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Trey Ideker

TitleAdjunct Professor
InstitutionUniversity of California San Diego
DepartmentBioengineering
Address9500 Gilman Drive #0688
La Jolla CA 92093
Phone858-822-4558
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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
    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 - Apr 30, 2020
    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
    Comparative Analysis of Genetic Interaction Networks
    NIH/NIGMS R01GM084279Aug 1, 2008 - Feb 28, 2018
    Role: Principal Investigator
    San Diego Center for Systems Biology: From Maps to Models
    NIH/NIGMS P50GM085764Jul 1, 2008 - May 31, 2019
    Role: Principal Investigator
    A Systems Approach to Mapping the DNA Damage Response
    NIH/NIEHS R01ES014811Sep 26, 2005 - Aug 31, 2022
    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 - Apr 30, 2017
    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 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.
    List All   |   Timeline
    1. Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nat Commun. 2018 Oct 08; 9(1):4159. PMID: 30297789.
      View in: PubMed
    2. Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell. 2018 Sep 20; 71(6):882-895. PMID: 30241605.
      View in: PubMed
    3. Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ. Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med. 2018 Sep 14; 10(1):69. PMID: 30217226.
      View in: PubMed
    4. Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 Sep 12. PMID: 30209081.
      View in: PubMed
    5. van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res. 2018 Sep 08. PMID: 30203048.
      View in: PubMed
    6. Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 Jul 26; 174(3):505-520. PMID: 30053424.
      View in: PubMed
    7. Zhang W, Ma J, Ideker T. Classifying tumors by supervised network propagation. Bioinformatics. 2018 Jul 01; 34(13):i484-i493. PMID: 29949979.
      View in: PubMed
    8. Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000Res. 2018; 7:800. PMID: 29983926.
      View in: PubMed
    9. Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. J Mol Biol. 2018 Jun 19. PMID: 29932943.
      View in: PubMed
    10. Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T. Visible Machine Learning for Biomedicine. Cell. 2018 Jun 14; 173(7):1562-1565. PMID: 29906441.
      View in: PubMed
    11. Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T. Disruption of NSD1 in head and neck cancer promotes favorable chemotherapeutic responses linked to hypomethylation. Mol Cancer Ther. 2018 Apr 10. PMID: 29636367.
      View in: PubMed
    12. Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr; 50(4):613-620. PMID: 29610481.
      View in: PubMed
    13. Huang JK, Jia T, Carlin DE, Ideker T. pyNBS: A Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018 Mar 28. PMID: 29608663.
      View in: PubMed
    14. Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018 Apr 25; 6(4):484-495.e5. PMID: 29605183.
      View in: PubMed
    15. Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nat Methods. 2018 Apr; 15(4):290-298. PMID: 29505029.
      View in: PubMed
    16. Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 Mar 01; 69(5):915. PMID: 29499140.
      View in: PubMed
    17. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 Feb 15; 69(4):699-708.e7. PMID: 29452643.
      View in: PubMed
    18. Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F, Kelso J. ndexr-an R package to interface with the network data exchange. Bioinformatics. 2018 Feb 15; 34(4):716-717. PMID: 29087446.
      View in: PubMed
    19. Neal S, Jaeger PA, Duttke SH, Benner C, K Glass C, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 Jan 18; 69(2):306-320.e4. PMID: 29351849.
      View in: PubMed
    20. Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Mol Cell. 2018 Jan 18; 69(2):321-333.e3. PMID: 29351850.
      View in: PubMed
    21. Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T. Annotating gene sets by mining large literature collections with protein networks. Pac Symp Biocomput. 2018; 23:602-613. PMID: 29218918.
      View in: PubMed
    22. Shen JP, Ideker T. Correcting CRISPR for copy number. Nat Genet. 2017 Nov 29; 49(12):1674-1675. PMID: 29186130.
      View in: PubMed
    23. Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Res. 2017 11 01; 77(21):e58-e61. PMID: 29092941.
