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ORCIDBMC Bioinformatics, Volume 26
Volume 26, Number 1, December 2025
- Tongjun Xiang, Huibao Feng, Xin-hui Xing, Chong Zhang:
GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes. 1 - M. Eremeyeva, Y. Din, N. Shirokii, N. Serov:
SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes. 2 - Mohamed Elmanzalawi, Takatomo Fujisawa, Hiroshi Mori, Yasukazu Nakamura, Yasuhiro Tanizawa:
DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes. 3 - James P. Long, Yumeng Yang, Shohei Shimizu, Thong Pham, Kim-Anh Do:
Causal models and prediction in cell line perturbation experiments. 4 - Xianfang Tang, Yawen Hou, Yajie Meng, Zhaojing Wang, Changcheng Lu, Juan Lv, Xinrong Hu, Junlin Xu, Jialiang Yang:
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction. 5 - Weijie Yang, Jingsi Ji, Gang Fang:
A metric and its derived protein network for evaluation of ortholog database inconsistency. 6 - Leonardo Campillos Llanos, Ana Valverde-Mateos, Adrián Capllonch-Carrión:
Hybrid natural language processing tool for semantic annotation of medical texts in Spanish. 7 - Cristian Iperi, Álvaro Fernández-Ochoa, Guillermo Barturen, Jacques-Olivier Pers, Nathan Foulquier, Eléonore Bettacchioli, Marta E. Alarcón-Riquelme, Divi Cornec, Anne Bordron, Christophe Jamin
:
BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data. 8 - Olga Fourkioti, Matt De Vries, Reed Naidoo, Chris Bakal:
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology. 9 - Zixin Chen, Chengming Ji, Wenwen Xu, Jianfeng Gao, Ji Huang, Huanliang Xu, Guoliang Qian, Junxian Huang:
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides. 10 - Guang Yang, Yinbo Liu, Sijian Wen, Wenxi Chen, Xiaolei Zhu, Yongmei Wang:
DTI-MHAPR: optimized drug-target interaction prediction via PCA-enhanced features and heterogeneous graph attention networks. 11 - Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk, Samuel Sihvonen:
Solu: a cloud platform for real-time genomic pathogen surveillance. 12 - Jianwei Li, Xukun Zhang, Bing Li, Ziyu Li, Zhenzhen Chen:
MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks. 13 - Gabriele Moro, Rossano Atzeni, Ali Al-Subhi, Maria Giovanna Marche:
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes. 14 - Lujun Luo, Tarikul I. Milon, Elijah K. Tandoh, Walter J. Galdamez, Andrei Y. Chistoserdov, Jianping Yu, Jan Kern, Yingchun Wang, Wu Xu:
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I. 15 - Leixia Tian, Qi Wang, Zhiheng Zhou, Xiya Liu, Ming Zhang, Guiying Yan:
Predicting drug combination side effects based on a metapath-based heterogeneous graph neural network. 16 - Minindu Weerakoon, Sangjin Lee, Emily Mitchell, Haynes Heaton:
TopoQual polishes circular consensus sequencing data and accurately predicts quality scores. 17 - Xiaomin Liu, Yi-Ju Li, Qiao Fan:
Zim4rv: an R package to modeling zero-inflated count phenotype on regional-based rare variants. 18 - Dhekra Saeed, Huanlai Xing, Barakat AlBadani, Li Feng, Raeed Al-Sabri, Monir Abdullah, Amir Rehman:
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction. 19 - Arash Shahbazpoor Shahbazi, Farzin Irandoost, Reza Mahdavian, Seyedehsamaneh Shojaeilangari, Abdollah Allahvardi, Hossein Naderi-manesh:
A multi-stage weakly supervised design for spheroid segmentation to explore mesenchymal stem cell differentiation dynamics. 20 - Thomas J. Booth, Simon Shaw, Pablo Cruz-Morales, Tilmann Weber:
getphylo: rapid and automatic generation of multi-locus phylogenetic trees. 21 - Jinming Cheng, Xinyi Jin, Gordon K. Smyth, Yunshun Chen:
Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. 22 - Xiao Zhang, Qian Liu:
A graph neural network approach for hierarchical mapping of breast cancer protein communities. 23 - Stefan Pastore, Philipp Hillenbrand, Nils Molnar, Irina Kovlyagina, Monika Chanu Chongtham, Stanislav Sys, Beat Lutz, Margarita Tevosian, Susanne Gerber:
ClearFinder: a Python GUI for annotating cells in cleared mouse brain. 24 - Azam Shirali, Vitalii Stebliankin, Ukesh Karki, Jimeng Shi, Prem Chapagain, Giri Narasimhan:
A comprehensive survey of scoring functions for protein docking models. 25 - Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer:
Joint embedding-classifier learning for interpretable collaborative filtering. 26 - Tatiana A. Semashko, Gleb Y. Fisunov, Georgiy Y. Shevelev, Vadim M. Govorun:
BAC-browser: the tool for synthetic biology. 27 - Jinchen Sun, Haoran Zheng:
HDN-DDI: a novel framework for predicting drug-drug interactions using hierarchical molecular graphs and enhanced dual-view representation learning. 28 - Qifeng Liu, Tao Zhou, Chi Cheng, Jin Ma, Marzia Hoque Tania:
