Trey Ideker - RankMe

62 papers A 1B 5Misc 4Journal 48Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis. CoRR Zhen Wang, Yiming Gao, Jieyuan Liu, Enze Ma, Jefferson Chen, Mark Antkowiak, Mengzhou Hu, JungHo Kong, Dexter Pratt, Zhiting Hu, Wei Wang, Trey Ideker, Eric P. Xing
2025	B	`conf`	An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. RECOMB Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan
2025	J	`jnl`	Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. CoRR Elizabeth Fahsbender, Alma Andersson, Jeremy Ash, Polina Binder, Daniel Burkhardt, Benjamin Chang, Georg K. Gerber, Anthony Gitter, Patrick Godau, Ankit Gupta, Genevieve Haliburton, Siyu He, Trey Ideker, Ivana Jelic, Aly Khan, Yang-Joon Kim, Aditi Krishnapriyan, Jon M. Laurent, Tianyu Liu, Emma Lundberg, Shalin B. Mehta, Rob Moccia, Angela Oliveira Pisco, Katherine S. Pollard, Suresh Ramani, Julio Saez-Rodriguez, Yasin Senbabaoglu, Elana Simon, Srinivasan Sivanandan, Gustavo Stolovitzky, Marc Valer, Bo Wang, Xikun Zhang, James Zou, Katrina Kalantar
2025	J	`jnl`	Bridge2AI: Building A Cross-disciplinary Curriculum Towards AI-Enhanced Biomedical and Clinical Care. CoRR John Rincon, Alexander Russell Pelletier, Destiny Gilliland, Wei Wang, Ding Wang, Simha Sankar Baradwaj, Lori Scott-Sheldon, Samson Gebreab, William Hersh, Parisa Rashidi, Sally Baxter, Wade Schulz, Trey Ideker, Yael Bensoussan, Paul C. Boutros, Alex A. T. Bui, Colin Walsh, Karol E. Watson, Peipei Ping
2025	J	`jnl`	Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization. Bioinform. Joanna Lenkiewicz, Christopher Churas, Mengzhou Hu, Gege Qian, Mayank Jain, Maxwell Adam Levinson, Sadnan Al Manir, Yue Qin, Dylan Fong, Keiichiro Ono, Jing Chen, Chengzhan Gao, Dexter Pratt, Jillian Parker, Timothy W. Clark, Trey Ideker, Leah V. Schaffer
2024	J	`jnl`	Multi-modal contrastive learning of subcellular organization using DICE. Bioinform. Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan
2024	J	`jnl`	Representing mutations for predicting cancer drug response. Bioinform. Patrick Wall, Trey Ideker
2023	J	`jnl`	Evaluation of large language models for discovery of gene set function. CoRR Mengzhou Hu, Sahar Alkhairy, Ingoo Lee, Rudolf T. Pillich, Robin Bachelder, Trey Ideker, Dexter Pratt
2023	J	`jnl`	NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 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
2021	J	`jnl`	Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput. Biol. Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker
2020	J	`jnl`	Multiscale community detection in Cytoscape. PLoS Comput. Biol. Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker
2019	J	`jnl`	Classifying tumors by supervised network propagation. Bioinform. Wei Zhang, Jianzhu Ma, Trey Ideker
2019	B	`conf`	Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. RECOMB Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
2019	J	`jnl`	On entropy and information in gene interaction networks. Bioinform. Z. S. Wallace, Sara Brin Rosenthal, Kathleen M. Fisch, Trey Ideker, Roman Sásik
2019	J	`jnl`	Rare variant phasing using paired tumor: normal sequence data. BMC Bioinform. Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork
2018	Misc	`conf`	Annotating gene sets by mining large literature collections with protein networks. PSB Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker
2018	J	`jnl`	Classifying tumors by supervised network propagation. Bioinform. Wei Zhang, Jianzhu Ma, Trey Ideker
2018	B	`conf`	Deciphering Signaling Specificity with Deep Neural Networks. RECOMB Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
2018	J	`jnl`	The Cytoscape Automation app article collection. F1000Research 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, Benno Schwikowski, Piet Molenaar, Trey Ideker
2018	J	`jnl`	ndexr - an R package to interface with the network data exchange. Bioinform. Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer
2018	J	`jnl`	pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinform. Justin K. Huang, Tongqiu Jia, Daniel E. Carlin, Trey Ideker
2017	J	`jnl`	A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research Daniel E. Carlin, Kassi Kosnicki, Sara Garamszegi, Trey Ideker, Helga Thorvaldsdóttir, Michael Reich, Jill P. Mesirov
2017	J	`jnl`	Network approaches and applications in biology. PLoS Comput. Biol. Trey Ideker, Ruth Nussinov
2017	J	`jnl`	Network propagation in the cytoscape cyberinfrastructure. PLoS Comput. Biol. Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker
2014	J	`jnl`	Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Research Keiichiro Ono, Barry Demchak, Trey Ideker
2014	J	`jnl`	Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Research Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael E. Smoot, Trey Ideker, Jill P. Mesirov
