Hook and
Winston Timp and
Albert J. Keung and
James M. Tuck},
title = {FrameD: framework for DNA-based data storage design, verification,
and validation},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad572},
doi = {10.1093/BIOINFORMATICS/BTAD572},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VolkelLHTKT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VolpeD23,
author = {Massimiliano Volpe and
Jyotirmoy Das},
title = {methylR: a graphical interface for comprehensive {DNA} methylation
array data analysis},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad184},
doi = {10.1093/BIOINFORMATICS/BTAD184},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VolpeD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VozzaBTFFBSZZM23,
author = {Gianluca Vozza and
Emanuele Bonetti and
Giulia Tini and
Valentina Favalli and
Gianmaria Frige and
Gabriele Bucci and
Simona De Summa and
Mario Zanfardino and
Francesco Zapelloni and
Luca Mazzarella},
title = {Benchmarking and improving the performance of variant-calling pipelines
with RecallME},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad722},
doi = {10.1093/BIOINFORMATICS/BTAD722},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VozzaBTFFBSZZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VuKFE23,
author = {Ha Vu and
Zane Koch and
Petko Fiziev and
Jason Ernst},
title = {A framework for group-wise summarization and comparison of chromatin
state annotations},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac722},
doi = {10.1093/BIOINFORMATICS/BTAC722},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VuKFE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VuLLPLBKK23,
author = {Thao Vu and
Elizabeth Litkowski and
Weixuan Liu and
Katherine A. Pratte and
Leslie Lange and
Russell Bowler and
Farnoush Banaei Kashani and
Katerina J. Kechris},
title = {NetSHy: network summarization via a hybrid approach leveraging topological
properties},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac818},
doi = {10.1093/BIOINFORMATICS/BTAC818},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VuLLPLBKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WagnerR23,
author = {Vincent Wagner and
Nicole Radde},
title = {The impossible challenge of estimating non-existent moments of the
Chemical Master Equation},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {440--447},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad205},
doi = {10.1093/BIOINFORMATICS/BTAD205},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WagnerR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Wallner23,
author = {Bj{\"{o}}rn Wallner},
title = {AFsample: improving multimer prediction with AlphaFold using massive
sampling},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad573},
doi = {10.1093/BIOINFORMATICS/BTAD573},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Wallner23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WalterSV23,
author = {Florin C. Walter and
Oliver Stegle and
Britta Velten},
title = {FISHFactor: a probabilistic factor model for spatial transcriptomics
data with subcellular resolution},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad183},
doi = {10.1093/BIOINFORMATICS/BTAD183},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WalterSV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Wang23,
author = {Shulei Wang},
title = {Multiscale adaptive differential abundance analysis in microbial compositional
data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad178},
doi = {10.1093/BIOINFORMATICS/BTAD178},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Wang23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangBPWBBIYDS23,
author = {Zhikang Wang and
Yue Bi and
Tong Pan and
Xiaoyu Wang and
Chris Bain and
Richard Bassed and
Seiya Imoto and
Jianhua Yao and
Roger J. Daly and
Jiangning Song},
title = {Targeting tumor heterogeneity: multiplex-detection-based multiple
instance learning for whole slide image classification},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad114},
doi = {10.1093/BIOINFORMATICS/BTAD114},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangBPWBBIYDS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangBWTCTLM23,
author = {Weiwen Wang and
James Barbetti and
Thomas Wong and
Bryan Thornlow and
Russell Corbett{-}Detig and
Yatish Turakhia and
Robert Lanfear and
Bui Quang Minh},
title = {DecentTree: scalable Neighbour-Joining for the genomic era},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad536},
doi = {10.1093/BIOINFORMATICS/BTAD536},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangBWTCTLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangDLAJV23,
author = {Xinyue Wang and
Leonard Dervishi and
Wen Tao Li and
Erman Ayday and
Xiaoqian Jiang and
Jaideep Vaidya},
title = {Privacy-preserving federated genome-wide association studies via dynamic
sampling},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad639},
doi = {10.1093/BIOINFORMATICS/BTAD639},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangDLAJV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangGC23,
author = {Yanli Wang and
Zhiye Guo and
Jianlin Cheng},
title = {Single-cell Hi-C data enhancement with deep residual and generative
adversarial networks},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad458},
doi = {10.1093/BIOINFORMATICS/BTAD458},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangGKL23,
author = {Chen Wang and
Harikumar Govindarajan and
Panagiotis Katsonis and
Olivier Lichtarge},
title = {ShinyBioHEAT: an interactive shiny app to identify phenotype driver
genes in \emph{E.coli} and \emph{B.subtilis}},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad467},
doi = {10.1093/BIOINFORMATICS/BTAD467},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangGKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangGLM23,
author = {Xiao Wang and
Wei{-}Cheng Gu and
Jie Li and
Bin{-}Guang Ma},
title = {{EVRC:} reconstruction of chromosome 3D structure models using error-vector
resultant algorithm with clustering coefficient},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad638},
doi = {10.1093/BIOINFORMATICS/BTAD638},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangGLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangGZ23,
author = {Jinxian Wang and
Jihong Guan and
Shuigeng Zhou},
title = {Molecular property prediction by contrastive learning with attention-guided
positive sample selection},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad258},
doi = {10.1093/BIOINFORMATICS/BTAD258},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangHYWWWSML23,
author = {Xuesong Wang and
Zhihang Hu and
Tingyang Yu and
Yixuan Wang and
Ruijie Wang and
Yumeng Wei and
Juan Shu and
Jianzhu Ma and
Yu Li},
title = {Con-AAE: contrastive cycle adversarial autoencoders for single-cell
multi-omics alignment and integration},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad162},
doi = {10.1093/BIOINFORMATICS/BTAD162},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangHYWWWSML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLAWY23,
author = {Ruimin Wang and
Miaoshan Lu and
Shaowei An and
Jinyin Wang and
Changbin Yu},
title = {3D-MSNet: a point cloud-based deep learning model for untargeted feature
detection and quantification in profile {LC-HRMS} data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad195},
doi = {10.1093/BIOINFORMATICS/BTAD195},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLAWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLBPM23,
author = {Xinran Wang and
Zeyun Lu and
Arjun Bhattacharya and
Bogdan Pasaniuc and
Nicholas Mancuso},
title = {twas{\_}sim, a Python-based tool for simulation and power analysis
of transcriptome-wide association analysis},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad288},
doi = {10.1093/BIOINFORMATICS/BTAD288},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLBPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLHYFV23,
author = {Ruogu Wang and
Alex A. Lemus and
Colin M. Henneberry and
Yiming Ying and
Yunlong Feng and
Alex M. Valm},
title = {Unmixing biological fluorescence image data with sparse and low-rank
Poisson regression},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad159},
doi = {10.1093/BIOINFORMATICS/BTAD159},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLHYFV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLL23,
author = {Jinjuan Wang and
Mingya Long and
Qizhai Li},
title = {A maximum kernel-based association test to detect the pleiotropic
genetic effects on multiple phenotypes},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad291},
doi = {10.1093/BIOINFORMATICS/BTAD291},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLLM23,
author = {Feifei Wang and
Dongzuo Liang and
Yang Li and
Shuangge Ma},
title = {Prior information-assisted integrative analysis of multiple datasets},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad452},
doi = {10.1093/BIOINFORMATICS/BTAD452},
timestamp = {Tue, 06 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLLW23,
author = {Bin Wang and
Kun Liu and
Yaohang Li and
Jianxin Wang},