      View in: PubMed
    24. Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017 Nov 30; 171(6):1272-1283.e15. PMID: 29107334.
      View in: PubMed
    25. Ideker T, Nussinov R. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct; 13(10):e1005771. PMID: 29023447.
      View in: PubMed
    26. Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct; 13(10):e1005598. PMID: 29023449.
      View in: PubMed
    27. Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017 09; 18(9):551-562. PMID: 28607512.
      View in: PubMed
    28. Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 06 12; 18(1):458. PMID: 28606096.
      View in: PubMed
    29. Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017; 6:784. PMID: 29487738.
      View in: PubMed
    30. Farré JC, Kramer M, Ideker T, Subramani S. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 03; 13(7):1248-1249. PMID: 28486053.
      View in: PubMed
    31. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun; 14(6):577-580. PMID: 28481362.
      View in: PubMed
    32. Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Systems biology guided by XCMS Online metabolomics. Nat Methods. 2017 Apr 27; 14(5):461-462. PMID: 28448069.
      View in: PubMed
    33. Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 2017 03 28; 18(1):57. PMID: 28351423.
      View in: PubMed
    34. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. PMID: 28319113.
      View in: PubMed
    35. Carter H, Ideker T. Common genetic variation in the germline influences where and how tumors develop. Mol Cell Oncol. 2017; 4(3):e1302905. PMID: 28616579.
      View in: PubMed
    36. Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 04; 7(4):410-423. PMID: 28188128.
      View in: PubMed
    37. Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell. 2017 Feb 16; 65(4):761-774.e5. PMID: 28132844.
      View in: PubMed
    38. Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D'Agati V, Beyret E, Belmonte JC, Anders HJ, Sharma K. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016 Oct 20; 1(17):e87877. PMID: 27777973.
      View in: PubMed
    39. Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 09 27; 113(39):10750-8. PMID: 27638202.
      View in: PubMed
    40. Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell. 2016 08 04; 63(3):514-25. PMID: 27453043.
      View in: PubMed
    41. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun. 2016 Jul 15; 7:12096. PMID: 27417679.
      View in: PubMed
    42. Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener. 2016 May 23; 11(1):42. PMID: 27216421.
      View in: PubMed
    43. Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hoffree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener. 2016 Apr 26; 11:31. PMID: 27112350; PMCID: PMC4845325.
    44. Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016 04 21; 62(2):157-168. PMID: 27105112.
      View in: PubMed
    45. Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer. 2016 07 15; 139(2):373-82. PMID: 26949921.
      View in: PubMed
    46. Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst. 2016 Feb 24; 2(2):77-88. PMID: 26949740.
      View in: PubMed
    47. Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar; 13(3):245-247. PMID: 26780094; PMCID: PMC4767623.
    48. Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife. 2015 Dec 18; 4. PMID: 26682651.
      View in: PubMed
    49. Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. PLoS One. 2015; 10(11):e0142618. PMID: 26555223.
      View in: PubMed
    50. Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, Sobol RW, Ideker T. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. 2015 Nov 03; 6(34):35755-69. PMID: 26437225; PMCID: PMC4742139.
    51. Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28; 1(4):302-305. PMID: 26594663.
      View in: PubMed
    52. Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. J Proteome Res. 2015 Dec 04; 14(12):4995-5006. PMID: 26435392.
      View in: PubMed
    53. Liss MA, DeConde R, Caovan D, Hofler J, Gabe M, Palazzi KL, Patel ND, Lee HJ, Ideker T, Van Poppel H, Karow D, Aertsen M, Casola G, Derweesh IH. Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy. J Endourol. 2016 Jan; 30(1):114-21. PMID: 26192380; PMCID: PMC4841003 [Available on 01/01/17].
    54. Gross AM, Ideker T. Molecular networks in context. Nat Biotechnol. 2015 Jul; 33(7):720-1. PMID: 26154012.
      View in: PubMed
    55. Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One. 2015; 10(6):e0126898. PMID: 26083491; PMCID: PMC4470586.
