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Trey Ideker

Title(s)Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #0688
La Jolla CA 92093
Phone8/8-22--4558
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    Collapse Biography 
    Collapse Awards and Honors
    Duke University Talent Identification Program2009Distinguished Alumni Award
    2009Selected as member of Faculty of 1000 (f1000.com)
    International Society for Computational Biology (ISCB)2009Overton Prize
    2006Selected by Technology Review Top 10 Innovators of 2006
    2005Selected by Technology Review Top 35 Young Innovators of 2005
    David and Lucile Packard Foundation2004 Fellowship Award

    Collapse Overview 
    Collapse Overview
    Education
    - 2001 - Ph. D. (Molecular Biotechnology), University of Washington, Seattle, WA
    - 1995 - M.E. (Electrical Engineering and Computer Science), Massachusetts Institute of Technology, Cambridge, MA
    - 1995 - B.S. (Electrical Engineering and Computer Science), Minor in Cognitive Science. Massachusetts Institute of Technology, Cambridge, MA

    Employment
    - 2010 - Pres: Professor, Medicine and Bioengineering, University of California, San Diego, CA
    - 2009 - Pres: Division Chief of Medical Genetics, University of California, San Diego, CA
    - 2006- Pres: Associate Professor of Bioengineering, University of California, San Diego, CA
    - 2006- Pres: Adjunct Professor of Computer Science, University of California, San Diego, CA
    - 2003 – 2006: Assistant Professor of Bioengineering, University of California, San Diego, CA
    - 2001 – 2003: Pfizer Fellow in Computational Biology, Whitehead Institute for Biomedical Research, MIT, Cambridge, MA
    - 1996 – 2001: Doctoral Dissertation, Leroy Hood Laboratory, Institute for Systems Biology / University of Washington Seattle, WA
    - 1999: Yeast Genetics Advanced Course, Cold Spring Harbor Laboratory Cold Spring Harbor, NY

