Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data. - Trey Ideker; Vesteinn Thorsson; Andrew F. Siegel; Leroy E. Hood (J. Comput. Biol., 2000)

Discovering regulatory and signalling circuits in molecular interaction networks. - Trey Ideker; Owen Ozier; Benno Schwikowski; Andrew F. Siegel (ISMB, 2002)

Session Introduction. - Trey Ideker; Erik K. Neumann; Vincent Schächter (Pacific Symposium on Biocomputing, 2004)

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. - Roded Sharan; Trey Ideker; Brian P. Kelley; Ron Shamir; Richard M. Karp (RECOMB, 2004)

Physical Network Models. - Chen-Hsiang Yeang; Trey Ideker; Tommi S. Jaakkola (J. Comput. Biol., 2004)

PathBLAST: a tool for alignment of protein interaction networks. - Brian P. Kelley; Bingbing Yuan; Fran Lewitter; Roded Sharan; Brent R. Stockwell; Trey Ideker (Nucleic Acids Res., 2004)

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. - Jacob Scott; Trey Ideker; Richard M. Karp; Roded Sharan (RECOMB, 2005)

Comparison of Protein-Protein Interaction Confidence Assignment Schemes. - Silpa Suthram; Tomer Shlomi; Eytan Ruppin; Roded Sharan; Trey Ideker (Systems Biology and Regulatory Genomics, 2005)

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. - Albert Hsiao; Trey Ideker; Jerrold M. Olefsky; Shankar Subramaniam (Nucleic Acids Res., 2005)

enoLOGOS: a versatile web tool for energy normalized sequence logos. - Christopher T. Workman; Yutong Yin; David L. Corcoran; Trey Ideker; Gary D. Stormo; Panayiotis V. Benos (Nucleic Acids Res., 2005)

Discovering Regulated Networks During HIV-1 Latency and Reactivation. - Sourav Bandyopadhyay; Ryan M. Kelley; Trey Ideker (Pacific Symposium on Biocomputing, 2006)

Bioinformatics in the human interactome project. - Trey Ideker; Alfonso Valencia (Bioinform., 2006)

A direct comparison of protein interaction confidence assignment schemes. - Silpa Suthram; Tomer Shlomi; Eytan Ruppin; Roded Sharan; Trey Ideker (BMC Bioinform., 2006)

Integrated Assessment and Prediction of Transcription Factor Binding. - Andreas Beyer; Christopher T. Workman; Jens Hollunder; Dörte Radke; Ulrich Möller; Thomas Wilhelm 003; Trey Ideker (PLoS Comput. Biol., 2006)

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. - Oved Ourfali; Tomer Shlomi; Trey Ideker; Eytan Ruppin; Roded Sharan (ISMB/ECCB (Supplement of Bioinformatics), 2007)

CellCircuits: a database of protein network models. - H. Craig Mak; Mike Daly; Bianca Gruebel; Trey Ideker (Nucleic Acids Res., 2007)

NetworkBLAST: comparative analysis of protein networks. - Maxim Kalaev; Michael E. Smoot; Trey Ideker; Roded Sharan (Bioinform., 2008)

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. - Ryan M. Kelley; Hoda Feizi; Trey Ideker (Bioinform., 2008)

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. - Sourav Bandyopadhyay; Ryan M. Kelley; Nevan J. Krogan; Trey Ideker (PLoS Comput. Biol., 2008)

Inferring Pathway Activity toward Precise Disease Classification. - Eunjung Lee; Han-Yu Chuang; Jong-Won Kim 001; Trey Ideker; Doheon Lee (PLoS Comput. Biol., 2008)

Papers on normalization, variable selection, classification or clustering of microarray data. - David M. Rocke; Trey Ideker; Olga G. Troyanskaya; John Quackenbush; Joaquín Dopazo (Bioinform., 2009)

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. - Carlo Vittorio Cannistraci; Timothy Ravasi; Franco Maria Montevecchi; Trey Ideker; Massimo Alessio (Bioinform., 2010)

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. - Konstantin Pentchev; Keiichiro Ono; Ralf Herwig; Trey Ideker; Atanas Kamburov (Bioinform., 2010)

PiNGO: a Cytoscape plugin to find candidate genes in biological networks. - Michael E. Smoot; Keiichiro Ono; Trey Ideker; Steven Maere (Bioinform., 2011)

Cytoscape 2.8: new features for data integration and network visualization. - Michael E. Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker (Bioinform., 2011)

Protein Networks as Logic Functions in Development and Cancer. - Janusz Dutkowski; Trey Ideker (PLoS Comput. Biol., 2011)

Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. - Ann Atwood; Robert DeConde; Susanna S. Wang; Todd C. Mockler; Jamal S. M. Sabir; Trey Ideker; Steve A. Kay (Proc. Natl. Acad. Sci. USA, 2011)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Trey Ideker; Joel S. Bader (Pacific Symposium on Biocomputing, 2013)

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. - Erhan Bilal; Janusz Dutkowski; Justin Guinney; In Sock Jang; Benjamin A. Logsdon; Gaurav Pandey 002; Benjamin A. Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H. Mecham; Oscar M. Rueda; Jorg Tost; et al. (PLoS Comput. Biol., 2013)

Inferring gene ontologies from pairwise similarity data. - Michael Kramer; Janusz Dutkowski; Michael Yu; Vineet Bafna; Trey Ideker (Bioinform., 2014)