    56. Jaeger PA, McElfresh C, Wong LR, Ideker T. 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. PMID: 26070672; PMCID: PMC4510171.
    57. 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. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 2015 May 30; 4:e06602. PMID: 26026149; PMCID: PMC4477441.
    58. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21; 58(4):690-8. PMID: 26000852.
      View in: PubMed
    59. 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. Transcriptional repression of IFNß1 by ATF2 confers melanoma resistance to therapy. Oncogene. 2015 Nov 12; 34(46):5739-48. PMID: 25728676; PMCID: PMC4558399.
    60. 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. 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. PMID: 25735654; PMCID: PMC4427339.
    61. Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015; 11(9):1652-67. PMID: 26103419; PMCID: PMC4590607.
    62. Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell. 2015 Jan 08; 57(1):55-68. PMID: 25544559; PMCID: PMC4373083.
    63. 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. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell. 2015 Jan 22; 57(2):273-89. PMID: 25533186.
      View in: PubMed
    64. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. PMID: 25417114; PMCID: PMC4243044.
    65. 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. Mitochondria, energetics, epigenetics, and cellular responses to stress. Environ Health Perspect. 2014 Dec; 122(12):1271-8. PMID: 25127496.
      View in: PubMed
    66. 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. 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. PMID: 25091190; PMCID: PMC4469264.
    67. 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. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep; 46(9):939-43. PMID: 25086664; PMCID: PMC4146706.
    68. Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A. 2014 Jul 29; 111(30):E3157-66. PMID: 25028499; PMCID: PMC4121818.
    69. Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014; 3:151. PMID: 25165537.
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    70. Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 2014; 3:143. PMID: 25520778.
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    71. 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. The Cytoscape app article collection. F1000Res. 2014; 3:138. PMID: 25580224; PMCID: PMC4288400.
    72. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15; 30(12):i34-42. PMID: 24932003; PMCID: PMC4058954.
    73. Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. PLoS One. 2014; 9(5):e96687. PMID: 24817247; PMCID: PMC4016004.
    74. Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One. 2014; 9(4):e95893. PMID: 24770346; PMCID: PMC4000195.
    75. Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell. 2014 Apr 24; 157(3):534-8. PMID: 24766803; PMCID: PMC4154484.
    76. 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. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014 Jan 31; 343(6170):506-511. PMID: 24482476; PMCID: PMC4157572.
    77. Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial "omics". PLoS One. 2014; 9(1):e85177. PMID: 24465499; PMCID: PMC3897414.
    78. 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. 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. PMID: 24360959; PMCID: PMC4136507.
    79. Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014 Jan; 42(Database issue):D1269-74. PMID: 24271398; PMCID: PMC3965056.
    80. Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. PMID: 24238873; PMCID: PMC3866044.
    81. 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. Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal. 2013 Oct 15; 6(297):ra90. PMID: 24129700; PMCID: PMC4075427.
    82. 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. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol. 2013 Nov; 24(11):1901-12. PMID: 23949796; PMCID: PMC3810086.
    83. Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013 Oct; 14(10):719-32. PMID: 24045689; PMCID: PMC3940161.
    84. Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov; 10(11):1108-15. PMID: 24037242; PMCID: PMC3866081.
    85. Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD. Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep. 2013 Jul 11; 4(1):174-88. PMID: 23810556; PMCID: PMC3855057.
    86. 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. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11; 2:e00675. PMID: 23795294; PMCID: PMC3679525.
    87. 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. 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. PMID: 23749869; PMCID: PMC3696746.
    88. 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. 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. PMID: 23647160; PMCID: PMC4142215.
    89. Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. Proteome-wide discovery of mislocated proteins in cancer. Genome Res. 2013 Aug; 23(8):1283-94. PMID: 23674306; PMCID: PMC3730102.
