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Trey Ideker

Title(s)Professor, Medicine
SchoolHealth Sciences
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
    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.
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    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. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Syst. 2020 Jul 01. Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Kreisberg JF, Adams PD, Carvunis AR, Bannasch DL, Ostrander EA, Ideker T. PMID: 32619550.
      View in: PubMed   Mentions: 1     Fields:    
    2. Decoding of persistent multiscale structures in complex biological networks. bioRxiv. 2020 Jun 18. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. PMID: 32587977.
      View in: PubMed   Mentions:
    3. A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. J Cell Sci. 2020 May 22; 133(10). Ming Sun S, Batté A, Elmer M, van der Horst SC, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. PMID: 32299836.
      View in: PubMed   Mentions:    Fields:    
    4. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    5. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Ann Hum Genet. 2020 May; 84(3):214-220. Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. PMID: 32232836.
      View in: PubMed   Mentions: 1     Fields:    
    6. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. PMID: 32511329.
      View in: PubMed   Mentions:
    7. A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2020 04; 20(4):233-246. Kuenzi BM, Ideker T. PMID: 32066900.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 02 07; 11(1):781. Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR. PMID: 32034123.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    9. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17; 9. Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. PMID: 31951200.
      View in: PubMed   Mentions:    Fields:    
    10. The great hairball gambit. PLoS Genet. 2019 11; 15(11):e1008519. Flint J, Ideker T. PMID: 31770365.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    11. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 2019 11 25; 20(1):249. Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. PMID: 31767039.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    12. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Rep. 2019 08 27; 28(9):2317-2330.e8. Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. PMID: 31461649.
      View in: PubMed   Mentions:    Fields:    
    13. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 02; 54:110-117. Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. PMID: 31288129.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 2019 05 30; 177(6):1375-1383. van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. PMID: 31150618.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    15. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 29; 10(1):2415. Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. PMID: 31142745.
      View in: PubMed   Mentions:    Fields:    
    16. Rare variant phasing using paired tumor:normal sequence data. BMC Bioinformatics. 2019 May 27; 20(1):265. Buckley AR, Ideker T, Carter H, Schork NJ. PMID: 31132991.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. A Fast and Flexible Framework for Network-Assisted Genomic Association. iScience. 2019 Jun 28; 16:155-161. Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T. PMID: 31174177.
      View in: PubMed   Mentions:
    18. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 05 16; 10(1):2188. Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. PMID: 31097695.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    19. Transcriptional responses to DNA damage. DNA Repair (Amst). 2019 07; 79:40-49. Silva E, Ideker T. PMID: 31102970.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    20. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 04 24; 8(4):275-280. Fong SH, Carlin DE, Ozturk K, Ideker T. PMID: 31022372.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    21. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 04 18; 177(3):572-586.e22. Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. PMID: 30955884.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    22. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst. 2019 03 27; 8(3):267-273.e3. Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. PMID: 30878356.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    23. On entropy and information in gene interaction networks. Bioinformatics. 2019 03 01; 35(5):815-822. Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. PMID: 30102349.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    24. Classifying tumors by supervised network propagation. Bioinformatics. 2019 07; 35(14):2528. Zhang W, Ma J, Ideker T. PMID: 30726869.
      View in: PubMed   Mentions:    Fields:    
    25. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. Methods Mol Biol. 2019; 2049:73-85. Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. PMID: 31602605.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    26. A Blueprint for Systems Biology. Clin Chem. 2019 02; 65(2):342-344. Ideker T, Hood L. PMID: 30593465.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    27. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res. 2018 11 30; 46(21):11251-11261. 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. PMID: 30203048.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    28. Typing tumors using pathways selected by somatic evolution. Nat Commun. 2018 10 08; 9(1):4159. Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. PMID: 30297789.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    29. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell. 2018 09 20; 71(6):882-895. Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD. PMID: 30241605.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    30. Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med. 2018 09 14; 10(1):69. Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ. PMID: 30217226.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    31. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 11; 8(11):1474-1489. 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. PMID: 30209081.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    32. pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018 08 15; 34(16):2859-2861. Huang JK, Jia T, Carlin DE, Ideker T. PMID: 29608663.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    33. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 07 26; 174(3):505-520. 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. PMID: 30053424.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    34. Classifying tumors by supervised network propagation. Bioinformatics. 2018 07 01; 34(13):i484-i493. Zhang W, Ma J, Ideker T. PMID: 29949979.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    35. The Cytoscape Automation app article collection. F1000Res. 2018; 7:800. 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. PMID: 29983926.