title = {DFHiC: a dilated full convolution model to enhance the resolution
of Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad211},
doi = {10.1093/BIOINFORMATICS/BTAD211},
timestamp = {Thu, 04 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLYHN23,
author = {Kangwei Wang and
Zhengwei Li and
Zhu{-}Hong You and
Pengyong Han and
Ru Nie},
title = {Adversarial dense graph convolutional networks for single-cell classification},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad043},
doi = {10.1093/BIOINFORMATICS/BTAD043},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLYHN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLZZHWRSYH23,
author = {Yuwei Wang and
Bin Lian and
Haohui Zhang and
Yuanke Zhong and
Jie He and
Fashuai Wu and
Knut Reinert and
Xuequn Shang and
Hui Yang and
Jialu Hu},
title = {A multi-view latent variable model reveals cellular heterogeneity
in complex tissues for paired multimodal single-cell data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad005},
doi = {10.1093/BIOINFORMATICS/BTAD005},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLZZHWRSYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangN23,
author = {Junmin Wang and
Steven Novick},
title = {{DOSE-L1000:} unveiling the intricate landscape of compound-induced
transcriptional changes},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad683},
doi = {10.1093/BIOINFORMATICS/BTAD683},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangNZZ23,
author = {Victor Wang and
Ardalan Naseri and
Shaojie Zhang and
Degui Zhi},
title = {Syllable-PBWT for space-efficient haplotype long-match query},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac734},
doi = {10.1093/BIOINFORMATICS/BTAC734},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangNZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangSXLZ23,
author = {Lin Wang and
Chenhao Sun and
Xianyu Xu and
Jia Li and
Wenjuan Zhang},
title = {A neighborhood-regularization method leveraging multiview data for
predicting the frequency of drug-side effects},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad532},
doi = {10.1093/BIOINFORMATICS/BTAD532},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangSXLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangWHWDL23,
author = {Qian Wang and
Zhiqiang Wei and
Xiaotong Hu and
Zhuoya Wang and
Yujie Dong and
Hao Liu},
title = {Molecular generation strategy and optimization based on {A2C} reinforcement
learning in de novo drug design},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad693},
doi = {10.1093/BIOINFORMATICS/BTAD693},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangWHWDL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangXSL23,
author = {Chuan{-}Yuan Wang and
Shiyu Xu and
Duanchen Sun and
Zhi{-}Ping Liu},
title = {ActivePPI: quantifying protein-protein interaction network activity
with Markov random fields},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad567},
doi = {10.1093/BIOINFORMATICS/BTAD567},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangXSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangXYZZ23,
author = {Zixuan Wang and
Shuwen Xiong and
Yun Yu and
Jiliu Zhou and
Yongqing Zhang},
title = {{HAMPLE:} deciphering {TF-DNA} binding mechanism in different cellular
environments by characterizing higher-order nucleotide dependency},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad299},
doi = {10.1093/BIOINFORMATICS/BTAD299},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangXYZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangYLBLWL23,
author = {Yunhe Wang and
Zhuohan Yu and
Shaochuan Li and
Chuang Bian and
Yanchun Liang and
Ka{-}Chun Wong and
Xiangtao Li},
title = {scBGEDA: deep single-cell clustering analysis via a dual denoising
autoencoder with bipartite graph ensemble clustering},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad075},
doi = {10.1093/BIOINFORMATICS/BTAD075},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangYLBLWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangYXWWZWP23,
author = {Tao Wang and
Jinjin Yang and
Yifu Xiao and
Jingru Wang and
Yuxian Wang and
Xi Zeng and
Yongtian Wang and
Jiajie Peng},
title = {DFinder: a novel end-to-end graph embedding-based method to identify
drug-food interactions},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac837},
doi = {10.1093/BIOINFORMATICS/BTAC837},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangYXWWZWP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangZSWLC23,
author = {Ran Wang and
Xubin Zheng and
Fangda Song and
Man Hon Wong and
Kwong{-}Sak Leung and
Lixin Cheng},
title = {Deciphering associations between gut microbiota and clinical factors
using microbial modules},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad213},
doi = {10.1093/BIOINFORMATICS/BTAD213},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangZSWLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeberBLKHWL23,
author = {Leon Weber and
Fabio Barth and
Leonie Lorenz and
Fabian Konrath and
Kirsten Huska and
Jana Wolf and
Ulf Leser},
title = {{PEDL+:} protein-centered relation extraction from PubMed at your
fingertip},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad603},
doi = {10.1093/BIOINFORMATICS/BTAD603},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeberBLKHWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeberCK23,
author = {Thomas Weber and
Marco Raffaele Cosenza and
Jan Korbel},
title = {MosaiCatcher v2: a single-cell structural variations detection and
analysis reference framework based on Strand-seq},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad633},
doi = {10.1093/BIOINFORMATICS/BTAD633},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeberCK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WebsterDCFSHPCM23,
author = {Jace Webster and
Ha X. Dang and
Pradeep S. Chauhan and
Wenjia Feng and
Alex Shiang and
Peter K. Harris and
Russell K. Pachynski and
Aadel A Chaudhuri and
Christopher A. Maher},
title = {{PACT:} a pipeline for analysis of circulating tumor {DNA}},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad489},
doi = {10.1093/BIOINFORMATICS/BTAD489},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WebsterDCFSHPCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WebsterMLM23,
author = {Jace Webster and
Hung Mai and
Amy Ly and
Christopher Maher},
title = {INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization
of fusion-derived circular {RNA}},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad569},
doi = {10.1093/BIOINFORMATICS/BTAD569},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WebsterMLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WegG23,
author = {Karel J. van der Weg and
Holger Gohlke},
title = {TopEnzyme: a framework and database for structural coverage of the
functional enzyme space},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad116},
doi = {10.1093/BIOINFORMATICS/BTAD116},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WegG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WegnerK23,
author = {Martin Wegner and
Manuel Kaulich},
title = {ReCo: automated {NGS} \emph{re} ad- \emph{co} unting of single and
combinatorial {CRISPR} gRNAs},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad448},
doi = {10.1093/BIOINFORMATICS/BTAD448},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WegnerK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiBZLQW23,
author = {Ze{-}Gang Wei and
Peng{-}Yu Bu and
Xiao{-}Dan Zhang and
Fei Liu and
Yu Qian and
Fang{-}Xiang Wu},
title = {invMap: a sensitive mapping tool for long noisy reads with inversion
structural variants},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad726},
doi = {10.1093/BIOINFORMATICS/BTAD726},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiBZLQW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiLILL23,
author = {Chih{-}Hsuan Wei and
Ling Luo and
Rezarta Islamaj and
Po{-}Ting Lai and
Zhiyong Lu},
title = {GNorm2: an improved gene name recognition and normalization system},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad599},
doi = {10.1093/BIOINFORMATICS/BTAD599},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiLILL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiMK23,
author = {Wei Wei and
Andrew Millward and
David Koslicki},
title = {Finding phylogeny-aware and biologically meaningful averages of metagenomic
samples: \emph{L}2UniFrac},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {57--65},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad238},
doi = {10.1093/BIOINFORMATICS/BTAD238},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiMK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeidnerHRS23,
author = {Leopold Weidner and
Daniel Hemmler and
Michael Rychlik and
Philippe Schmitt{-}Kopplin},
title = {DBDIpy: a Python library for processing of untargeted datasets from
real-time plasma ionization mass spectrometry},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad088},
doi = {10.1093/BIOINFORMATICS/BTAD088},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeidnerHRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeilandtSMFDHH23,