    90. 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. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013; 9(5):e1003047. PMID: 23671412; PMCID: PMC3649990.
    91. Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling epigenetic and genetic effects through systematic analysis of gene position. Cell Rep. 2013 Jan 31; 3(1):128-37. PMID: 23291096; PMCID: PMC3563736.
    92. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2013 Jan; 31(1):38-45. PMID: 23242164; PMCID: PMC3654867.
    93. Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. Dissection of DNA damage responses using multiconditional genetic interaction maps. Mol Cell. 2013 Jan 24; 49(2):346-58. PMID: 23273983; PMCID: PMC3633480.
    94. Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26; 13(12):R123. PMID: 23268787; PMCID: PMC4056373.
    95. Jaeger PA, Doherty C, Ideker T. Modeling transcriptome dynamics in a complex world. Cell. 2012 Dec 07; 151(6):1161-2. PMID: 23217702.
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    96. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013 Jan 24; 49(2):359-367. PMID: 23177740; PMCID: PMC3780611.
    97. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76. PMID: 23132118.
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    98. Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. J Proteome Res. 2012 Oct 05; 11(10):4983-91. PMID: 22909323; PMCID: PMC3495236.
    99. Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One. 2012; 7(8):e41134. PMID: 22916103; PMCID: PMC3420874.
    100. Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet. 2012 Jul 27; 44(8):841-7. PMID: 22836096; PMCID: PMC3593099.
    101. Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T, Kipps TJ. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 2012 Sep 27; 120(13):2639-49. PMID: 22837534; PMCID: PMC3460686.
    102. Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ. Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 08; 46(5):691-704. PMID: 22681890; PMCID: PMC3380636.
    103. Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J. 2012 Apr 04; 31(7):1811-22. PMID: 22333915; PMCID: PMC3321207.
    104. Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 03; 148(3):543-55. PMID: 22304920; PMCID: PMC3615433.
    105. Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol. 2012 Jan 17; 8:565. PMID: 22252388; PMCID: PMC3296360.
    106. Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, Geum D, Wei X, Zhu J, Ideker T, Oka C, Wang N, Yang Z, Shaw PX, Zhang K. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-ß family member growth differentiation factor 6. J Biol Chem. 2012 Jan 06; 287(2):1520-6. PMID: 22049084; PMCID: PMC3256864.
    107. Atwood A, DeConde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc Natl Acad Sci U S A. 2011 Nov 08; 108(45):18560-5. PMID: 22042857; PMCID: PMC3215069.
    108. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep; 7(9):e1002180. PMID: 21980275; PMCID: PMC3182870.
    109. Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 2011 Sep 23; 35(3):413-25. PMID: 21903424; PMCID: PMC3183365.
    110. Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc. 2011 Aug 11; 6(9):1308-23. PMID: 21886098; PMCID: PMC3383003.
    111. Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 2011 Mar 18; 144(6):860-3. PMID: 21414478; PMCID: PMC3102020.
    112. Friend SH, Ideker T. Point: Are we prepared for the future doctor visit? Nat Biotechnol. 2011 Mar; 29(3):215-8. PMID: 21390021.
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    113. Smoot M, Ono K, Ideker T, Maere S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics. 2011 Apr 01; 27(7):1030-1. PMID: 21278188; PMCID: PMC3065683.
    114. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011 Feb 01; 27(3):431-2. PMID: 21149340; PMCID: PMC3031041.
    115. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science. 2010 Dec 03; 330(6009):1385-9. PMID: 21127252; PMCID: PMC3006187.
    116. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec; 20(12):1672-8. PMID: 20978140; PMCID: PMC2989993.
    117. Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nat Methods. 2010 Oct; 7(10):801-5. PMID: 20936779; PMCID: PMC2967489.
    118. Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics. 2010 Nov 01; 26(21):2796-7. PMID: 20847220; PMCID: PMC2958747.