      View in: PubMed   Mentions:    Fields:    
    36. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. J Mol Biol. 2018 09 14; 430(18 Pt A):2900-2912. Shen JP, Ideker T. PMID: 29932943.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    37. Visible Machine Learning for Biomedicine. Cell. 2018 06 14; 173(7):1562-1565. Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T. PMID: 29906441.
      View in: PubMed   Mentions: 8     Fields:    
    38. Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol Cancer Ther. 2018 07; 17(7):1585-1594. 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. PMID: 29636367.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    39. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 04; 50(4):613-620. 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. PMID: 29610481.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    40. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018 Apr 25; 6(4):484-495.e5. Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. PMID: 29605183.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    41. Using deep learning to model the hierarchical structure and function of a cell. Nat Methods. 2018 04; 15(4):290-298. Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. PMID: 29505029.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    42. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 03 01; 69(5):915. Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. PMID: 29499140.
      View in: PubMed   Mentions: 1     Fields:    
    43. ndexr-an R package to interface with the network data exchange. Bioinformatics. 2018 02 15; 34(4):716-717. Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. PMID: 29087446.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    44. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 02 15; 69(4):699-708.e7. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. PMID: 29452643.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    45. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Mol Cell. 2018 01 18; 69(2):321-333.e3. Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. PMID: 29351850.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    46. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 01 18; 69(2):306-320.e4. Neal S, Jaeger PA, Duttke SH, Benner C, K Glass C, Ideker T, Hampton RY. PMID: 29351849.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    47. Annotating gene sets by mining large literature collections with protein networks. Pac Symp Biocomput. 2018; 23:602-613. Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T. PMID: 29218918.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    48. Correcting CRISPR for copy number. Nat Genet. 2017 11 29; 49(12):1674-1675. Shen JP, Ideker T. PMID: 29186130.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    49. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Res. 2017 11 01; 77(21):e58-e61. Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. PMID: 29092941.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    50. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017 Nov 30; 171(6):1272-1283.e15. 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. PMID: 29107334.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    51. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct; 13(10):e1005771. Ideker T, Nussinov R. PMID: 29023447.
      View in: PubMed   Mentions: 5     Fields:    
    52. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct; 13(10):e1005598. Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. PMID: 29023449.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    53. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 06 12; 18(1):458. Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. PMID: 28606096.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    54. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017 09; 18(9):551-562. Cowen L, Ideker T, Raphael BJ, Sharan R. PMID: 28607512.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    55. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017; 6:784. Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. PMID: 29487738.
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    56. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 03; 13(7):1248-1249. Farré JC, Kramer M, Ideker T, Subramani S. PMID: 28486053.
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    57. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun; 14(6):577-580. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. PMID: 28481362.
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    58. Systems biology guided by XCMS Online metabolomics. Nat Methods. 2017 04 27; 14(5):461-462. 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. PMID: 28448069.
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    59. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 2017 03 28; 18(1):57. Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. PMID: 28351423.
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    60. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. 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. PMID: 28319113.
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    61. Common genetic variation in the germline influences where and how tumors develop. Mol Cell Oncol. 2017; 4(3):e1302905. Carter H, Ideker T. PMID: 28616579.
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    62. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 04; 7(4):410-423. 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. PMID: 28188128.
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    63. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell. 2017 Feb 16; 65(4):761-774.e5. Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. PMID: 28132844.
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    64. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016 Oct 20; 1(17):e87877. 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 JCI, Anders HJ, Sharma K. PMID: 27777973.
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    65. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 09 27; 113(39):10750-8. 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. PMID: 27638202.
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    66. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell. 2016 08 04; 63(3):514-25. 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. PMID: 27453043.
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    67. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun. 2016 07 15; 7:12096. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. PMID: 27417679.
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    68. Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener. 2016 05 23; 11(1):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. PMID: 27216421.
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    69. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener. 2016 04 26; 11:31. 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. PMID: 27112350.
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    70. 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. 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. PMID: 27105112.
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    71. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer. 2016 07 15; 139(2):373-82. Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. PMID: 26949921.
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    72. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst. 2016 Feb 24; 2(2):77-88. Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. PMID: 26949740.