author = {Daniel Weilandt and
Pierre Salvy and
Maria Masid and
Georgios Fengos and
Robin Denhardt{-}Erikson and
Zhaleh Hosseini and
Vassily Hatzimanikatis},
title = {Symbolic kinetic models in python (SKiMpy): intuitive modeling of
large-scale biological kinetic models},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac787},
doi = {10.1093/BIOINFORMATICS/BTAC787},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeilandtSMFDHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeinerLKG23,
author = {Rockwell J. Weiner and
Chirag M. Lakhani and
David A. Knowles and
Gamze G{\"{u}}rsoy},
title = {LDmat: efficiently queryable compression of linkage disequilibrium
matrices},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad092},
doi = {10.1093/BIOINFORMATICS/BTAD092},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeinerLKG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WelshXSKCS23,
author = {Ciaran M. Welsh and
Jin Xu and
Lucian P. Smith and
Matthias K{\"{o}}nig and
Kiri Choi and
Herbert M. Sauro},
title = {libRoadRunner 2.0: a high performance {SBML} simulation and analysis
library},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac770},
doi = {10.1093/BIOINFORMATICS/BTAC770},
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biburl = {https://dblp.org/rec/journals/bioinformatics/WelshXSKCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WenL23,
author = {Gang Wen and
Limin Li},
title = {FGCNSurv: dually fused graph convolutional network for multi-omics
survival prediction},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad472},
doi = {10.1093/BIOINFORMATICS/BTAD472},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WenL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WenZRPLCZHCBHGCLLZC23,
author = {Jun Wen and
Xiang Zhang and
Everett Neil Rush and
Vidul Ayakulangara Panickan and
Xingyu Li and
Tianrun Cai and
Doudou Zhou and
Yuk{-}Lam Ho and
Lauren Costa and
Edmon Begoli and
Chuan Hong and
J. Michael Gaziano and
Kelly Cho and
Junwei Lu and
Katherine P. Liao and
Marinka Zitnik and
Tianxi Cai},
title = {Multimodal representation learning for predicting molecule-disease
relations},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad085},
doi = {10.1093/BIOINFORMATICS/BTAD085},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WenZRPLCZHCBHGCLLZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WharrieYRMGWMOKMPLG23,
author = {Sophie Wharrie and
Zhiyu Yang and
Vishnu Raj and
Remo Monti and
Rahul Gupta and
Ying Wang and
Alicia Martin and
Luke J. O'Connor and
Samuel Kaski and
Pekka Marttinen and
Pier Francesco Palamara and
Christoph Lippert and
Andrea Ganna},
title = {{HAPNEST:} efficient, large-scale generation and evaluation of synthetic
datasets for genotypes and phenotypes},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad535},
doi = {10.1093/BIOINFORMATICS/BTAD535},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WharrieYRMGWMOKMPLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WierczeikoPMBDHBG23,
author = {Anna Wierczeiko and
Stefan Pastore and
Stefan M{\"{u}}ndnich and
Anne M. Busch and
Vincent Dietrich and
Mark Helm and
Tamer Butto and
Susanne Gerber},
title = {NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional
analysis},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad492},
doi = {10.1093/BIOINFORMATICS/BTAD492},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WierczeikoPMBDHBG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiewiorkaSSG23,
author = {Marek S. Wiewi{\'{o}}rka and
Agnieszka Szmurlo and
Pawel Stankiewicz and
Tomasz Gambin},
title = {Cloud-native distributed genomic pileup operations},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac804},
doi = {10.1093/BIOINFORMATICS/BTAC804},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiewiorkaSSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WilliamsRTAH23,
author = {Nathan P. Williams and
Carlos H. M. Rodrigues and
Jia Truong and
David B. Ascher and
Jessica K. Holien},
title = {DockNet: high-throughput protein-protein interface contact prediction},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac797},
doi = {10.1093/BIOINFORMATICS/BTAC797},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WilliamsRTAH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiltonS23,
author = {Richard Wilton and
Alexander S. Szalay},
title = {Short-read aligner performance in germline variant identification},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad480},
doi = {10.1093/BIOINFORMATICS/BTAD480},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiltonS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WlasnowolskiGRKP23,
author = {Michal Wlasnowolski and
Pawel Z. Grabowski and
Damian Roszczyk and
Krzysztof Kaczmarski and
Dariusz Plewczynski},
title = {cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad588},
doi = {10.1093/BIOINFORMATICS/BTAD588},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WlasnowolskiGRKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WlodzimierzHH23,
author = {Piotr Wlodzimierz and
Michael Hong and
Ian R. Henderson},
title = {{TRASH:} Tandem Repeat Annotation and Structural Hierarchy},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad308},
doi = {10.1093/BIOINFORMATICS/BTAD308},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WlodzimierzHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WoicikZXMW23,
author = {Addie Woicik and
Mingxin Zhang and
Hanwen Xu and
Sara Mostafavi and
Sheng Wang},
title = {Gemini: memory-efficient integration of hundreds of gene networks
with high-order pooling},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {504--512},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad247},
doi = {10.1093/BIOINFORMATICS/BTAD247},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WoicikZXMW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WongPKFJ23,
author = {Serene W. H. Wong and
Chiara Pastrello and
Max Kotlyar and
Christos Faloutsos and
Igor Jurisica},
title = {\emph{USNAP}: fast unique dense region detection and its application
to lung cancer},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad477},
doi = {10.1093/BIOINFORMATICS/BTAD477},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WongPKFJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuDGGL23,
author = {Jialun Wu and
Yuxin Dong and
Zeyu Gao and
Tieliang Gong and
Chen Li},
title = {Dual Attention and Patient Similarity Network for drug recommendation},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad003},
doi = {10.1093/BIOINFORMATICS/BTAD003},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuDGGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuDZPCZSY23,
author = {Qunzhuo Wu and
Zhaohong Deng and
Wei Zhang and
Xiaoyong Pan and
Kup{-}Sze Choi and
Yun Zuo and
Hong{-}Bin Shen and
Dong{-}Jun Yu},
title = {{MLNGCF:} circRNA-disease associations prediction with multilayer
attention neural graph-based collaborative filtering},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad499},
doi = {10.1093/BIOINFORMATICS/BTAD499},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuDZPCZSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuGC23,
author = {Tianqi Wu and
Zhiye Guo and
Jianlin Cheng},
title = {Atomic protein structure refinement using all-atom graph representations
and SE(3)-equivariant graph transformer},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad298},
doi = {10.1093/BIOINFORMATICS/BTAD298},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuGJ0023,
author = {Zhourun Wu and
Mingyue Guo and
Xiaopeng Jin and
Junjie Chen and
Bin Liu},
title = {{CFAGO:} cross-fusion of network and attributes based on attention
mechanism for protein function prediction},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad123},
doi = {10.1093/BIOINFORMATICS/BTAD123},
timestamp = {Sun, 16 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuGJ0023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuHSHBZ23,
author = {Xiaojing Wu and
Mingfei Han and
Xinyu Song and
Song He and
Xiaochen Bo and
Yunping Zhu},
title = {{COMMO:} a web server for the identification and analysis of consensus
gene modules across multiple methods},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad708},
doi = {10.1093/BIOINFORMATICS/BTAD708},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuHSHBZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuJLX23,
author = {Fandi Wu and
Xiaoyang Jing and
Xiao Luo and
Jinbo Xu},
title = {Improving protein structure prediction using templates and sequence
embedding},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac723},
doi = {10.1093/BIOINFORMATICS/BTAC723},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuJLX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuLLXWZXBX23,
author = {Jiawei Wu and
Qingrui Liu and
Min Li and
Jiliang Xu and
Chen Wang and
Junyin Zhang and
Minfeng Xiao and
Yannan Bin and
Junfeng Xia},
title = {PhaGAA: an integrated web server platform for phage genome annotation
and analysis},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad120},
