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Trey Ideker
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2020 – today
- 2023
- [j36]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) - [i6]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 abs/2309.04019 (2023) - 2021
- [j35]Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker:
Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput. Biol. 17(9) (2021) - 2020
- [j34]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)
2010 – 2019
- 2019
- [j33]Z. S. Wallace, Sara Brin Rosenthal, Kathleen M. Fisch, Trey Ideker, Roman Sásik:
On entropy and information in gene interaction networks. Bioinform. 35(5): 815-822 (2019) - [j32]Wei Zhang, Jianzhu Ma, Trey Ideker:
Classifying tumors by supervised network propagation. Bioinform. 35(14): 2528 (2019) - [j31]Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork:
Rare variant phasing using paired tumor: normal sequence data. BMC Bioinform. 20(1): 265:1-265:11 (2019) - [c11]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: 305-307 - 2018
- [j30]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): 716-717 (2018) - [j29]Wei Zhang, Jianzhu Ma, Trey Ideker:
Classifying tumors by supervised network propagation. Bioinform. 34(13): i484-i493 (2018) - [j28]Justin K. Huang, Tongqiu Jia, Daniel E. Carlin, Trey Ideker:
pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinform. 34(16): 2859-2861 (2018) - [c10]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: 601-613 - [c9]Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng:
Deciphering Signaling Specificity with Deep Neural Networks. RECOMB 2018: 266-268 - [i5]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: 800 (2018) - 2017
- [j27]Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker:
Network propagation in the cytoscape cyberinfrastructure. PLoS Comput. Biol. 13(10) (2017) - [j26]Trey Ideker, Ruth Nussinov:
Network approaches and applications in biology. PLoS Comput. Biol. 13(10) (2017) - [i4]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: 784- (2017) - 2014
- [j25]Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker:
Inferring gene ontologies from pairwise similarity data. Bioinform. 30(12): 34-42 (2014) - [j24]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): 1269-1274 (2014) - [i3]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: 138 (2014) - [i2]Keiichiro Ono, Barry Demchak, Trey Ideker:
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Research 3: 143 (2014) - [i1]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: 151 (2014) - 2013
- [j23]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) - [c8]Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader:
Session Introduction. Pacific Symposium on Biocomputing 2013: 103-110 - 2011
- [j22]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): 431-432 (2011) - [j21]Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere:
PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinform. 27(7): 1030-1031 (2011) - [j20]Janusz Dutkowski, Trey Ideker:
Protein Networks as Logic Functions in Development and Cancer. PLoS Comput. Biol. 7(9) (2011) - [j19]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): 18560-18565 (2011) - 2010
- [j18]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) - [j17]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): 2796-2797 (2010)
2000 – 2009
- 2009
- [j16]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): 701-702 (2009) - 2008
- [j15]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): 71-77 (2008) - [j14]Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan:
NetworkBLAST: comparative analysis of protein networks. Bioinform. 24(4): 594-596 (2008) - [j13]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) - [j12]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) - 2007
- [j11]H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker:
CellCircuits: a database of protein network models. Nucleic Acids Res. 35(Database-Issue): 538-545 (2007) - [c7]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: 359-366 - [e2]Trey Ideker, Vineet Bafna:
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. Lecture Notes in Computer Science 4532, Springer 2007, ISBN 978-3-540-73059-0 [contents] - 2006
- [j10]Trey Ideker, Alfonso Valencia:
Bioinformatics in the human interactome project. Bioinform. 22(24): 2973-2974 (2006) - [j9]Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker:
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. 7: 360 (2006) - [j8]Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. J. Comput. Biol. 13(2): 133-144 (2006) - [j7]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) - [c6]Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker:
Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pacific Symposium on Biocomputing 2006: 354-366 - [e1]Eleazar Eskin, Trey Ideker, Benjamin J. Raphael, Christopher T. Workman:
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. Lecture Notes in Computer Science 4023, Springer 2006, ISBN 978-3-540-48293-2 [contents] - 2005
- [j6]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): 835-846 (2005) - [j5]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) - [j4]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): 627-632 (2005) - [c5]Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. RECOMB 2005: 1-13 - [c4]Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker:
Comparison of Protein-Protein Interaction Confidence Assignment Schemes. Systems Biology and Regulatory Genomics 2005: 39-50 - 2004
- [j3]Chen-Hsiang Yeang, Trey Ideker, Tommi S. Jaakkola:
Physical Network Models. J. Comput. Biol. 11(2/3): 243-262 (2004) - [j2]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): 83-88 (2004) - [c3]Trey Ideker, Erik K. Neumann, Vincent Schächter:
Session Introduction. Pacific Symposium on Biocomputing 2004: 471-473 - [c2]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: 282-289 - 2002
- [c1]Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel:
Discovering regulatory and signalling circuits in molecular interaction networks. ISMB 2002: 233-240 - 2000
- [j1]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): 805-817 (2000)
Coauthor Index
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