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Trey Ideker

Research Profile

Procedures

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Saccharomyces cerevisiae

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Chemicals & Drugs

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Physiology

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Menzies Chen; Katherine Licon; Rei Otsuka; Lorraine Pillus; Trey Ideker
Decoupling epigenetic and genetic effects through systematic analysis of gene position.
Gregory Hannum; Guy Hughes; Trey Ideker; Brandy Klotzle; Indika Rajapakse; SriniVas Sadda; Marina Bibikova; Menzies Chen; Rob Deconde; Jian-Bing Fan; Stephen Friend; Yuan Gao; Justin Guinney; Li Zhang; Ling Zhao; Kang Zhang
Genome-wide methylation profiles reveal quantitative views of human aging rates.
Janusz Dutkowski; Rama Balakrishnan; J Michael Cherry; Michael Kramer; Nevan J Krogan; Michal A Surma; Trey Ideker
A gene ontology inferred from molecular networks.

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All Publications

2013: Menzies Chen; Katherine Licon; Rei Otsuka; Lorraine Pillus; Trey Ideker
Decoupling epigenetic and genetic effects through systematic analysis of gene position.
Cell reports 2013;3(1):128-37.
2013: Gregory Hannum; Guy Hughes; Trey Ideker; Brandy Klotzle; Indika Rajapakse; SriniVas Sadda; Marina Bibikova; Menzies Chen; Rob Deconde; Jian-Bing Fan; Stephen Friend; Yuan Gao; Justin Guinney; Li Zhang; Ling Zhao; Kang Zhang
Genome-wide methylation profiles reveal quantitative views of human aging rates.
Molecular cell 2013;49(2):359-67.
2013: Janusz Dutkowski; Rama Balakrishnan; J Michael Cherry; Michael Kramer; Nevan J Krogan; Michal A Surma; Trey Ideker
A gene ontology inferred from molecular networks.
Nature biotechnology 2013;31(1):38-45.
2012: Philipp A Jaeger; Colleen Doherty; Trey Ideker
Modeling transcriptome dynamics in a complex world.
Cell 2012;151(6):1161-2.
2012: Rintaro Saito; Michael E Smoot; Peng-Liang Wang; Gary D Bader; Samad Lotia; Keiichiro Ono; Alexander R Pico; Johannes Ruscheinski; Trey Ideker
A travel guide to Cytoscape plugins.
Nature methods 2012;9(11):1069-76.
2012: Anna Travesa; John R Yates; Aaron S. Aslanian; Robertus A M de Bruin; Marisela Guaderrama; Trey Ideker; Tatyana I Kalashnikova; Dwight Kuo; Marcus B Smolka; Kevin Thai; Curt Wittenberg
DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1.
The EMBO journal 2012;31(7):1811-22.
2012: Steven J Bark; Trey Ideker; Qi Ma; Daniel T O'Connor; Michael Smoot; LAURENT TAUPENOT; Jill Wegrzyn; Michael Ziegler; Vivian Hook
The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases.
PloS one 2012;7(8):e41134.
2012: Trey Ideker; Nevan J Krogan
Differential network biology.
Molecular systems biology 2012;8():565.
2011: Ann Atwood; Robert DeConde; Trey Ideker; Todd C Mockler; Jamal S M Sabir; Susanna S Wang; Steve A Kay
Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(45):18560-5.
2011: Elinore M Mercer; Mikael Sigvardsson; Christopher Benner; Janusz Dutkowski; Martha Flores; Christopher K Glass; Trey Ideker; Suchit Jhunjhunwala; Yin C Lin; Cornelis Murre
Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors.
Immunity 2011;35(3):413-25.
2011: Janusz Dutkowski; Trey Ideker
Protein networks as logic functions in development and cancer.
PLoS computational biology 2011;7(9):e1002180.
2011: Rohith Srivas; Peng-Liang Wang; Gregory Hannum; Keiichoro Ono; Johannes Ruscheinski; Michael Smoot; Trey Ideker
Assembling global maps of cellular function through integrative analysis of physical and genetic networks.
Nature protocols 2011;6(9):1308-23.
2011: Trey Ideker; Janusz Dutkowski; Leroy Hood
Boosting signal-to-noise in complex biology: prior knowledge is power.
Cell 2011;144(6):860-3.
2011: Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Cytoscape 2.8: new features for data integration and network visualization.
Bioinformatics (Oxford, England) 2011;27(3):431-2.
2010: Sourav Bandyopadhyay; Monika Mehta; Dwight Kuo; Min-Kyung Sung; Ryan Chuang; Eric J Jaehnig; Bernd Bodenmiller; Katherine Licon; Wilbert Copeland; Michael Shales; Dorothea Fiedler; Janusz Dutkowski; Aude Guénolé; Haico Van Attikum; Kevan M Shokat; Richard D Kolodner; Won-Ki Huh; Ruedi Aebersold; Michael-Christopher Keogh; Nevan J Krogan; Trey Ideker