    Collapse Research 
    Collapse Research Activities and Funding
    The Psychiatric Cell Map Initiative: Connecting Genomics, Subcellular Networks, and Higher Order Phenotypes
    NIH/NIMH U01MH115747Sep 5, 2018 - Jun 30, 2023
    Role: Co-Principal Investigator
    Research Center for Cancer Systems Biology: Cancer Cell Map Initiative
    NIH/NCI U54CA209891May 11, 2017 - Apr 30, 2022
    Role: Co-Principal Investigator
    NDEx - the Network Data Exchange A Network Commons for Biologists
    NIH/NCI U24CA184427May 1, 2014 - Apr 30, 2022
    Role: Principal Investigator
    National Resource for Network Biology (NRNB)
    NIH/NIGMS P41GM103504Sep 13, 2010 - Jun 30, 2015
    Role: Principal Investigator
    Resource for Analysis, Vizualization, and Integration of Networks (RAVIN)
    NIH/NCRR P41RR031228Sep 13, 2010 - Jun 30, 2015
    Role: Principal Investigator
    Massively parallel epigenomics: building new value with current resources
    NIH/NHGRI R21HG005252Feb 1, 2010 - Jan 31, 2013
    Role: Principal Investigator
    A Systems Approach to Mapping the DNA Damage Response
    NIH/NIEHS R01ES014811Sep 4, 2009 - Jul 31, 2010
    Role: Principal Investigator
    Comparative Analysis of Genetic Interaction Networks
    NIH/NIGMS R01GM084279Aug 1, 2008 - Jul 31, 2014
    Role: Principal Investigator
    San Diego Center for Systems Biology: From Maps to Models
    NIH/NIGMS P50GM085764Jul 1, 2008 - May 31, 2019
    Role: Principal Investigator
    Cytoscape: A Modeling Platform for Biomolecular Networks
    NIH/NHGRI R01HG009979Jun 1, 2004 - Jun 30, 2021
    Role: Principal Investigator
    Cytoscape: A Modeling Platform for Biomolecular Networks
    NIH/NIGMS R01GM070743Jun 1, 2004 - May 31, 2009
    Role: Principal Investigator
    Integrated Proteome Technologies for Pathway Mapping
    NIH P41RR018627Sep 30, 2003 - Jul 31, 2010
    Role: Co-Investigator
    Chronic HIV infection and Aging in NeuroAIDS (CHAIN) Center
    NIH P30MH062261Sep 30, 2000 - Feb 28, 2017
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments. Appl Environ Microbiol. 2015 Aug 15; 81(16):5639-49. Jaeger PA, McElfresh C, Wong LR, Ideker T. PMID: 26070672.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    2. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 2015 May 30; 4:e06602. Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, Mikati MA, Incecik F, Azam M, Borgatti R, Romaniello R, Boustany RM, Clericuzio CL, D'Arrigo S, Strømme P, Boltshauser E, Stanzial F, Mirabelli-Badenier M, Moroni I, Bertini E, Emma F, Steinlin M, Hildebrandt F, Johnson CA, Freilinger M, Vaux KK, Gabriel SB, Aza-Blanc P, Heynen-Genel S, Ideker T, Dynlacht BD, Lee JE, Valente EM, Kim J, Gleeson JG. PMID: 26026149.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    3. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21; 58(4):690-8. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. PMID: 26000852.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    4. Transcriptional repression of IFNß1 by ATF2 confers melanoma resistance to therapy. Oncogene. 2015 Nov 12; 34(46):5739-48. Lau E, Sedy J, Sander C, Shaw MA, Feng Y, Scortegagna M, Claps G, Robinson S, Cheng P, Srivas R, Soonthornvacharin S, Ideker T, Bosenberg M, Gonzalez R, Robinson W, Chanda SK, Ware C, Dummer R, Hoon D, Kirkwood JM, Ronai ZA. PMID: 25728676.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    5. Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma. Oral Oncol. 2015 May; 51(5):470-5. Raju SC, Hauff SJ, Lemieux AJ, Orosco RK, Gross AM, Nguyen LT, Savariar E, Moss W, Whitney M, Cohen EE, Lippman SM, Tsien RY, Ideker T, Advani SJ, Nguyen QT. PMID: 25735654.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    6. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell. 2015 Jan 08; 57(1):55-68. Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M. PMID: 25544559.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    7. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell. 2015 Jan 22; 57(2):273-89. Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. PMID: 25533186.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    8. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. PMID: 25417114.
      View in: PubMed   Mentions: 558     Fields:    Translation:Humans
    9. Mitochondria, energetics, epigenetics, and cellular responses to stress. Environ Health Perspect. 2014 Dec; 122(12):1271-8. Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol RW, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL. PMID: 25127496.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansCellsPHPublic Health
    10. Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice. Otolaryngol Head Neck Surg. 2014 Oct; 151(4):612-8. Hauff SJ, Raju SC, Orosco RK, Gross AM, Diaz-Perez JA, Savariar E, Nashi N, Hasselman J, Whitney M, Myers JN, Lippman SM, Tsien RY, Ideker T, Nguyen QT. PMID: 25091190.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    11. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep; 46(9):939-43. Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. PMID: 25086664.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    12. Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A. 2014 Jul 29; 111(30):E3157-66. Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. PMID: 25028499.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    13. The Cytoscape app article collection. F1000Res. 2014; 3:138. Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. PMID: 25580224.
      View in: PubMed   Mentions: 3     Fields:    
    14. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014; 3:151. Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. PMID: 25165537.
      View in: PubMed   Mentions: 26     Fields:    
    15. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 2014; 3:143. Ono K, Demchak B, Ideker T. PMID: 25520778.
      View in: PubMed   Mentions: 7     Fields:    
    16. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15; 30(12):i34-42. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. PMID: 24932003.
      View in: PubMed   Mentions: 20     Fields:    Translation:Animals
    17. An integrated map of HIV-human protein complexes that facilitate viral infection. PLoS One. 2014; 9(5):e96687. Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. PMID: 24817247.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    18. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One. 2014; 9(4):e95893. Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. PMID: 24770346.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    19. Siri of the cell: what biology could learn from the iPhone. Cell. 2014 Apr 24; 157(3):534-8. Carvunis AR, Ideker T. PMID: 24766803.
      View in: PubMed   Mentions: 13     Fields:    
    20. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014 Jan 31; 343(6170):506-511. Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GMH, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, El Din Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG. PMID: 24482476.
      View in: PubMed   Mentions: 159     Fields:    Translation:HumansAnimalsCells
    21. Development of ultra-high-density screening tools for microbial "omics". PLoS One. 2014; 9(1):e85177. Bean GJ, Jaeger PA, Bahr S, Ideker T. PMID: 24465499.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    22. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. Cell Rep. 2013 Dec 26; 5(6):1714-24. Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T. PMID: 24360959.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    23. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014 Jan; 42(Database issue):D1269-74. Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. PMID: 24271398.
      View in: PubMed   Mentions: 8     Fields:    
    24. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. Carter H, Hofree M, Ideker T. PMID: 24238873.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    25. Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal. 2013 Oct 15; 6(297):ra90. Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, Lewis RE, MacMillan JB, White MA. PMID: 24129700.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    26. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol. 2013 Nov; 24(11):1901-12. Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, Ideker T, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, Nyhan WL, Naviaux RK. PMID: 23949796.
      View in: PubMed   Mentions: 128     Fields:    Translation:Humans
    27. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013 Oct; 14(10):719-32. Mitra K, Carvunis AR, Ramesh SK, Ideker T. PMID: 24045689.
      View in: PubMed   Mentions: 141     Fields:    Translation:Humans
    28. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov; 10(11):1108-15. Hofree M, Shen JP, Carter H, Gross A, Ideker T. PMID: 24037242.
      View in: PubMed   Mentions: 246     Fields:    Translation:Humans
    29. Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep. 2013 Jul 11; 4(1):174-88. Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD. PMID: 23810556.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    30. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11; 2:e00675. Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR. PMID: 23795294.
      View in: PubMed   Mentions: 113     Fields:    Translation:AnimalsCells
    31. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proc Natl Acad Sci U S A. 2013 Jun 25; 110(26):10717-22. Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, Vinh J, Hoffmann JA. PMID: 23749869.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    32. Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. J Proteome Res. 2013 Jun 07; 12(6):2805-17. Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS. PMID: 23647160.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    33. Proteome-wide discovery of mislocated proteins in cancer. Genome Res. 2013 Aug; 23(8):1283-94. Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. PMID: 23674306.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    34. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013; 9(5):e1003047. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. PMID: 23671412.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    35. Decoupling epigenetic and genetic effects through systematic analysis of gene position. Cell Rep. 2013 Jan 31; 3(1):128-37. Chen M, Licon K, Otsuka R, Pillus L, Ideker T. PMID: 23291096.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    36. Dissection of DNA damage responses using multiconditional genetic interaction maps. Mol Cell. 2013 Jan 24; 49(2):346-58. Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. PMID: 23273983.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    37. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 2011 Mar 18; 144(6):860-3. Ideker T, Dutkowski J, Hood L. PMID: 21414478.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
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