doi = {10.1093/BIOINFORMATICS/BTAD120},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuLLXWZXBX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuMRMDRV23,
author = {Kwan{-}Ling Wu and
Melisa A. Martinez{-}Paniagua and
Kate Reichel and
Prashant Menon and
Shravani Deo and
Badrinath Roysam and
Navin Varadarajan},
title = {Automated detection of apoptotic bodies and cells in label-free time-lapse
high-throughput video microscopy using deep convolutional neural networks},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad584},
doi = {10.1093/BIOINFORMATICS/BTAD584},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuMRMDRV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuOQZRSWTLS23,
author = {Jun Wu and
Jian Ouyang and
Haipeng Qing and
Jiajia Zhou and
Ruth Roberts and
Rania Siam and
Lan Wang and
Weida Tong and
Zhichao Liu and
Tieliu Shi},
title = {{PLM-ARG:} antibiotic resistance gene identification using a pretrained
protein language model},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad690},
doi = {10.1093/BIOINFORMATICS/BTAD690},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuOQZRSWTLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuQWDZM23,
author = {Yiming Wu and
Bing Qian and
Anqi Wang and
Heng Dong and
Enqiang Zhu and
Baoshan Ma},
title = {iLSGRN: inference of large-scale gene regulatory networks based on
multi-model fusion},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad619},
doi = {10.1093/BIOINFORMATICS/BTAD619},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuQWDZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuRP23,
author = {Yujie Wu and
Boyu Ren and
Prasad Patil},
title = {A pairwise strategy for imputing predictive features when combining
multiple datasets},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac839},
doi = {10.1093/BIOINFORMATICS/BTAC839},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuRP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuSWL23,
author = {Xingqi Wu and
Yi Shi and
Minghui Wang and
Ao Li},
title = {{CAMR:} cross-aligned multimodal representation learning for cancer
survival prediction},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad025},
doi = {10.1093/BIOINFORMATICS/BTAD025},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuSWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23,
title = {Correction to: {FASTRAL:} improving scalability of phylogenomic analysis},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad010},
doi = {10.1093/BIOINFORMATICS/BTAD010},
timestamp = {Tue, 21 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23a,
title = {Correction to: Automated classification of cytogenetic abnormalities
in hematolymphoid neoplasms},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac826},
doi = {10.1093/BIOINFORMATICS/BTAC826},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23aa,
title = {Correction to: {BIODICA:} a computational environment for Independent
Component Analysis of omics data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad597},
doi = {10.1093/BIOINFORMATICS/BTAD597},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23aa.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ab,
title = {Correction to: Reducing cost in DNA-based data storage by sequence
analysis-aided soft information decoding of variable-length reads},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad697},
doi = {10.1093/BIOINFORMATICS/BTAD697},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ab.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ac,
title = {Correction to: Snapper: high-sensitive detection of methylation motifs
based on Oxford Nanopore reads},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad770},
doi = {10.1093/BIOINFORMATICS/BTAD770},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ac.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ad,
title = {Correction to: Prediction of gene co-expression from chromatin contacts
with graph attention network},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad769},
doi = {10.1093/BIOINFORMATICS/BTAD769},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ad.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ae,
title = {Correction to: {KR4SL:} knowledge graph reasoning for explainable
prediction of synthetic lethality},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad768},
doi = {10.1093/BIOINFORMATICS/BTAD768},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ae.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23af,
title = {Correction to: {GIL:} a python package for designing custom indexing
primers},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad735},
doi = {10.1093/BIOINFORMATICS/BTAD735},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23af.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ag,
title = {Correction to: NeoFox: annotating neoantigen candidates with neoantigen
features},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad763},
doi = {10.1093/BIOINFORMATICS/BTAD763},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ag.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ah,
title = {Correction to: {PEMT:} a patent enrichment tool for drug discovery},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad758},
doi = {10.1093/BIOINFORMATICS/BTAD758},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ah.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23ai,
title = {Correction to: DeepFold: enhancing protein structure prediction through
optimized loss functions, improved template features, and re-optimized
energy function},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad762},
doi = {10.1093/BIOINFORMATICS/BTAD762},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23ai.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23b,
title = {Correction to: wpLogicNet: logic gate and structure inference in gene
regulatory networks},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad304},
doi = {10.1093/BIOINFORMATICS/BTAD304},
timestamp = {Mon, 29 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23c,
title = {Correction to: Python interfaces for the Smoldyn simulator},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad558},
doi = {10.1093/BIOINFORMATICS/BTAD558},
timestamp = {Wed, 04 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23c.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23d,
title = {Correction to: CITEdb: a manually curated database of cell-cell interactions
in human},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad669},
doi = {10.1093/BIOINFORMATICS/BTAD669},
timestamp = {Wed, 29 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23d.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23e,
title = {Correction to: HunFlair: an easy-to-use tool for state-of-the-art
biomedical named entity recognition},
journal = {Bioinform.},
volume = {39},
number = {11},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad705},
doi = {10.1093/BIOINFORMATICS/BTAD705},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23e.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23f,
title = {Correction to: Targeted metabolomics analyses for brain tumor margin
assessment during surgery},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad009},
doi = {10.1093/BIOINFORMATICS/BTAD009},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23f.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23g,
title = {Expression of Concern: Overcoming the inadaptability of sparse group
lasso for data with various group structures by stacking},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac758},
doi = {10.1093/BIOINFORMATICS/BTAC758},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23g.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23h,
title = {Correction to: Biomedical evidence engineering for data-driven discovery},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad026},
doi = {10.1093/BIOINFORMATICS/BTAD026},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23h.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23i,
title = {Correction to: {ELIXIR} biovalidator for semantic validation of life
science metadata},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac835},
doi = {10.1093/BIOINFORMATICS/BTAC835},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23i.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23j,
title = {{CCPLS} reveals cell-type-specific spatial dependence of transcriptomes
in single cells},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad033},
doi = {10.1093/BIOINFORMATICS/BTAD033},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23j.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23k,
title = {Correction to: {HOMELETTE:} a unified interface to homology modelling
software},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad086},
doi = {10.1093/BIOINFORMATICS/BTAD086},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23k.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23l,
title = {Correction to: Improving annotation propagation on molecular networks
through random walks: introducing ChemWalker},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad147},