Hybrid generative adversarial network based on frequency and spatial domain for histopathological image synthesis. 29 - Gregory Teicher, R. Madison Riffe, Wayne Barnaby, Gabrielle Martin, Benjamin E. Clayton, Josef G. Trapani, Gerald B. Downes:
Marigold: a machine learning-based web app for zebrafish pose tracking. 30 - Pere Palmer-Rodríguez, Ricardo Alberich, Mariana Reyes-Prieto, José A. Castro, Mercè Llabrés:
Metadag: a web tool to generate and analyse metabolic networks. 31 - Christopher Thron, Farhad Jafari:
Correcting scale distortion in RNA sequencing data. 32 - Xiaoxu Cui, Renkai Wu, Yinghao Liu, Peizhan Chen, Qing Chang, Pengchen Liang, Changyu He:
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder. 33 - Ram Chandra Bhushan, Rakesh Kumar Donthi, Yojitha Chilukuri, Ulligaddala Srinivasarao, Polisetty Swetha:
Biomedical named entity recognition using improved green anaconda-assisted Bi-GRU-based hierarchical ResNet model. 34 - Meng Zhang, Joel Parker, Lingling An, Yiwen Liu, Xiaoxiao Sun:
Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach. 35 - Jia Tian, Ziyu Gao, Minghao Li, Ergude Bao, Jin Zhao:
Accurate assembly of full-length consensus for viral quasispecies. 36 - Qiaowang Li, Yaser Gamallat, Jon G. Rokne, Tarek A. Bismar, Reda Alhajj:
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse. 37 - Antoine Allard, Maxime Liboz, Raphaël Crépin, Sid Labdi, Olek Maciejak, Michel Malo, Clément Campillo, Guillaume Lamour:
CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope. 38 - Samuel Boyd, Chad Slawson, Jeffrey A. Thompson:
AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs. 39 - Dimitrios Kioroglou:
Omilayers: a Python package for efficient data management to support multi-omic analysis. 40 - Francesco Caredda, Andrea Pagnani:
Direct coupling analysis and the attention mechanism. 41 - Bo Guan, Guangdi Chu, Ziying Wang, Jianmin Li, Bo Yi:
Instance-level semantic segmentation of nuclei based on multimodal structure encoding. 42 - Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha Bayer, Ingo Hein:
Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. 43 - Masahiro Ono:
TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis. 44 - Chi-Jane Chen, Haidong Yi, Natalie Stanley:
Conditional similarity triplets enable covariate-informed representations of single-cell data. 45 - Yansong Wang, Yundong Sun, Baohui Lin, Haotian Zhang, Xiaoling Luo, Yumeng Liu, Xiaopeng Jin, Dongjie Zhu:
SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction. 46 - Simon Schlumbohm, Julia E. Neumann, Philipp Neumann:
HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation. 47 - Luke Kennedy, Jagdeep K. Sandhu, Mary-Ellen Harper, Miroslava Cuperlovic-Culf:
A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers. 48 - Yao Sun, Jing Gao:
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer. 49 - Tianjiao Zhang, Liang Chen, Haibin Zhu, Garry Wong:
Mammalian piRNA target prediction using a hierarchical attention model. 50 - Diane M. Walker, Wendy A. Smith, Lia Gale, Jacob T. Wolff, Connor P. Healy, Hannah F. Van Hollebeke, Ashlie Stephenson, Marianne Kim:
CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity. 51 - Pia Keukeleire, Jonathan D. Rosen, Angelina Göbel-Knapp, Kilian Salomon, Max Schubach, Martin Kircher:
Using individual barcodes to increase quantification power of massively parallel reporter assays. 52 - Peng Sun, Yu Yang, Mengjie Yuan, Qin Tang:
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes. 53 - Junheng Chen, Fangfang Han, Mingxiu He, Yiyang Shi, Yongming Cai:
A novel weighted pseudo-labeling framework based on matrix factorization for adverse drug reaction prediction. 54 - Jiashan Li, Xinqi Gong:
Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity. 55 - Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya:
Identifying risk factors for Alzheimer's disease from multivariate longitudinal clinical data using temporal pattern mining. 56 - Na Quan, Shicheng Ma, Kai Zhao, Xuehua Bi, Linlin Zhang:
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism. 57 - Na Sun, Qiang Han, Yu Wang, Mengtong Sun, Ziqing Sun, Hongpeng Sun, Yueping Shen:
BHCox: Bayesian heredity-constrained Cox proportional hazards models for detecting gene-environment interactions. 58 - Lena Morrill Gavarró, Dominique-Laurent Couturier, Florian Markowetz:
A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures. 59 - Weiyin Zhou, Wen-Yi Huang, Neal D. Freedman, Mitchell J. Machiela:
Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region. 60
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