Rewiring of genetic networks in response to DNA damage.
Science (New York, N.Y.) 2010;330(6009):1385-9.
2010: Dwight Kuo; Katherine Licon; Sourav Bandyopadhyay; Ryan Chuang; Colin Luo; Justin Catalana; Timothy Ravasi; Kai Tan; Trey Ideker
Coevolution within a transcriptional network by compensatory trans and cis mutations.
Genome research 2010;20(12):1672-8.
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.
Bioinformatics (Oxford, England) 2010;26(21):2796-7.
2010: Sourav Bandyopadhyay; Chih-yuan Chiang; Jyoti Srivastava; Merril Gersten; Suhaila White; Russell Bell; Cornelia Kurschner; Christopher H Martin; Mike Smoot; Sudhir Sahasrabudhe; Diane L Barber; Sumit K Chanda; Trey Ideker
A human MAP kinase interactome.
Nature methods 2010;7(10):801-5.
2010: Yin C Lin; Suchit Jhunjhunwala; Christopher Benner; Sven Heinz; Eva Welinder; Robert Mansson; Mikael Sigvardsson; James Hagman; Celso A Espinoza; Janusz Dutkowski; Trey Ideker; Christopher K Glass; Cornelis Murre
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.
Nature immunology 2010;11(7):635-43.
2010: Joon Kim; Ji Eun Lee; Susanne Heynen-Genel; Eigo Suyama; Keiichiro Ono; Kiyoung Lee; Trey Ideker; Pedro Aza-Blanc; Joseph G Gleeson
Functional genomic screen for modulators of ciliogenesis and cilium length.
Nature 2010;464(7291):1048-51.
2010: Dwight Kuo; Kai Tan; Guy Zinman; Timothy Ravasi; Ziv Bar-Joseph; Trey Ideker
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.
Genome biology 2010;11(7):R77.
2010: Han-Yu Chuang; Matan Hofree; Trey Ideker
A decade of systems biology.
Annual review of cell and developmental biology 2010;26():721-44.
2009: Gregory Hannum; Rohith Srivas; Aude Guénolé; Haico Van Attikum; Nevan J Krogan; Richard M Karp; Trey Ideker
Genome-wide association data reveal a global map of genetic interactions among protein complexes.
PLoS genetics 2009;5(12):e1000782.
2009: Merril Gersten; mehrdad alirezaei; Maria Cecilia Garibaldi Marcondes; Claudia Flynn; Timothy Ravasi; Trey Ideker; Howard S Fox
An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2009;29(40):12467-76.
2009: H Craig Mak; Lorraine Pillus; Trey Ideker
Dynamic reprogramming of transcription factors to and from the subtelomere.
Genome research 2009;19(6):1014-25.
2009: Ryan Kelley; Trey Ideker
Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide.
PLoS genetics 2009;5(5):e1000488.
2009: Joel Moxley; Michael C Jewett; Maciek Antoniewicz; Silas G Villas-Boas; Hal Alper; Robert Wheeler; Lily Tong; Alan G Hinnebusch; Trey Ideker; Jens Nielsen; Gregory Stephanopoulos
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(16):6477-82.
2009: Ariel S Schwartz; Jingkai Yu; Kyle R Gardenour; Russell L Finley; Trey Ideker
Cost-effective strategies for completing the interactome.
Nature methods 2009;6(1):55-61.
2008: Kiyoung Lee; Han-Yu Chuang; Andreas Beyer; Min-Kyung Sung; Won-Ki Huh; Bonghee Lee; Trey Ideker
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species.
Nucleic acids research 2008;36(20):e136.
2008: Trey Ideker
Forging new ties between E. coli genes.
Cell 2008;133(7):1135-7.
2008: Sourav Bandyopadhyay; Ryan Kelley; Nevan J Krogan; Trey Ideker
Functional maps of protein complexes from quantitative genetic interaction data.
PLoS computational biology 2008;4(4):e1000065.
2008: Trey Ideker; Roded Sharan
Protein networks in disease.
Genome research 2008;18(4):644-52.
2008: Maxim Kalaev; Mike Smoot; Trey Ideker; Roded Sharan
NetworkBLAST: comparative analysis of protein networks.
Bioinformatics (Oxford, England) 2008;24(4):594-6.
2008: Silpa Suthram; Andreas Beyer; Richard M Karp; Yonina Eldar; Trey Ideker
eQED: an efficient method for interpreting eQTL associations using protein networks.
Molecular systems biology 2008;4():162.
2008: Ryan Kelley; Hoda Feizi; Trey Ideker
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.
Bioinformatics (Oxford, England) 2008;24(1):71-7.
2007: Andreas Beyer; Sourav Bandyopadhyay; Trey Ideker
Integrating physical and genetic maps: from genomes to interaction networks.
Nature reviews. Genetics 2007;8(9):699-710.
2007: Oved Ourfali; Tomer Shlomi; Trey Ideker; Eytan Ruppin; Roded Sharan
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.