doi = {10.1093/BIOINFORMATICS/BTAD147},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23l.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23m,
title = {Correction to: On the feasibility of deep learning applications using
raw mass spectrometry data},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad106},
doi = {10.1093/BIOINFORMATICS/BTAD106},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23m.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23n,
title = {Correction to: SVJedi: genotyping structural variations with long
reads},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad129},
doi = {10.1093/BIOINFORMATICS/BTAD129},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23n.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23o,
title = {Correction to: SBbadger: biochemical reaction networks with definable
degree distributions},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad117},
doi = {10.1093/BIOINFORMATICS/BTAD117},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23o.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23p,
title = {Correction to: Benchmarking the empirical accuracy of short-read sequencing
across the \emph{M. tuberculosis} genome},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad107},
doi = {10.1093/BIOINFORMATICS/BTAD107},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23p.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23q,
title = {Correction to: Multi-omic integration by machine learning (MIMaL)},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad146},
doi = {10.1093/BIOINFORMATICS/BTAD146},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23q.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23r,
title = {Correction to: Continuous chromatin state feature annotation of the
human epigenome},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad163},
doi = {10.1093/BIOINFORMATICS/BTAD163},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23r.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23s,
title = {Correction to: Phylovar: toward scalable phylogeny-aware inference
of single-nucleotide variations from single-cell {DNA} sequencing
data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad321},
doi = {10.1093/BIOINFORMATICS/BTAD321},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23s.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23t,
title = {Correction to: Integrative analysis of individual-level data and high-dimensional
summary statistics},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad324},
doi = {10.1093/BIOINFORMATICS/BTAD324},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23t.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23u,
title = {Correction to: Joint registration of multiple point clouds for fast
particle fusion in localization microscopy},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad500},
doi = {10.1093/BIOINFORMATICS/BTAD500},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23u.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23v,
title = {Correction to: Clustering spatial transcriptomics data},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad574},
doi = {10.1093/BIOINFORMATICS/BTAD574},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23v.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23w,
title = {Correction to: "Retraction of: DeepCRISTL: deep transfer learning
to predict CRISPR/Cas9 functional and endogenous on-target editing
efficiency"},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad562},
doi = {10.1093/BIOINFORMATICS/BTAD562},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23w.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23x,
title = {Correction to: Optimal adjustment sets for causal query estimation
in partially observed biomolecular networks},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad559},
doi = {10.1093/BIOINFORMATICS/BTAD559},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23x.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23y,
title = {Correction to: Robust joint clustering of multi-omics single-cell
data via multi-modal high-order neighborhood Laplacian matrix optimization},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad554},
doi = {10.1093/BIOINFORMATICS/BTAD554},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23y.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X23z,
title = {Correction to: Online bias-aware disease module mining with ROBUST-Web},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad566},
doi = {10.1093/BIOINFORMATICS/BTAD566},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X23z.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XieCZS23,
author = {Hongjing Xie and
Xuewei Cao and
Shuanglin Zhang and
Qiuying Sha},
title = {Joint analysis of multiple phenotypes for extremely unbalanced case-control
association studies using multi-layer network},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad707},
doi = {10.1093/BIOINFORMATICS/BTAD707},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XieCZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XieVK23,
author = {Xuezhi Xie and
Pedro A. Valiente and
Philip M. Kim},
title = {HelixGAN a deep-learning methodology for conditional \emph{de novo}
design of {\(\alpha\)}-helix structures},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad036},
doi = {10.1093/BIOINFORMATICS/BTAD036},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XieVK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XinLCLSSCH23,
author = {Tong Xin and
Yanan Lv and
Haoran Chen and
Linlin Li and
Lijun Shen and
Guangcun Shan and
Xi Chen and
Hua Han},
title = {A novel registration method for long-serial section images of {EM}
with a serial split technique based on unsupervised optical flow network},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad436},
doi = {10.1093/BIOINFORMATICS/BTAD436},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XinLCLSSCH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiongBZ23,
author = {Guangzhi Xiong and
Stefan Bekiranov and
Aidong Zhang},
title = {ProtoCell4P: an explainable prototype-based neural network for patient
classification using single-cell RNA-seq},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad493},
doi = {10.1093/BIOINFORMATICS/BTAD493},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiongBZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiongLSLXW23,
author = {Zehao Xiong and
Jiawei Luo and
Wanwan Shi and
Ying Liu and
Zhongyuan Xu and
Bo Wang},
title = {scGCL: an imputation method for scRNA-seq data based on graph contrastive
learning},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad098},
doi = {10.1093/BIOINFORMATICS/BTAD098},
timestamp = {Thu, 08 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiongLSLXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuHGZSLYZN23,
author = {Cuifang Xu and
Jiating Huang and
Yongqiang Gao and
Weixing Zhao and
Yiqi Shen and
Feihong Luo and
Gang Yu and
Feng Zhu and
Yan Ni},
title = {OBMeta: a comprehensive web server to analyze and validate gut microbial
features and biomarkers for obesity-associated metabolic diseases},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad715},
doi = {10.1093/BIOINFORMATICS/BTAD715},
timestamp = {Fri, 09 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuHGZSLYZN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuJS23,
author = {Jin Xu and
Jessie Jiang and
Herbert M. Sauro},
title = {SBMLDiagrams: a python package to process and visualize {SBML} layout
and render},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac730},
doi = {10.1093/BIOINFORMATICS/BTAC730},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuJS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuLLZLXW23,
author = {Yunpei Xu and
Hong{-}Dong Li and
Cui{-}Xiang Lin and
Ruiqing Zheng and
Yaohang Li and
Jinhui Xu and
Jianxin Wang},
title = {CellBRF: a feature selection method for single-cell clustering using
cell balance and random forest},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {368--376},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad216},
doi = {10.1093/BIOINFORMATICS/BTAD216},
timestamp = {Tue, 04 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuLLZLXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuYYYWSL23,
author = {Xiaoming Xu and
Zekun Yin and
Lifeng Yan and
Huiguang Yi and
Hua Wang and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitKSSD: accelerating genome distance estimation on modern multi-core
architectures},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad695},
doi = {10.1093/BIOINFORMATICS/BTAD695},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuYYYWSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuZLZ23,
author = {Jing Xu and
Aidi Zhang and
Fang Liu and
Xiujun Zhang},
title = {{STGRNS:} an interpretable transformer-based method for inferring
gene regulatory networks from single-cell transcriptomic data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad165},
doi = {10.1093/BIOINFORMATICS/BTAD165},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuZLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XueZHKSPLSMT23,