2014	J	`jnl`	Inferring gene ontologies from pairwise similarity data. Bioinform. Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker
2014	J	`jnl`	NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker
2014	J	`jnl`	The Cytoscape app article collection. F1000Research 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, Benno Schwikowski, David Welker, Trey Ideker
2013	J	`jnl`	Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. PLoS Comput. Biol. Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin
2013	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
2011	J	`jnl`	Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc. Natl. Acad. Sci. USA Ann Atwood, Robert DeConde, Susanna S. Wang, Todd C. Mockler, Jamal S. M. Sabir, Trey Ideker, Steve A. Kay
2011	J	`jnl`	Cytoscape 2.8: new features for data integration and network visualization. Bioinform. Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker
2011	J	`jnl`	PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinform. Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere
2011	J	`jnl`	Protein Networks as Logic Functions in Development and Cancer. PLoS Comput. Biol. Janusz Dutkowski, Trey Ideker
2010	J	`jnl`	Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinform. Konstantin Pentchev, Keiichiro Ono, Ralf Herwig, Trey Ideker, Atanas Kamburov
2010	J	`jnl`	Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinform. Carlo Vittorio Cannistraci, Timothy Ravasi, Franco Maria Montevecchi, Trey Ideker, Massimo Alessio
2009	J	`jnl`	Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
2008	J	`jnl`	Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinform. Ryan M. Kelley, Hoda Feizi, Trey Ideker
2008	J	`jnl`	Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. PLoS Comput. Biol. Sourav Bandyopadhyay, Ryan M. Kelley, Nevan J. Krogan, Trey Ideker
2008	J	`jnl`	Inferring Pathway Activity toward Precise Disease Classification. PLoS Comput. Biol. Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee
2008	J	`jnl`	NetworkBLAST: comparative analysis of protein networks. Bioinform. Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan
2007	J	`jnl`	CellCircuits: a database of protein network models. Nucleic Acids Res. H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker
2007	—	`conf`	SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ISMB/ECCB (Supplement of Bioinformatics) Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan
2007	—	`ed.`	Systems Biology and Computational Proteomics, Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers Systems Biology and Computational Proteomics Trey Ideker, Vineet Bafna
2006	J	`jnl`	A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
2006	J	`jnl`	Bioinformatics in the human interactome project. Bioinform. Trey Ideker, Alfonso Valencia
2006	Misc	`conf`	Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pacific Symposium on Biocomputing Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker
2006	J	`jnl`	Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. J. Comput. Biol. Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan
2006	J	`jnl`	Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Comput. Biol. Andreas Beyer, Christopher T. Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
2006	—	`ed.`	Systems Biology and Regulatory Genomics, Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers Systems Biology and Regulatory Genomics Eleazar Eskin, Trey Ideker, Benjamin J. Raphael, Christopher T. Workman
2005	—	`conf`	Comparison of Protein-Protein Interaction Confidence Assignment Schemes. Systems Biology and Regulatory Genomics Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
2005	B	`conf`	Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. RECOMB Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan
2005	J	`jnl`	Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. J. Comput. Biol. Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp
2005	J	`jnl`	VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, Shankar Subramaniam
2005	J	`jnl`	enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos
2004	B	`conf`	Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. RECOMB Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp
2004	J	`jnl`	PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, Trey Ideker
2004	J	`jnl`	Physical Network Models. J. Comput. Biol. Chen-Hsiang Yeang, Trey Ideker, Tommi S. Jaakkola
2004	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Trey Ideker, Erik K. Neumann, Vincent Schächter
2002	A	`conf`	Discovering regulatory and signalling circuits in molecular interaction networks. ISMB Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel
2000	J	`jnl`	Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data. J. Comput. Biol. Trey Ideker, Vesteinn Thorsson, Andrew F. Siegel, Leroy E. Hood