Bioinformatics (Oxford, England) 2007;23(13):i359-66.
2007: Kai Tan; Tomer Shlomi; Hoda Feizi; Trey Ideker; Roded Sharan
Transcriptional regulation of protein complexes within and across species.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(4):1283-8.
2007: Han-Yu Chuang; Eunjung Lee; Yu-Tsueng Liu; Doheon Lee; Trey Ideker
Network-based classification of breast cancer metastasis.
Molecular systems biology 2007;3():140.
2007: Jodi R Parrish; Jingkai Yu; Guozhen Liu; Julie A Hines; Jason E Chan; Bernie A Mangiola; Huamei Zhang; Svetlana Pacifico; Farshad Fotouhi; Victor J DiRita; Trey Ideker; Phillip Andrews; Russell L Finley
A proteome-wide protein interaction map for Campylobacter jejuni.
Genome biology 2007;8(7):R130.
2007: Trey Ideker; Vineet Bafna; Thomas Lemberger
Integrating scientific cultures.
Molecular systems biology 2007;3():105.
2007: Trey Ideker
Network genomics.
Ernst Schering Research Foundation workshop 2007;(61):89-115.
2007: H Craig Mak; Mike Daly; Bianca Gruebel; Trey Ideker
CellCircuits: a database of protein network models.
Nucleic acids research 2007;35(Database issue):D538-45.
2006: Trey Ideker; Alfonso Valencia
Bioinformatics in the human interactome project.
Bioinformatics (Oxford, England) 2006;22(24):2973-4.
2006: Trey Ideker; L Raimond Winslow; Douglas A Lauffenburger
Bioengineering and systems biology.
Annals of biomedical engineering 2006;34(7):1226-33.
2006: Andreas Beyer; Christopher T Workman; Jens Hollunder; Dörte Radke; Ulrich Möller; Thomas Wilhelm; Trey Ideker
Integrated assessment and prediction of transcription factor binding.
PLoS computational biology 2006;2(6):e70.
2006: Christopher T Workman; H Craig Mak; Scott McCuine; Jean-Bosco Tagne; Maya Agarwal; Owen Ozier; Thomas Begley; Leona D Samson; Trey Ideker
A systems approach to mapping DNA damage response pathways.
Science (New York, N.Y.) 2006;312(5776):1054-9.
2006: Roded Sharan; Trey Ideker
Modeling cellular machinery through biological network comparison.
Nature biotechnology 2006;24(4):427-33.
2006: Jacob Scott; Trey Ideker; Richard M Karp; Roded Sharan
Efficient algorithms for detecting signaling pathways in protein interaction networks.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):133-44.
2006: Sourav Bandyopadhyay; Roded Sharan; Trey Ideker
Systematic identification of functional orthologs based on protein network comparison.
Genome research 2006;16(3):428-35.
2006: Trey Ideker; L Raimond Winslow; A Douglas Lauffenburger
Bioengineering and systems biology.
Annals of biomedical engineering 2006;34(2):257-64.
2006: Sourav Bandyopadhyay; Ryan Kelley; Trey Ideker
Discovering regulated networks during HIV-1 latency and reactivation.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():354-66.
2006: Silpa Suthram; Tomer Shlomi; Eytan Ruppin; Roded Sharan; Trey Ideker
A direct comparison of protein interaction confidence assignment schemes.
BMC bioinformatics 2006;7():360.
2006: Teresa Reguly; Ashton Breitkreutz; Lorrie Boucher; Bobby-Joe Breitkreutz; Gary C Hon; Chad L Myers; Ainslie Parsons; Helena Friesen; Rose Oughtred; Amy Tong; Chris Stark; Yuen Ho; David Botstein; Brenda Andrews; Charles Boone; Olga G Troyanskya; Trey Ideker; Kara Dolinski; Nizar N Batada; Mike Tyers
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.
Journal of biology 2006;5(4):11.
2006: Adam M Feist; Johannes Scholten; Bernhard Ø Palsson; Fred J Brockman; Trey Ideker
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
Molecular systems biology 2006;2():2006.0004.
2006: Guy J Warner; Yeyejide A Adeleye; Trey Ideker
Interactome networks: the state of the science.
Genome biology 2006;7(1):301.
2005: Silpa Suthram; Taylor Sittler; Trey Ideker
The Plasmodium protein network diverges from those of other eukaryotes.
Nature 2005;438(7064):108-12.
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.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(6):835-46.
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 research 2005;33(Web Server issue):W627-32.
2005: Christopher T Workman; Yutong Yin; David L Corcoran; Trey Ideker; Gary stormo; Panayiotis V Benos
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Nucleic acids research 2005;33(Web Server issue):W389-92.
2005: Ryan Kelley; Trey Ideker
