Trey Ideker

According to our database, Trey Ideker authored at least 50 papers between 2000 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

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., March, 2023

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

2021

Genetic dissection of complex traits using hierarchical biological knowledge.

Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker

PLoS Comput. Biol., 2021

2020

Multiscale community detection in Cytoscape.

Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker

PLoS Comput. Biol., 2020

2019

Rare variant phasing using paired tumor: normal sequence data.

Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork

BMC Bioinform., 2019

On entropy and information in gene interaction networks.

Z. S. Wallace, Sara Brin Rosenthal, Kathleen M. Fisch, Trey Ideker, Roman Sásik

Bioinform., 2019

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning.

Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2019

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, Benno Schwikowski, Piet Molenaar, Trey Ideker

F1000Research, 2018

Classifying tumors by supervised network propagation.

Wei Zhang, Jianzhu Ma, Trey Ideker

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

ndexr - an R package to interface with the network data exchange.

Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer

Bioinform., 2018

Deciphering Signaling Specificity with Deep Neural Networks.

Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng

Proceedings of the Research in Computational Molecular Biology, 2018

Annotating gene sets by mining large literature collections with protein networks.

Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2017

Network approaches and applications in biology.

Trey Ideker, Ruth Nussinov

PLoS Comput. Biol., 2017

Network propagation in the cytoscape cyberinfrastructure.

Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker

PLoS Comput. Biol., 2017

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

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

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, Benno Schwikowski, David Welker, Trey Ideker

F1000Research, 2014

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

Keiichiro Ono, Barry Demchak, Trey Ideker

F1000Research, 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

Inferring gene ontologies from pairwise similarity data.

Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker

Bioinform., 2014

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, 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

PLoS Comput. Biol., 2013

Session Introduction.

Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

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

Protein Networks as Logic Functions in Development and Cancer.

Janusz Dutkowski, Trey Ideker

PLoS Comput. Biol., 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

PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere

Bioinform., 2011

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

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

2009

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

2008

Inferring Pathway Activity toward Precise Disease Classification.

Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee

PLoS Comput. Biol., 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

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.

Ryan M. Kelley, Hoda Feizi, Trey Ideker

Bioinform., 2008

NetworkBLAST: comparative analysis of protein networks.

Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan

Bioinform., 2008

2007

CellCircuits: a database of protein network models.

H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker

Nucleic Acids Res., 2007

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Integrated Assessment and Prediction of Transcription Factor Binding.

Andreas Beyer, Christopher T. Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker

PLoS Comput. Biol., 2006

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.

Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan

J. Comput. Biol., 2006

A direct comparison of protein interaction confidence assignment schemes.

Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker

BMC Bioinform., 2006

Bioinformatics in the human interactome project.

Trey Ideker, Alfonso Valencia

Bioinform., 2006

Discovering Regulated Networks During HIV-1 Latency and Reactivation.

Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker

Proceedings of the Biocomputing 2006, 2006

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

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

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

J. Comput. Biol., 2005

Comparison of Protein-Protein Interaction Confidence Assignment Schemes.

Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker

Proceedings of the Systems Biology and Regulatory Genomics, 2005

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

Physical Network Models.

Chen-Hsiang Yeang, Trey Ideker, Tommi S. Jaakkola

J. Comput. Biol., 2004

Session Introduction.

Trey Ideker, Erik K. Neumann, Vincent Schächter

Proceedings of the Biocomputing 2004, 2004

2002

Discovering regulatory and signalling circuits in molecular interaction networks.

Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2000

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