Trey Ideker

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 17

Top Topics

Inclusion Dependencies

Pairwise Similarities

Top Venues

PLoS Comput. Biol.

Publications

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
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 39 (3) (2023)
Mengzhou Hu, Sahar Alkhairy, Ingoo Lee, Rudolf T. Pillich, Robin Bachelder, Trey Ideker, Dexter Pratt
Evaluation of large language models for discovery of gene set function. CoRR (2023)
Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker
Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput. Biol. 17 (9) (2021)
Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker
Multiscale community detection in Cytoscape. PLoS Comput. Biol. 16 (10) (2020)
Wei Zhang, Jianzhu Ma, Trey Ideker
Classifying tumors by supervised network propagation. Bioinform. 35 (14) (2019)
Z. S. Wallace, Sara Brin Rosenthal, Kathleen M. Fisch, Trey Ideker, Roman Sásik
On entropy and information in gene interaction networks. Bioinform. 35 (5) (2019)
Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork
Rare variant phasing using paired tumor: normal sequence data. BMC Bioinform. 20 (1) (2019)
Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. RECOMB (2019)
Justin K. Huang, Tongqiu Jia, Daniel E. Carlin, Trey Ideker
pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinform. 34 (16) (2018)
Wei Zhang, Jianzhu Ma, Trey Ideker
Classifying tumors by supervised network propagation. Bioinform. 34 (13) (2018)
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
The Cytoscape Automation app article collection. F1000Research 7 (2018)
Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer
ndexr - an R package to interface with the network data exchange. Bioinform. 34 (4) (2018)
Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
Deciphering Signaling Specificity with Deep Neural Networks. RECOMB (2018)
Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker
Annotating gene sets by mining large literature collections with protein networks. PSB (2018)
Daniel E. Carlin, Kassi Kosnicki, Sara Garamszegi, Trey Ideker, Helga Thorvaldsdóttir, Michael Reich, Jill P. Mesirov
A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research 6 (2017)
Trey Ideker, Ruth Nussinov
Network approaches and applications in biology. PLoS Comput. Biol. 13 (10) (2017)
Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker
Network propagation in the cytoscape cyberinfrastructure. PLoS Comput. Biol. 13 (10) (2017)
Keiichiro Ono, Barry Demchak, Trey Ideker
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Research 3 (2014)
Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael E. Smoot, Trey Ideker, Jill P. Mesirov
Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Research 3 (2014)
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
The Cytoscape app article collection. F1000Research 3 (2014)
Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker
Inferring gene ontologies from pairwise similarity data. Bioinform. 30 (12) (2014)
Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker
NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 42 (Database-Issue) (2014)
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
Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. PLoS Comput. Biol. 9 (5) (2013)
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
Session Introduction. Pacific Symposium on Biocomputing (2013)
Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker
Cytoscape 2.8: new features for data integration and network visualization. Bioinform. 27 (3) (2011)
Janusz Dutkowski, Trey Ideker
Protein Networks as Logic Functions in Development and Cancer. PLoS Comput. Biol. 7 (9) (2011)
Ann Atwood, Robert DeConde, Susanna S. Wang, Todd C. Mockler, Jamal S. M. Sabir, Trey Ideker, Steve A. Kay
Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc. Natl. Acad. Sci. USA 108 (45) (2011)
Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere
PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinform. 27 (7) (2011)
Carlo Vittorio Cannistraci, Timothy Ravasi, Franco Maria Montevecchi, Trey Ideker, Massimo Alessio
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinform. 26 (18) (2010)
Konstantin Pentchev, Keiichiro Ono, Ralf Herwig, Trey Ideker, Atanas Kamburov
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinform. 26 (21) (2010)
David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. 25 (6) (2009)
Ryan M. Kelley, Hoda Feizi, Trey Ideker
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinform. 24 (1) (2008)
Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee
Inferring Pathway Activity toward Precise Disease Classification. PLoS Comput. Biol. 4 (11) (2008)
Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan
NetworkBLAST: comparative analysis of protein networks. Bioinform. 24 (4) (2008)
Sourav Bandyopadhyay, Ryan M. Kelley, Nevan J. Krogan, Trey Ideker
Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. PLoS Comput. Biol. 4 (4) (2008)
H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker
CellCircuits: a database of protein network models. Nucleic Acids Res. 35 (Database-Issue) (2007)
Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Andreas Beyer, Christopher T. Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Comput. Biol. 2 (6) (2006)
Trey Ideker, Alfonso Valencia
Bioinformatics in the human interactome project. Bioinform. 22 (24) (2006)
Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. 7 (2006)
Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. J. Comput. Biol. 13 (2) (2006)
Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker
Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pacific Symposium on Biocomputing (2006)
Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. RECOMB (2005)
Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
Comparison of Protein-Protein Interaction Confidence Assignment Schemes. Systems Biology and Regulatory Genomics (2005)
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) (2005)
Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, Shankar Subramaniam
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. J. Comput. Biol. 12 (6) (2005)
Trey Ideker, Erik K. Neumann, Vincent Schächter
Session Introduction. Pacific Symposium on Biocomputing (2004)
Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, Trey Ideker
PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Chen-Hsiang Yeang, Trey Ideker, Tommi S. Jaakkola
Physical Network Models. J. Comput. Biol. 11 (2/3) (2004)
Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. RECOMB (2004)
Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel
Discovering regulatory and signalling circuits in molecular interaction networks. ISMB (2002)
Trey Ideker, Vesteinn Thorsson, Andrew F. Siegel, Leroy E. Hood
Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data. J. Comput. Biol. 7 (6) (2000)