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Journal Articles
- 2024
[j24]Nephi A. Walton, Radhakrishnan Nagarajan, Chen Wang
, Murat Sincan, Robert R. Freimuth, David B. Everman, Derek C. Walton, Scott P. McGrath, Dominick J. Lemas, Panayiotis V. Benos, Alexander V. Alekseyenko, Qianqian Song, Ece D. Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams:
Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. J. Am. Medical Informatics Assoc. 31(2): 536-541 (2024)- 2023
- [j23]Ali Tugrul Balci, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina:
An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinform. 39(Supplement-1): 413-422 (2023) - 2022
- [j22]Xin Bing, Tyler Lovelace, Florentina Bunea, Marten H. Wegkamp, Sudhir Pai Kasturi, Harinder Singh, Panayiotis V. Benos, Jishnu Das:
Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets. Patterns 3(5): 100473 (2022) - 2021
- [j21]Vineet K. Raghu, Xiaoyu Ge, Arun Balajiee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis:
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE ACM Trans. Comput. Biol. Bioinform. 18(3): 811-822 (2021) - 2020
- [j20]Kristina Buschur, Maria Chikina, Panayiotis V. Benos:
Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinform. 36(8): 2515-2521 (2020) - [j19]Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello, Claudia Coronnello:
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs. BMC Bioinform. 21-S(8): 201 (2020) - [j18]Xiaoyu Ge, Vineet K. Raghu, Panos K. Chrysanthis, Panayiotis V. Benos:
CausalMGM: an interactive web-based causal discovery tool. Nucleic Acids Res. 48(Webserver-Issue): W597-W602 (2020) - 2019
- [j17]Andrew J. Sedgewick, Kristina Buschur, Ivy Shi, Joseph D. Ramsey, Vineet K. Raghu, Dimitris V. Manatakis, Yingze Zhang, Jessica Bon, Divay Chandra, Chad Karoleski, Frank C. Sciurba, Peter Spirtes, Clark Glymour, Panayiotis V. Benos:
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis. Bioinform. 35(7): 1204-1212 (2019) - 2018
- [j16]Artemis G. Hatzigeorgiou, Pantelis G. Bagos, Panayiotis V. Benos, Christoforos Nikolaou, Yves Moreau, Ioannis Kavakiotis:
ECCB 2018: The 17th European Conference on Computational Biology. Bioinform. 34(17): i595-i598 (2018) - [j15]Dimitris V. Manatakis, Vineet K. Raghu, Panayiotis V. Benos:
piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks. Bioinform. 34(17): i848-i856 (2018) - [j14]Vineet K. Raghu, Joseph D. Ramsey, Alison Morris, Dimitrios V. Manatakis, Peter Spirtes, Panos K. Chrysanthis, Clark Glymour, Panayiotis V. Benos:
Comparison of strategies for scalable causal discovery of latent variable models from mixed data. Int. J. Data Sci. Anal. 6(1): 33-45 (2018) - 2016
- [j13]Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan, Panayiotis V. Benos:
Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC Bioinform. 17(S-5): S175 (2016) - 2015
- [j12]Gregory F. Cooper, Ivet Bahar, Michael J. Becich, Panayiotis V. Benos, Jeremy M. Berg, Jeremy U. Espino, Clark Glymour, Rebecca Crowley Jacobson, Michelle Kienholz, Adrian V. Lee, Xinghua Lu, Richard Scheines:
The center for causal discovery of biomedical knowledge from big data. J. Am. Medical Informatics Assoc. 22(6): 1132-1136 (2015) - 2013
- [j11]Claudia Coronnello, Panayiotis V. Benos:
ComiR: combinatorial microRNA target prediction tool. Nucleic Acids Res. 41(Webserver-Issue): 159-164 (2013) - 2012
- [j10]Claudia Coronnello, Ryan J. Hartmaier, Arshi Arora, Luai Huleihel, Kusum V. Pandit, Abha S. Bais, Michael Butterworth, Naftali Kaminski, Gary D. Stormo, Steffi Oesterreich, Panayiotis V. Benos:
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j9]Grace T. Huang, Charalambos Athanassiou, Panayiotis V. Benos:
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 39(Web-Server-Issue): 416-423 (2011) - 2009
- [j8]Sabah Kadri, Veronica F. Hinman, Panayiotis V. Benos:
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinform. 10(S-1) (2009) - [j7]Alain B. Tchagang, Kevin V. Bui, Thomas McGinnis, Panayiotis V. Benos:
Extracting biologically significant patterns from short time series gene expression data. BMC Bioinform. 10 (2009) - 2007
- [j6]Shaun Mahony, Panayiotis V. Benos:
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35(Web-Server-Issue): 253-258 (2007) - [j5]Shaun Mahony, Philip E. Auron, Panayiotis V. Benos:
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput. Biol. 3(3) (2007) - 2006
- [j4]Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden:
Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Networks 19(6-7): 950-962 (2006) - 2005
- [j3]Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos:
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 33(Web-Server-Issue): 389-392 (2005) - [j2]David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos:
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res. 33(Web-Server-Issue): 442-446 (2005) - [j1]Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panayiotis V. Benos, Massimo Trucco:
SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms. Nucleic Acids Res. 33(Web-Server-Issue): 548-552 (2005)
Conference and Workshop Papers
- 2022
- [c10]Haiyi Mao, Hongfu Liu, Jason Xiaotian Dou, Panayiotis V. Benos:
Towards Cross-Modal Causal Structure and Representation Learning. ML4H@NeurIPS 2022: 120-140 - 2020
- [c9]Haiyi Mao, Matthew J. Broerman, Panayiotis V. Benos:
Interpretable Factors in scRNA-seq Data with Disentangled Generative Models. BIBE 2020: 85-88 - 2018
- [c8]Vineet K. Raghu, Allen Poon, Panayiotis V. Benos:
Evaluation of Causal Structure Learning Methods on Mixed Data Types. CD@KDD 2018: 48-65 - 2017
- [c7]Vineet K. Raghu, Xiaoyu Ge, Panos K. Chrysanthis, Panayiotis V. Benos:
Integrated Theory-and Data-Driven Feature Selection in Gene Expression Data Analysis. ICDE 2017: 1525-1532 - 2015
- [c6]Grace T. Huang, Ioannis Tsamardinos, Vineet K. Raghu, Naftali Kaminski, Panayiotis V. Benos:
T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes. Pacific Symposium on Biocomputing 2015: 431-442 - 2013
- [c5]Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla:
Spectral Clustering Strategies for Heterogeneous Disease Data. Pacific Symposium on Biocomputing 2013: 212-223 - 2008
- [c4]Alain B. Tchagang, Ahmed H. Tewfik, Panayiotis V. Benos:
Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data. ICASSP 2008: 637-640 - 2007
- [c3]Shaun Mahony, Philip E. Auron, Panayiotis V. Benos:
Inferring protein-DNA dependencies using motif alignments and mutual information. ISMB/ECCB (Supplement of Bioinformatics) 2007: 297-304 - 2005
- [c2]Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos:
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. ISMB (Supplement of Bioinformatics) 2005: 283-291 - 2001
- [c1]Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo:
SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing 2001: 115-126
Parts in Books or Collections
- 2011
- [p1]Alain B. Tchagang, Youlian Pan, Fazel Famili, Ahmed H. Tewfik, Panayiotis V. Benos:
Biclustering of DNA Microarray Data: Theory, Evaluation, and Applications. Handbook of Research on Computational and Systems Biology 2011: 148-186
Informal and Other Publications
- 2022
- [i3]Haiyi Mao, Minxue Jia, Jason Xiaotian Dou, Haotian Zhang, Panayiotis V. Benos:
COEM: Cross-Modal Embedding for MetaCell Identification. CoRR abs/2207.07734 (2022) - 2020
- [i2]Vineet K. Raghu, Xiaoyu Ge, Arun Balajee, Daniel J. Shirer, Isha Das, Panayiotis V. Benos, Panos K. Chrysanthis:
A Pipeline for Integrated Theory and Data-Driven Modeling of Genomic and Clinical Data. CoRR abs/2005.02521 (2020) - 2017
- [i1]Andrew J. Sedgewick, Joseph D. Ramsey, Peter Spirtes, Clark Glymour, Panayiotis V. Benos:
Mixed Graphical Models for Causal Analysis of Multi-modal Variables. CoRR abs/1704.02621 (2017)
Coauthor Index
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