author = {Xiangning Xue and
Wei Zong and
Zhiguang Huo and
Kyle D. Ketchesin and
Madeline R. Scott and
Kaitlyn A Petersen and
Ryan W. Logan and
Marianne L. Seney and
Colleen A. Mcclung and
George C. Tseng},
title = {DiffCircaPipeline: a framework for multifaceted characterization of
differential rhythmicity},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad039},
doi = {10.1093/BIOINFORMATICS/BTAD039},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XueZHKSPLSMT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YamamotoLCX23,
author = {Ryo Yamamoto and
Zhiheng Liu and
Mudra Choudhury and
Xinshu Xiao},
title = {dsRID: \emph{in silico} identification of dsRNA regions using long-read
RNA-seq data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad649},
doi = {10.1093/BIOINFORMATICS/BTAD649},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YamamotoLCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanGL23,
author = {Ke Yan and
Yichen Guo and
Bin Liu},
title = {PreTP-2L: identification of therapeutic peptides and their types using
two-layer ensemble learning framework},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad125},
doi = {10.1093/BIOINFORMATICS/BTAD125},
timestamp = {Mon, 29 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanLGPL23,
author = {Ke Yan and
Hongwu Lv and
Yichen Guo and
Wei Peng and
Bin Liu},
title = {sAMPpred-GAT: prediction of antimicrobial peptide by graph attention
network and predicted peptide structure},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac715},
doi = {10.1093/BIOINFORMATICS/BTAC715},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanLGPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanMY23,
author = {Jiaqian Yan and
Ming Ma and
Zhenhua Yu},
title = {bmVAE: a variational autoencoder method for clustering single-cell
mutation data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac790},
doi = {10.1093/BIOINFORMATICS/BTAC790},
timestamp = {Sun, 31 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanMY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanS23,
author = {Lulu Yan and
Xiaoqiang Sun},
title = {Benchmarking and integration of methods for deconvoluting spatial
transcriptomic data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac805},
doi = {10.1093/BIOINFORMATICS/BTAC805},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanZCL23,
author = {Xuhua Yan and
Ruiqing Zheng and
Jinmiao Chen and
Min Li},
title = {scNCL: transferring labels from scRNA-seq to scATAC-seq data with
neighborhood contrastive regularization},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad505},
doi = {10.1093/BIOINFORMATICS/BTAD505},
timestamp = {Sun, 24 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanZCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanZWL23,
author = {Xuhua Yan and
Ruiqing Zheng and
Fang{-}Xiang Wu and
Min Li},
title = {{CLAIRE:} contrastive learning-based batch correction framework for
better balance between batch mixing and preservation of cellular heterogeneity},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad099},
doi = {10.1093/BIOINFORMATICS/BTAD099},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Yang023,
author = {Muyu Yang and
Jian Ma},
title = {{UNADON:} transformer-based model to predict genome-wide chromosome
spatial position},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {553--562},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad246},
doi = {10.1093/BIOINFORMATICS/BTAD246},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Yang023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangHZJZHZ23,
author = {Minghao Yang and
Zhi{-}An Huang and
Wei Zhou and
Junkai Ji and
Jun Zhang and
Shan He and
Zexuan Zhu},
title = {{MIX-TPI:} a flexible prediction framework for TCR-pMHC interactions
based on multimodal representations},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad475},
doi = {10.1093/BIOINFORMATICS/BTAD475},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangHZJZHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangJ23,
author = {Yiyan Yang and
Xiaofang Jiang},
title = {Evolink: a phylogenetic approach for rapid identification of genotype-phenotype
associations in large-scale microbial multispecies data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad215},
doi = {10.1093/BIOINFORMATICS/BTAD215},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangKZDY23,
author = {Bowen Yang and
Minal Khatri and
Jinfang Zheng and
Jitender S. Deogun and
Yanbin Yin},
title = {Genome mining for anti-CRISPR operons using machine learning},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad309},
doi = {10.1093/BIOINFORMATICS/BTAD309},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangKZDY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangMCBCZ23,
author = {Chen Yang and
Jiahao Mai and
Xuan Cao and
Aaron Burberry and
Fabio Cominelli and
Liangliang Zhang},
title = {ggpicrust2: an {R} package for PICRUSt2 predicted functional profile
analysis and visualization},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad470},
doi = {10.1093/BIOINFORMATICS/BTAD470},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangMCBCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangQHZYZLLGLX23,
author = {Min Yang and
Bo Qiu and
Guo{-}You He and
Jian{-}Yuan Zhou and
Hao{-}Jie Yu and
Yu{-}Ying Zhang and
Yan{-}Shang Li and
Tai{-}Song Li and
Jin{-}Cheng Guo and
Xue{-}Cang Li and
Jian{-}Jun Xie},
title = {eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts
in multi-species},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad173},
doi = {10.1093/BIOINFORMATICS/BTAD173},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangQHZYZLLGLX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangWLCXXJCQPYNJLX23,
author = {Wenyi Yang and
Pingping Wang and
Meng Luo and
Yideng Cai and
Chang Xu and
Guangfu Xue and
Xiyun Jin and
Rui Cheng and
Jinhao Que and
Fenglan Pang and
Yuexin Yang and
Huan Nie and
Qinghua Jiang and
Zhigang Liu and
Zhaochun Xu},
title = {DeepCCI: a deep learning framework for identifying cell-cell interactions
from single-cell {RNA} sequencing data},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad596},
doi = {10.1093/BIOINFORMATICS/BTAD596},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangWLCXXJCQPYNJLX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YaziciVCADKKA23,
author = {G{\"{o}}zde Yazici and
Burcu Kurt Vatandaslar and
Ilknur Aydin Canturk and
Fatmagul I Aydinli and
Ozge Arici Duz and
Emre Karako{\c{c}} and
Bilal Ersen Kerman and
Can Alkan},
title = {Identification of protein-protein interaction bridges for multiple
sclerosis},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad175},
doi = {10.1093/BIOINFORMATICS/BTAD175},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YaziciVCADKKA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YeHPM23,
author = {Tiantian Ye and
Yangyang Hu and
Sydney Pun and
Wenxiu Ma},
title = {HiCube: interactive visualization of multiscale and multimodal Hi-C
and 3D genome data},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad154},
doi = {10.1093/BIOINFORMATICS/BTAD154},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YeHPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YounisTSYSAKBC23,
author = {Omar G. Younis and
Matteo Turchetta and
Daniel Ariza Suarez and
Steven Yates and
Bruno Studer and
Ioannis N. Athanasiadis and
Andreas Krause and
Joachim M. Buhmann and
Luca Corinzia},
title = {ChromaX: a fast and scalable breeding program simulator},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad691},
doi = {10.1093/BIOINFORMATICS/BTAD691},
timestamp = {Tue, 13 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YounisTSYSAKBC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuCRK23,
author = {Dingquan Yu and
Grzegorz Chojnowski and
Maria Rosenthal and
Jan Kosinski},
title = {AlphaPulldown - a python package for protein-protein interaction screens
using AlphaFold-Multimer},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac749},
doi = {10.1093/BIOINFORMATICS/BTAC749},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuCRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuCS23,
author = {Runzhou Yu and
Dehan Cai and
Yanni Sun},
title = {AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation
sequencing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac827},
doi = {10.1093/BIOINFORMATICS/BTAC827},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuJLNPG23,
author = {Hui Yu and
Limin Jiang and
Chung{-}I Li and
Scott Ness and
Sara G. M. Piccirillo and
Yan Guo},
title = {Somatic mutation effects diffused over microRNA dysregulation},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad520},
doi = {10.1093/BIOINFORMATICS/BTAD520},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuJLNPG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuWTCGNK23,
author = {Hanyi Yu and
Fusheng Wang and
George Teodoro and
Fan Chen and
Xiaoyuan Guo and
John Nickerson and
Jun Kong},
title = {Self-supervised semantic segmentation of retinal pigment epithelium