    119. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics. 2010 Sep 15; 26(18):i531-9. PMID: 20823318.
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    120. Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010; 11(7):R77. PMID: 20653936; PMCID: PMC2926788.
    121. Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul; 11(7):635-43. PMID: 20543837; PMCID: PMC2896911.
    122. Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 2010 Apr 15; 464(7291):1048-51. PMID: 20393563; PMCID: PMC2929961.
    123. Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. Plant Cell. 2010 Apr; 22(4):997-1005. PMID: 20371643; PMCID: PMC2879763.
    124. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010 Mar 05; 140(5):744-52. PMID: 20211142; PMCID: PMC2836267.
    125. König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK. Human host factors required for influenza virus replication. Nature. 2010 Feb 11; 463(7282):813-7. PMID: 20027183; PMCID: PMC2862546.
    126. Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annu Rev Cell Dev Biol. 2010; 26:721-44. PMID: 20604711; PMCID: PMC3371392.
    127. Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec; 5(12):e1000782. PMID: 20041197; PMCID: PMC2788232.
    128. van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res. 2010 Feb; 20(2):190-200. PMID: 20007327; PMCID: PMC2813475.
    129. Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci. 2009 Oct 07; 29(40):12467-76. PMID: 19812322; PMCID: PMC2802851.
    130. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437. PMID: 19478882; PMCID: PMC2682202.
    131. Kelley R, Ideker T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet. 2009 May; 5(5):e1000488. PMID: 19503593; PMCID: PMC2676504.
    132. Mak HC, Pillus L, Ideker T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res. 2009 Jun; 19(6):1014-25. PMID: 19372386; PMCID: PMC2694488.
    133. Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6477-82. PMID: 19346491; PMCID: PMC2672541.
    134. Schwartz AS, Yu J, Gardenour KR, Finley RL, Ideker T. Cost-effective strategies for completing the interactome. Nat Methods. 2009 Jan; 6(1):55-61. PMID: 19079254; PMCID: PMC2613168.
    135. Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell. 2008 Dec 05; 32(5):735-46. PMID: 19061648; PMCID: PMC2644724.
    136. Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol. 2008 Nov; 4(11):e1000217. PMID: 18989396; PMCID: PMC2563693.
    137. Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res. 2008 Nov; 36(20):e136. PMID: 18836191; PMCID: PMC2582614.
    138. König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008 Oct 03; 135(1):49-60. PMID: 18854154; PMCID: PMC2628946.
    139. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 2008 Oct 17; 322(5900):405-10. PMID: 18818364; PMCID: PMC2753251.
    140. Ideker T. Forging new ties between E. coli genes. Cell. 2008 Jun 27; 133(7):1135-7. PMID: 18585345; PMCID: PMC2806683.
    141. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000065. PMID: 18421374; PMCID: PMC2289880.
    142. Ideker T, Sharan R. Protein networks in disease. Genome Res. 2008 Apr; 18(4):644-52. PMID: 18381899; PMCID: PMC3863981.
    143. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol. 2008; 4:162. PMID: 18319721; PMCID: PMC2290938.
    144. Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A. 2008 Feb 26; 105(8):2934-9. PMID: 18287073; PMCID: PMC2268563.
    145. Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 2008 Feb 15; 24(4):594-6. PMID: 18174180.
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    146. Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007; 3:140. PMID: 17940530; PMCID: PMC2063581.
    147. Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet. 2007 Sep; 8(9):699-710. PMID: 17703239; PMCID: PMC2811081.
    148. Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics. 2008 Jan 01; 24(1):71-7. PMID: 17623705; PMCID: PMC2811084.
    149. Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 2007 Jul 01; 23(13):i359-66. PMID: 17646318.
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    150. Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol. 2007; 3:105. PMID: 17437030; PMCID: PMC1865587.
    151. Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A. 2007 Jan 23; 104(4):1283-8. PMID: 17227853; PMCID: PMC1783126.