Systematic interpretation of genetic interactions using protein networks.
Nature biotechnology 2005;23(5):561-6.
2005: Roded Sharan; Silpa Suthram; Ryan M Kelley; Tanja Kuhn; Scott McCuine; Peter Uetz; Taylor Sittler; Richard M Karp; Trey Ideker
Conserved patterns of protein interaction in multiple species.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(6):1974-9.
2005: Chen-Hsiang Yeang; H Craig Mak; Scott McCuine; Christopher T Workman; Tommi S Jaakkola; Trey Ideker
Validation and refinement of gene-regulatory pathways on a network of physical interactions.
Genome biology 2005;6(7):R62.
2004: Thomas Begley; Ari S Rosenbach; Trey Ideker; Leona D Samson
Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping.
Molecular cell 2004;16(1):117-25.
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 research 2004;32(Web Server issue):W83-8.
2004: Trey Ideker
Systems biology 101--what you need to know.
Nature biotechnology 2004;22(4):473-5.
2004: Astrid C Haugen; Ryan Kelley; Jennifer B Collins; Charles J Tucker; Changchun Deng; Cynthia A Afshari; J Martin Brown; Trey Ideker; Bennett Van Houten
Integrating phenotypic and expression profiles to map arsenic-response networks.
Genome biology 2004;5(12):R95.
2004: Chen-Hsiang Yeang; Trey Ideker; Tommi S Jaakkola
Physical network models.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):243-62.
2004: Trey Ideker
A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces.
Advances in experimental medicine and biology 2004;547():21-30.
2003: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome research 2003;13(11):2498-504.
2003: Brian P Kelley; Roded Sharan; Richard M Karp; Taylor Sittler; David E Root; Brent R Stockwell; Trey Ideker
Conserved pathways within bacteria and yeast as revealed by global protein network alignment.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11394-9.
2003: Elton T Young; Kenneth M Dombek; Christine Tachibana; Trey Ideker
Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8.
The Journal of biological chemistry 2003;278(28):26146-58.
2003: Trey Ideker; Douglas A Lauffenburger
Building with a scaffold: emerging strategies for high- to low-level cellular modeling.
Trends in biotechnology 2003;21(6):255-62.
2003: Owen Ozier; Nada Amin; Trey Ideker
Global architecture of genetic interactions on the protein network.
Nature biotechnology 2003;21(5):490-1.
2002: Thomas Begley; Ari S Rosenbach; Trey Ideker; Leona D Samson
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.
Molecular cancer research : MCR 2002;1(2):103-12.
2002: Jennifer J Smith; Marcello Marelli; Rowan H Christmas; Franco Vizeacoumar; David J Dilworth; Trey Ideker; Timothy Galitski; Krassen Dimitrov; Richard A Rachubinski; John D Aitchison
Transcriptome profiling to identify genes involved in peroxisome assembly and function.
The Journal of cell biology 2002;158(2):259-71.
2002: Timothy J Griffin; Steven P Gygi; Trey Ideker; Beate Rist; Jimmy Eng; Leroy Hood; Ruedi Aebersold
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae.
Molecular & cellular proteomics : MCP 2002;1(4):323-33.
2002: Trey Ideker; Owen Ozier; Benno Schwikowski; Andrew F Siegel
Discovering regulatory and signalling circuits in molecular interaction networks.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S233-40.
2001: Trey Ideker; Vesteinn Thorsson; Jeffrey A Ranish; Rowan H Christmas; J Buhler; Jimmy K Eng; Roger Bumgarner; David R Goodlett; Ruedi Aebersold; Leroy Hood
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
Science (New York, N.Y.) 2001;292(5518):929-34.
2001: Trey Ideker; Timothy Galitski; L Hood
A new approach to decoding life: systems biology.
Annual review of genomics and human genetics 2001;2():343-72.
2000: Trey Ideker; Vesteinn Thorsson; Andrew F Siegel; Leroy Hood
Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(6):805-17.
2000: Trey Ideker; Vesteinn Thorsson; R M Karp
Discovery of regulatory interactions through perturbation: inference and experimental design.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():305-16.
1999: Peter S Nelson; Vivian N Hawkins; Michèl Schummer; Roger Bumgarner; WL Ng; Trey Ideker; Camari Ferguson; Leroy Hood
Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays.
Genetic analysis : biomolecular engineering 1999;15(6):209-15.