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    73. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar; 13(3):245-247. 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. PMID: 26780094.
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    74. Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife. 2015 Dec 18; 4. Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. PMID: 26682651.
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    75. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. PLoS One. 2015; 10(11):e0142618. Gross AM, Kreisberg JF, Ideker T. PMID: 26555223.
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    76. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. 2015 Nov 03; 6(34):35755-69. 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. PMID: 26437225.
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    77. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28; 1(4):302-305. 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. PMID: 26594663.
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    78. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. J Proteome Res. 2015 Dec 04; 14(12):4995-5006. 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. PMID: 26435392.
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    79. 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. 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. PMID: 26192380.
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    80. Molecular networks in context. Nat Biotechnol. 2015 Jul; 33(7):720-1. Gross AM, Ideker T. PMID: 26154012.
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    81. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One. 2015; 10(6):e0126898. Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. PMID: 26083491.
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    82. 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.
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    83. 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.
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    84. 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.
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    85. 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.
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    86. 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.
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    87. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015; 11(9):1652-67. Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. PMID: 26103419.
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    88. 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.
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    89. 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.
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    90. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. PMID: 25417114.
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    91. 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.
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    92. 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.
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    93. 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.
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    94. 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.
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    95. 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.
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    96. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 2014; 3:143. Ono K, Demchak B, Ideker T. PMID: 25520778.
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    97. 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.
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    98. 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.
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    99. 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.
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    100. 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.
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    101. 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.
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    102. 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.
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    103. 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.
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    104. 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.
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    105. 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.
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    106. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. Carter H, Hofree M, Ideker T. PMID: 24238873.
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    107. 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.
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    108. 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.
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    109. 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.
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    110. 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.
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    111. 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.
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    112. 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.
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    113. 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.
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    114. 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.
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    115. 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.
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    116. 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.
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    117. 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.
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    118. A gene ontology inferred from molecular networks. Nat Biotechnol. 2013 Jan; 31(1):38-45. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. PMID: 23242164.
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    119. 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.
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    120. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26; 13(12):R123. Bean GJ, Ideker T. PMID: 23268787.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    121. Modeling transcriptome dynamics in a complex world. Cell. 2012 Dec 07; 151(6):1161-2. Jaeger PA, Doherty C, Ideker T. PMID: 23217702.
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    122. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013 Jan 24; 49(2):359-367. 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. PMID: 23177740.
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    123. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. PMID: 23132118.
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    124. Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. J Proteome Res. 2012 Oct 05; 11(10):4983-91. 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. PMID: 22909323.
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    125. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One. 2012; 7(8):e41134. Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. PMID: 22916103.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    126. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet. 2012 Jul 27; 44(8):841-7. Califano A, Butte AJ, Friend S, Ideker T, Schadt E. PMID: 22836096.
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    127. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 2012 Sep 27; 120(13):2639-49. Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T, Kipps TJ. PMID: 22837534.
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    128. Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 08; 46(5):691-704. 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. PMID: 22681890.
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    129. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J. 2012 Apr 04; 31(7):1811-22. Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C. PMID: 22333915.
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    130. PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 03; 148(3):543-55. Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PMID: 22304920.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    131. Differential network biology. Mol Syst Biol. 2012 Jan 17; 8:565. Ideker T, Krogan NJ. PMID: 22252388.
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    132. 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. 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. PMID: 22049084.
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    133. 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. Atwood A, DeConde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. PMID: 22042857.
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    134. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep; 7(9):e1002180. Dutkowski J, Ideker T. PMID: 21980275.
      View in: PubMed   Mentions: 31     Fields:    Translation:Humans
    135. 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. Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. PMID: 21903424.
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    136. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc. 2011 Aug 11; 6(9):1308-23. Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. PMID: 21886098.
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    137. 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.
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    138. Point: Are we prepared for the future doctor visit? Nat Biotechnol. 2011 Mar; 29(3):215-8. Friend SH, Ideker T. PMID: 21390021.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    139. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics. 2011 Apr 01; 27(7):1030-1. Smoot M, Ono K, Ideker T, Maere S. PMID: 21278188.
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    140. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011 Feb 01; 27(3):431-2. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. PMID: 21149340.
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    141. Rewiring of genetic networks in response to DNA damage. Science. 2010 Dec 03; 330(6009):1385-9. 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. PMID: 21127252.