    152. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMID: 17947979; PMCID: PMC3685583.
    153. Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, DiRita VJ, Ideker T, Andrews P, Finley RL. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007; 8(7):R130. PMID: 17615063; PMCID: PMC2323224.
    154. Ideker T, Valencia A. Bioinformatics in the human interactome project. Bioinformatics. 2006 Dec 15; 22(24):2973-4. PMID: 17142816.
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    155. Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan; 35(Database issue):D538-45. PMID: 17135207; PMCID: PMC1751555.
    156. Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 2006 Jul 26; 7:360. PMID: 16872496; PMCID: PMC1550431.
    157. Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Ann Biomed Eng. 2006 Jul; 34(7):1226-33. PMID: 16929563.
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    158. Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006 Jun 16; 2(6):e70. PMID: 16789814; PMCID: PMC1479087.
    159. Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006; 5(4):11. PMID: 16762047; PMCID: PMC1561585.
    160. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science. 2006 May 19; 312(5776):1054-9. PMID: 16709784; PMCID: PMC2811083.
    161. Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar; 16(3):428-35. PMID: 16510899; PMCID: PMC1415213.
    162. Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol. 2006 Mar; 13(2):133-44. PMID: 16597231.
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    163. Ideker T, Winslow LR, Lauffenburger AD. Bioengineering and systems biology. Ann Biomed Eng. 2006 Feb; 34(2):257-64. PMID: 16474915.
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    164. Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006; 2:2006.0004. PMID: 16738551; PMCID: PMC1681478.
    165. Warner GJ, Adeleye YA, Ideker T. Interactome networks: the state of the science. Genome Biol. 2006; 7(1):301. PMID: 16515723; PMCID: PMC1431712.
    166. Bandyopadhyay S, Kelley R, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006; 354-66. PMID: 17094252.
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    167. Suthram S, Sittler T, Ideker T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 2005 Nov 03; 438(7064):108-12. PMID: 16267557; PMCID: PMC2830740.
    168. Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W389-92. PMID: 15980495; PMCID: PMC1160200.
    169. Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W627-32. PMID: 15980550; PMCID: PMC1160204.
    170. Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 2005; 6(7):R62. PMID: 15998451; PMCID: PMC1175993.
    171. Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 2005 Jul-Aug; 12(6):835-46. PMID: 16108720.
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    172. Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol. 2005 May; 23(5):561-6. PMID: 15877074; PMCID: PMC2814446.
    173. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1974-9. PMID: 15687504; PMCID: PMC548573.
    174. Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 2004; 5(12):R95. PMID: 15575969; PMCID: PMC545798.
    175. Begley TJ, Rosenbach AS, Ideker T, Samson LD. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell. 2004 Oct 08; 16(1):117-25. PMID: 15469827.
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    176. Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W83-8. PMID: 15215356; PMCID: PMC441549.
    177. Ideker T. Systems biology 101--what you need to know. Nat Biotechnol. 2004 Apr; 22(4):473-5. PMID: 15085805.
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    178. Ideker T. A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. Adv Exp Med Biol. 2004; 547:21-30. PMID: 15230090.
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    179. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov; 13(11):2498-504. PMID: 14597658; PMCID: PMC403769.
    180. Ozier O, Amin N, Ideker T. Global architecture of genetic interactions on the protein network. Nat Biotechnol. 2003 May; 21(5):490-1. PMID: 12721566.
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    181. Young ET, Dombek KM, Tachibana C, Ideker T. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol Chem. 2003 Jul 11; 278(28):26146-58. PMID: 12676948.
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    182. Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res. 2002 Dec; 1(2):103-12. PMID: 12496357.
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    183. Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 2002 Jul 22; 158(2):259-71. PMID: 12135984; PMCID: PMC2173120.
    184. Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics. 2002 Apr; 1(4):323-33. PMID: 12096114.
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    185. Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002; 18 Suppl 1:S233-40. PMID: 12169552.
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