cells in flatmount fluorescent microscopy images},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad191},
doi = {10.1093/BIOINFORMATICS/BTAD191},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuWTCGNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuXCJWLY23,
author = {Xinyi Yu and
Jiashun Xiao and
Mingxuan Cai and
Yuling Jiao and
Xiang Wan and
Jin Liu and
Can Yang},
title = {{PALM:} a powerful and adaptive latent model for prioritizing risk
variants with functional annotations},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad068},
doi = {10.1093/BIOINFORMATICS/BTAD068},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuXCJWLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuanCD23,
author = {Musu Yuan and
Liang Chen and
Minghua Deng},
title = {Clustering single-cell multi-omics data with MoClust},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac736},
doi = {10.1093/BIOINFORMATICS/BTAC736},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuanCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuanSFGMQW23,
author = {Mingzhi Yuan and
Ao Shen and
Kexue Fu and
Jiaming Guan and
Yingfan Ma and
Qin Qiao and
Manning Wang},
title = {ProteinMAE: masked autoencoder for protein surface self-supervised
learning},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad724},
doi = {10.1093/BIOINFORMATICS/BTAD724},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuanSFGMQW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuzeirBGHSY23,
author = {Altay Yuzeir and
David Alejandro Bejarano and
Stephan Grein and
Jan Hasenauer and
Andreas Schlitzer and
Jiangyan Yu},
title = {IntestLine: a shiny-based application to map the rolled intestinal
tissue onto a line},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad140},
doi = {10.1093/BIOINFORMATICS/BTAD140},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuzeirBGHSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZadorozhnySFL23,
author = {Anton Zadorozhny and
Anton Smirnov and
Dmitry Filimonov and
Alexey Lagunin},
title = {Prediction of pathogenic single amino acid substitutions using molecular
fragment descriptors},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad484},
doi = {10.1093/BIOINFORMATICS/BTAD484},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZadorozhnySFL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZanettiOCM23,
author = {Jo{\~{a}}o Paulo Pereira Zanetti and
Lucas Peres Oliveira and
Leonid Chindelevitch and
Jo{\~{a}}o Meidanis},
title = {Generalizations of the genomic rank distance to indels},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad087},
doi = {10.1093/BIOINFORMATICS/BTAD087},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZanettiOCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZengML23,
author = {Pengcheng Zeng and
Yuanyuan Ma and
Zhixiang Lin},
title = {scAWMV: an adaptively weighted multi-view learning framework for the
integrative analysis of parallel scRNA-seq and scATAC-seq data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac739},
doi = {10.1093/BIOINFORMATICS/BTAC739},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZengML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZengWLYLDL23,
author = {Min Zeng and
Yifan Wu and
Yiming Li and
Rui Yin and
Chengqian Lu and
Junwen Duan and
Min Li},
title = {LncLocFormer: a Transformer-based deep learning model for multi-label
lncRNA subcellular localization prediction by using localization-specific
attention mechanism},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad752},
doi = {10.1093/BIOINFORMATICS/BTAD752},
timestamp = {Wed, 17 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZengWLYLDL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZengWYCYLGY23,
author = {Yuansong Zeng and
Zhuoyi Wei and
Qianmu Yuan and
Sheng Chen and
Weijiang Yu and
Yutong Lu and
Jianzhao Gao and
Yuedong Yang},
title = {Identifying B-cell epitopes using AlphaFold2 predicted structures
and pretrained language model},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad187},
doi = {10.1093/BIOINFORMATICS/BTAD187},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZengWYCYLGY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Zhang00F023,
author = {Ke Zhang and
Min Wu and
Yong Liu and
Yimiao Feng and
Jie Zheng},
title = {{KR4SL:} knowledge graph reasoning for explainable prediction of synthetic
lethality},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {158--167},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad261},
doi = {10.1093/BIOINFORMATICS/BTAD261},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Zhang00F023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangB23,
author = {Yanlin Zhang and
Mathieu Blanchette},
title = {Reference panel-guided super-resolution inference of Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {386--393},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad266},
doi = {10.1093/BIOINFORMATICS/BTAD266},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangBI23,
author = {Yao{-}zhong Zhang and
Zeheng Bai and
Seiya Imoto},
title = {Investigation of the {BERT} model on nucleotide sequences with non-standard
pre-training and evaluation of different k-mer embeddings},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad617},
doi = {10.1093/BIOINFORMATICS/BTAD617},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangBI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCWLR23,
author = {Weiyan Zhang and
Chuang Chen and
Jiacheng Wang and
Jingping Liu and
Tong Ruan},
title = {A co-adaptive duality-aware framework for biomedical relation extraction},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad301},
doi = {10.1093/BIOINFORMATICS/BTAD301},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCWLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangERM23,
author = {Haoting Zhang and
Carl Henrik Ek and
Magnus Rattray and
Marta Milo},
title = {SynBa: improved estimation of drug combination synergies with uncertainty
quantification},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {121--130},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad240},
doi = {10.1093/BIOINFORMATICS/BTAD240},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangERM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangKLZSZHMHKZHLWLHWBSW23,
author = {Xueli Zhang and
Lingcong Kong and
Shunming Liu and
Xiayin Zhang and
Xianwen Shang and
Zhuoting Zhu and
Yu Huang and
Shuo Ma and
Jason Ha and
Katerina V. Kiburg and
Chunwen Zheng and
Yunyan Hu and
Cong Li and
Guanrong Wu and
Yingying Liang and
Mengxia He and
Yan Wang and
Xiaohe Bai and
Danli Shi and
Wei Wang and
Chi Zhang and
Ke Zhao and
Haining Yuan and
Guang Hu and
Yijun Hu and
Huiying Liang and
Honghua Yu and
Lei Zhang and
Mingguang He},
title = {{EBD:} an eye biomarker database},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad194},
doi = {10.1093/BIOINFORMATICS/BTAD194},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangKLZSZHMHKZHLWLHWBSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangMS23,
author = {Hong Zhang and
Devan V. Mehrotra and
Judong Shen},
title = {{AWOT} and {CWOT} for genotype and genotype-by-treatment interaction
joint analysis in pharmacogenetics {GWAS}},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac834},
doi = {10.1093/BIOINFORMATICS/BTAC834},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangS23,
author = {Ziang Zhang and
Lei Sun},
title = {The hidden factor: accounting for covariate effects in power and sample
size computation for a binary trait},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad139},
doi = {10.1093/BIOINFORMATICS/BTAD139},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangSZLLZZ23,
author = {Weijie Zhang and
Yichu Shan and
Lili Zhao and
Zhen Liang and
Chao Liu and
Lihua Zhang and
Yukui Zhang},
title = {ComMap: a software to perform large-scale structure-based mapping
for cross-linking mass spectrometry},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad077},
doi = {10.1093/BIOINFORMATICS/BTAD077},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangSZLLZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangTWHCGLYLH23,
author = {Qinhu Zhang and
Pengrui Teng and
Siguo Wang and
Ying He and
Zhen Cui and
Zhenghao Guo and
Yixin Liu and
Changan Yuan and
Qi Liu and
De{-}Shuang Huang},
title = {Computational prediction and characterization of cell-type-specific
and shared binding sites},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac798},
doi = {10.1093/BIOINFORMATICS/BTAC798},
timestamp = {Tue, 09 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangTWHCGLYLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangWZLGSY23,
author = {Ying Zhang and
Zhikang Wang and
Yiwen Zhang and
Shanshan Li and
Yuming Guo and
Jiangning Song and
Dong{-}Jun Yu},
title = {Interpretable prediction models for widespread m6A {RNA} modification
across cell lines and tissues},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad709},
doi = {10.1093/BIOINFORMATICS/BTAD709},
timestamp = {Wed, 17 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangWZLGSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangXGZ23,
author = {Ziqiao Zhang and
Ailin Xie and
Jihong Guan and