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    142. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec; 20(12):1672-8. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. PMID: 20978140.
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    143. A human MAP kinase interactome. Nat Methods. 2010 Oct; 7(10):801-5. 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. PMID: 20936779.
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    144. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics. 2010 Nov 01; 26(21):2796-7. Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A. PMID: 20847220.
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    145. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics. 2010 Sep 15; 26(18):i531-9. Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. PMID: 20823318.
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    146. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010; 11(7):R77. Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. PMID: 20653936.
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    147. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul; 11(7):635-43. 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. PMID: 20543837.
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    148. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 2010 Apr 15; 464(7291):1048-51. Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. PMID: 20393563.
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    149. Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. Plant Cell. 2010 Apr; 22(4):997-1005. Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. PMID: 20371643.
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    150. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010 Mar 05; 140(5):744-52. 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. PMID: 20211142.
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    151. Human host factors required for influenza virus replication. Nature. 2010 Feb 11; 463(7282):813-7. 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. PMID: 20027183.
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    152. A decade of systems biology. Annu Rev Cell Dev Biol. 2010; 26:721-44. Chuang HY, Hofree M, Ideker T. PMID: 20604711.
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    153. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec; 5(12):e1000782. Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. PMID: 20041197.
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    154. Bayesian network analysis of targeting interactions in chromatin. Genome Res. 2010 Feb; 20(2):190-200. van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. PMID: 20007327.
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    155. An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci. 2009 Oct 07; 29(40):12467-76. Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. PMID: 19812322.
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    156. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437. 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. PMID: 19478882.
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    157. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet. 2009 May; 5(5):e1000488. Kelley R, Ideker T. PMID: 19503593.
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    158. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res. 2009 Jun; 19(6):1014-25. Mak HC, Pillus L, Ideker T. PMID: 19372386.
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    159. 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. Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. PMID: 19346491.
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    160. Cost-effective strategies for completing the interactome. Nat Methods. 2009 Jan; 6(1):55-61. Schwartz AS, Yu J, Gardenour KR, Finley RL, Ideker T. PMID: 19079254.
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    161. 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. 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. PMID: 19061648.
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    162. Inferring pathway activity toward precise disease classification. PLoS Comput Biol. 2008 Nov; 4(11):e1000217. Lee E, Chuang HY, Kim JW, Ideker T, Lee D. PMID: 18989396.
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    163. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res. 2008 Nov; 36(20):e136. Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. PMID: 18836191.
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    164. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 2008 Oct 03; 135(1):49-60. 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. PMID: 18854154.
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    165. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 2008 Oct 17; 322(5900):405-10. 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. PMID: 18818364.
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    166. Forging new ties between E. coli genes. Cell. 2008 Jun 27; 133(7):1135-7. Ideker T. PMID: 18585345.
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    167. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000065. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. PMID: 18421374.
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    168. Protein networks in disease. Genome Res. 2008 Apr; 18(4):644-52. Ideker T, Sharan R. PMID: 18381899.
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    169. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol. 2008; 4:162. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. PMID: 18319721.
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    170. 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. Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. PMID: 18287073.
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    171. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 2008 Feb 15; 24(4):594-6. Kalaev M, Smoot M, Ideker T, Sharan R. PMID: 18174180.
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    172. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007; 3:140. Chuang HY, Lee E, Liu YT, Lee D, Ideker T. PMID: 17940530.
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    173. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet. 2007 Sep; 8(9):699-710. Beyer A, Bandyopadhyay S, Ideker T. PMID: 17703239.
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    174. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics. 2008 Jan 01; 24(1):71-7. Kelley R, Feizi H, Ideker T. PMID: 17623705.
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    175. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 2007 Jul 01; 23(13):i359-66. Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. PMID: 17646318.
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    176. Integrating scientific cultures. Mol Syst Biol. 2007; 3:105. Ideker T, Bafna V, Lemberger T. PMID: 17437030.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    177. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A. 2007 Jan 23; 104(4):1283-8. Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. PMID: 17227853.
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    178. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. 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. PMID: 17947979.
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    179. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007; 8(7):R130. 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. PMID: 17615063.
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    180. Network genomics. Ernst Schering Res Found Workshop. 2007; (61):89-115. Ideker TE. PMID: 17249498.