Cytoscape: the network visualization tool for GenomeSpace workflows. - Barry Demchak; Tim Hull; Michael Reich; Ted Liefeld; Michael E. Smoot; Trey Ideker; Jill P. Mesirov (F1000Research, 2014)

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. - Keiichiro Ono; Barry Demchak; Trey Ideker (F1000Research, 2014)

The Cytoscape app article collection. - Alexander R. Pico; Gary D. Bader; Barry Demchak; Oriol Guitart Pla; Timothy Hull; William J. R. Longabaugh; Christian Tannus Lopes; Samad Lotia; Piet Molenaar; Jason Montojo; John H. Morris; Keiichiro Ono; et al. (F1000Research, 2014)

NeXO Web: the NeXO ontology database and visualization platform. - Janusz Dutkowski; Keiichiro Ono; Michael Kramer; Michael Yu; Dexter Pratt; Barry Demchak; Trey Ideker (Nucleic Acids Res., 2014)

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. - Daniel E. Carlin; Kassi Kosnicki; Sara Garamszegi; Trey Ideker; Helga Thorvaldsdóttir; Michael Reich; Jill P. Mesirov (F1000Research, 2017)

Network propagation in the cytoscape cyberinfrastructure. - Daniel E. Carlin; Barry Demchak; Dexter Pratt; Eric Sage; Trey Ideker (PLoS Comput. Biol., 2017)

Network approaches and applications in biology. - Trey Ideker; Ruth Nussinov (PLoS Comput. Biol., 2017)

Annotating gene sets by mining large literature collections with protein networks. - Sheng Wang 001; Jianzhu Ma; Michael Ku Yu; Fan Zheng; Edward W. Huang; Jiawei Han 001; Jian Peng 001; Trey Ideker (PSB, 2018)

Deciphering Signaling Specificity with Deep Neural Networks. - Yunan Luo; Jianzhu Ma; Yang Liu 097; Qing Ye; Trey Ideker; Jian Peng 001 (RECOMB, 2018)

ndexr - an R package to interface with the network data exchange. - Florian Auer; Zaynab Hammoud; Alexandr Ishkin; Dexter Pratt; Trey Ideker; Frank Kramer 001 (Bioinform., 2018)

pyNBS: a Python implementation for network-based stratification of tumor mutations. - Justin K. Huang; Tongqiu Jia; Daniel E. Carlin; Trey Ideker (Bioinform., 2018)

The Cytoscape Automation app article collection. - Barry Demchak; David Otasek; Alexander R. Pico; Gary D. Bader; Keiichiro Ono; Brett Settle; Eric Sage; John H. Morris; William J. R. Longabaugh; Christian Tannus Lopes; Michael Kucera; Adam Treister; et al. (F1000Research, 2018)

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. - Yunan Luo; Jianzhu Ma; Xiaoming Zhao 001; Yufeng Su; Yang Liu 097; Trey Ideker; Jian Peng 001 (RECOMB, 2019)

On entropy and information in gene interaction networks. - Z. S. Wallace; Sara Brin Rosenthal; Kathleen M. Fisch; Trey Ideker; Roman Sásik (Bioinform., 2019)

Classifying tumors by supervised network propagation. - Wei Zhang 067; Jianzhu Ma; Trey Ideker (Bioinform., 2019)

Rare variant phasing using paired tumor: normal sequence data. - Alexandra R. Buckley; Trey Ideker; Hannah Carter; Nicholas J. Schork (BMC Bioinform., 2019)

Multiscale community detection in Cytoscape. - Akshat Singhal; Song Cao; Christopher Churas; Dexter Pratt; Santo Fortunato; Fan Zheng; Trey Ideker (PLoS Comput. Biol., 2020)

Genetic dissection of complex traits using hierarchical biological knowledge. - Hidenori Tanaka; Jason F. Kreisberg; Trey Ideker (PLoS Comput. Biol., 2021)

Evaluation of large language models for discovery of gene set function. - Mengzhou Hu; Sahar Alkhairy; Ingoo Lee; Rudolf T. Pillich; Robin Bachelder; Trey Ideker; Dexter Pratt (CoRR, 2023)

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. - Rudolf T. Pillich; Jing Chen; Christopher Churas; Dylan Fong; Benjamin M. Gyori; Trey Ideker; Klas Karis; Sophie N. Liu; Keiichiro Ono; Alexander R. Pico; Dexter Pratt (Bioinform., 2023)

Multi-modal contrastive learning of subcellular organization using DICE. - Rami Nasser; Leah V. Schaffer; Trey Ideker; Roded Sharan (Bioinform., 2024)

Representing mutations for predicting cancer drug response. - Patrick Wall; Trey Ideker (Bioinform., 2024)

An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. - Rami Nasser; Leah V. Schaffer; Trey Ideker; Roded Sharan (RECOMB, 2025)

Bridge2AI: Building A Cross-disciplinary Curriculum Towards AI-Enhanced Biomedical and Clinical Care. - John Rincon; Alexander Russell Pelletier; Destiny Gilliland; Wei Wang 010; Ding Wang; Simha Sankar Baradwaj; Lori Scott-Sheldon; Samson Gebreab; William Hersh; Parisa Rashidi; Sally Baxter; Wade Schulz; et al. (CoRR, 2025)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang 009; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)