Shuigeng Zhou},
title = {Molecular property prediction by semantic-invariant contrastive learning},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad462},
doi = {10.1093/BIOINFORMATICS/BTAD462},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangXGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangZCZWS23,
author = {Mingqian Zhang and
Wenke Zhang and
Yuzhu Chen and
Jin Zhao and
Shunyao Wu and
Xiaoquan Su},
title = {Flex Meta-Storms elucidates the microbiome local beta-diversity under
specific phenotypes},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad148},
doi = {10.1093/BIOINFORMATICS/BTAD148},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangZCZWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoDGNP23,
author = {Chunyu Zhao and
Boris Dimitrov and
Miriam Goldman and
Stephen Nayfach and
Katherine S. Pollard},
title = {{MIDAS2:} Metagenomic Intra-species Diversity Analysis System},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac713},
doi = {10.1093/BIOINFORMATICS/BTAC713},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoDGNP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoQLYZYZDLYPCSWZWL23,
author = {Jianmei Zhao and
Fengcui Qian and
Xuecang Li and
Zhengmin Yu and
Jiang Zhu and
Rui Yu and
Yue Zhao and
Ke Ding and
Yanyu Li and
Yongsan Yang and
Qi Pan and
Jiaxin Chen and
Chao Song and
Qiuyu Wang and
Jian Zhang and
Guohua Wang and
Chunquan Li},
title = {CanMethdb: a database for genome-wide {DNA} methylation annotation
in cancers},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac783},
doi = {10.1093/BIOINFORMATICS/BTAC783},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoQLYZYZDLYPCSWZWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoSHHYH23,
author = {Bo{-}Wei Zhao and
Xiao{-}Rui Su and
Peng{-}Wei Hu and
Yu{-}An Huang and
Zhu{-}Hong You and
Lun Hu},
title = {iGRLDTI: an improved graph representation learning method for predicting
drug-target interactions over heterogeneous biological information
network},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad451},
doi = {10.1093/BIOINFORMATICS/BTAD451},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoSHHYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoSP023,
author = {Hanqing Zhao and
Matthijs Leon Souilljee and
Pavlos Pavlidis and
Nikolaos Alachiotis},
title = {Genome-wide scans for selective sweeps using convolutional neural
networks},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {194--203},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad265},
doi = {10.1093/BIOINFORMATICS/BTAD265},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoSP023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoZZLW23,
author = {Haochen Zhao and
Xiaoyu Zhang and
Qichang Zhao and
Yaohang Li and
Jianxin Wang},
title = {{MSDRP:} a deep learning model based on multisource data for predicting
drug response},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad514},
doi = {10.1093/BIOINFORMATICS/BTAD514},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoZZLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhapaCamachoKH23,
author = {Fernando Zhapa{-}Camacho and
Maxat Kulmanov and
Robert Hoehndorf},
title = {mOWL: Python library for machine learning with biomedical ontologies},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac811},
doi = {10.1093/BIOINFORMATICS/BTAC811},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhapaCamachoKH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengMW23,
author = {Weihua Zheng and
Wenwen Min and
Shunfang Wang},
title = {TsImpute: an accurate two-step imputation method for single-cell RNA-seq
data},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad731},
doi = {10.1093/BIOINFORMATICS/BTAD731},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengMW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengTZ23,
author = {Xiaobin Zheng and
Joseph R. Tran and
Yixian Zheng},
title = {CscoreTool-M infers 3D sub-compartment probabilities within cell population},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad314},
doi = {10.1093/BIOINFORMATICS/BTAD314},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhiyanovENST23,
author = {Anton Zhiyanov and
Narek Engibaryan and
Stepan A. Nersisyan and
Maxim U. Shkurnikov and
Alexander G. Tonevitsky},
title = {Differential co-expression network analysis with DCoNA reveals isomiR
targeting aberrations in prostate cancer},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad051},
doi = {10.1093/BIOINFORMATICS/BTAD051},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhiyanovENST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhongTW23,
author = {Cheng Zhong and
Tian Tian and
Zhi Wei},
title = {Hidden Markov random field models for cell-type assignment of spatially
resolved transcriptomics},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad641},
doi = {10.1093/BIOINFORMATICS/BTAD641},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhongTW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouDL0M023,
author = {Tianshuo Zhou and
Ning Dai and
Sizhen Li and
Max Ward and
David H. Mathews and
Liang Huang},
title = {{RNA} design via structure-aware multifrontier ensemble optimization},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {563--571},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad252},
doi = {10.1093/BIOINFORMATICS/BTAD252},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouDL0M023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouL23,
author = {Boyan Zhou and
Huilin Li},
title = {{STEMSIM:} a simulator of within-strain short-term evolutionary mutations
for longitudinal metagenomic data},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad302},
doi = {10.1093/BIOINFORMATICS/BTAD302},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouMD23,
author = {Chenxi Zhou and
Shane A. McCarthy and
Richard Durbin},
title = {YaHS: yet another Hi-C scaffolding tool},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac808},
doi = {10.1093/BIOINFORMATICS/BTAC808},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouMD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouYGSSLK23,
author = {Zhongliang Zhou and
Wayland Yeung and
Nathan Gravel and
Mariah Salcedo and
Saber Soleymani and
Sheng Li and
Natarajan Kannan},
title = {Phosformer: an explainable transformer model for protein kinase-specific
phosphorylation predictions},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad046},
doi = {10.1093/BIOINFORMATICS/BTAD046},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouYGSSLK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuCPPPGBH23,
author = {Wanying Zhu and
Hung{-}Hsin Chen and
Alexander S. Petty and
Lauren E. Petty and
Hannah G. Polikowsky and
Eric R. Gamazon and
Jennifer E. Below and
Heather M. Highland},
title = {IMMerge: merging imputation data at scale},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac750},
doi = {10.1093/BIOINFORMATICS/BTAC750},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuCPPPGBH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuSPY23,
author = {Kun Zhu and
Hong Su and
Zhenling Peng and
Jianyi Yang},
title = {A unified approach to protein domain parsing with inter-residue distance
matrix},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad070},
doi = {10.1093/BIOINFORMATICS/BTAD070},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuSPY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuZLWL23,
author = {Yan Zhu and
Yuhuan Zhou and
Yang Liu and
Xuan Wang and
Junyi Li},
title = {{SLGNN:} synthetic lethality prediction in human cancers based on
factor-aware knowledge graph neural network},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad015},
doi = {10.1093/BIOINFORMATICS/BTAD015},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuZLWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuZWWW23,
author = {Yan Zhu and
Lingling Zhao and
Naifeng Wen and
Junjie Wang and
Chunyu Wang},
title = {DataDTA: a multi-feature and dual-interaction aggregation framework
for drug-target binding affinity prediction},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad560},
doi = {10.1093/BIOINFORMATICS/BTAD560},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuZWWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZouSJW23,
author = {Huixi Zou and
Tianli Sun and
Bangqun Jin and
Shengqin Wang},
title = {sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters
from the human gut microbiome},
journal = {Bioinform.},
volume = {39},
number = {3},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad131},
doi = {10.1093/BIOINFORMATICS/BTAD131},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZouSJW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZurkowskiAS23,
author = {Michal Zurkowski and
Maciej Antczak and
Marta Szachniuk},
title = {High-quality, customizable heuristics for {RNA} 3D structure alignment},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad315},
doi = {10.1093/BIOINFORMATICS/BTAD315},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZurkowskiAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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