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    181. Bioinformatics in the human interactome project. Bioinformatics. 2006 Dec 15; 22(24):2973-4. Ideker T, Valencia A. PMID: 17142816.
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    182. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan; 35(Database issue):D538-45. Mak HC, Daly M, Gruebel B, Ideker T. PMID: 17135207.
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    183. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 2006 Jul 26; 7:360. Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. PMID: 16872496.
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    184. Bioengineering and systems biology. Ann Biomed Eng. 2006 Jul; 34(7):1226-33. Ideker T, Winslow LR, Lauffenburger DA. PMID: 16929563.
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    185. Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006 Jun 16; 2(6):e70. Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. PMID: 16789814.
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    186. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006; 5(4):11. 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. PMID: 16762047.
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    187. A systems approach to mapping DNA damage response pathways. Science. 2006 May 19; 312(5776):1054-9. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. PMID: 16709784.
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    188. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar; 16(3):428-35. Bandyopadhyay S, Sharan R, Ideker T. PMID: 16510899.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    189. Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol. 2006 Mar; 13(2):133-44. Scott J, Ideker T, Karp RM, Sharan R. PMID: 16597231.
      View in: PubMed   Mentions: 46     Fields:    Translation:AnimalsCells
    190. Bioengineering and systems biology. Ann Biomed Eng. 2006 Feb; 34(2):257-64. Ideker T, Winslow LR, Lauffenburger AD. PMID: 16474915.
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    191. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006; 2:2006.0004. Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. PMID: 16738551.
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    192. Interactome networks: the state of the science. Genome Biol. 2006; 7(1):301. Warner GJ, Adeleye YA, Ideker T. PMID: 16515723.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    193. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006; 354-66. Bandyopadhyay S, Kelley R, Ideker T. PMID: 17094252.
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    194. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 2005 Nov 03; 438(7064):108-12. Suthram S, Sittler T, Ideker T. PMID: 16267557.
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    195. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005 Jul 01; 33(Web Server issue):W389-92. Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. PMID: 15980495.
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    196. 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. Hsiao A, Ideker T, Olefsky JM, Subramaniam S. PMID: 15980550.
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    197. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 2005; 6(7):R62. Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. PMID: 15998451.
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    198. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 2005 Jul-Aug; 12(6):835-46. Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. PMID: 16108720.
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    199. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol. 2005 May; 23(5):561-6. Kelley R, Ideker T. PMID: 15877074.
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    200. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1974-9. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. PMID: 15687504.
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    201. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 2004; 5(12):R95. Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. PMID: 15575969.
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    202. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell. 2004 Oct 08; 16(1):117-25. Begley TJ, Rosenbach AS, Ideker T, Samson LD. PMID: 15469827.
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    203. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W83-8. Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PMID: 15215356.
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    204. Systems biology 101--what you need to know. Nat Biotechnol. 2004 Apr; 22(4):473-5. Ideker T. PMID: 15085805.
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    205. 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. Ideker T. PMID: 15230090.
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    206. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov; 13(11):2498-504. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. PMID: 14597658.
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    207. Global architecture of genetic interactions on the protein network. Nat Biotechnol. 2003 May; 21(5):490-1. Ozier O, Amin N, Ideker T. PMID: 12721566.
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    208. 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. Young ET, Dombek KM, Tachibana C, Ideker T. PMID: 12676948.
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    209. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res. 2002 Dec; 1(2):103-12. Begley TJ, Rosenbach AS, Ideker T, Samson LD. PMID: 12496357.
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    210. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 2002 Jul 22; 158(2):259-71. Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. PMID: 12135984.
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    211. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics. 2002 Apr; 1(4):323-33. Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. PMID: 12096114.
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    212. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002; 18 Suppl 1:S233-40. Ideker T, Ozier O, Schwikowski B, Siegel AF. PMID: 12169552.
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    213. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 2001 May 04; 292(5518):929-34. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. PMID: 11340206.
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    214. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001; 2:343-72. Ideker T, Galitski T, Hood L. PMID: 11701654.
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    215. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol. 2000; 7(6):805-17. Ideker T, Thorsson V, Siegel AF, Hood LE. PMID: 11382363.
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    216. Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays. Genet Anal. 1999 Dec 15; 15(6):209-15. Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L. PMID: 10609756.
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    217. Mining SNPs from EST databases. Genome Res. 1999 Feb; 9(2):167-74. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. PMID: 10022981.
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