Trey Ideker

Title(s)Professor, Medicine
SchoolVc-health Sciences-schools
ORCID ORCID Icon0000-0002-1708-8454 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Massachusetts Institute of Technology, Cambridge, MABS06/1994Elec. Eng. & Comp. Sci.
    Massachusetts Institute of Technology, Cambridge, MAMEng06/1995Elec. Eng. & Comp. Sci.
    University of Washington, Seattle. WAPhD06/2001Molecular Biotechnology
    Whitehead Institute for Biomedical Research, Cambridge, MA06/2003Whitehead Fellow
    Collapse Awards and Honors
    2020Clarivate Web of Science Highly Cited Researcher (top 1% of citations for field and year)
    2015Elected Fellow, American Association for the Advancement of Science (AAAS)
    2014Elected Fellow, American Institute for Medical and Biological Engineering (AIMBE)
    2009Overton Prize, International Society for Computational Biology (ISCB)
    2009Distinguished Alumni Award, Duke University Talent Identification Program
    2009Selected as member of Faculty of 1000 (f1000.com)
    2006Selected by Technology Review Top 10 Innovators of 2006
    2005Selected by Technology Review Top 35 Young Innovators of 2005
    2004 Fellowship Award, David and Lucile Packard Foundation

    Collapse Overview 
    Collapse Overview
    Employment
    (2010 – pres) Professor, Division of Genetics, Department of Medicine, UC San Diego
    (2010 – pres) Member, Moores Cancer Center, UC San Diego
    (2010 – pres) Adjunct Professor, Departments of Bioengineering & Computer Science
    (2009 – 2014) Division Chief of Genetics, Department of Medicine, UC San Diego
    (2007 – 2009) Associate Professor, Department of Bioengineering, UC San Diego
    (2003 – 2006) Assistant Professor, Department of Bioengineering, UC San Diego

    Advisory Boards and Consulting
    (2016 – 2021) NIH/NHGRI National Advisory Council for Human Genome Research
    (2015 – pres) Scientific Advisory Board, IDEAYA Biosciences, Menlo Park, CA
    (2014 – pres) Data4Cure, co-Founder and Chair of Scientific Advisory Board, La Jolla, CA
    (2007 – 2015) Scientific Advisory Board, Mendel Biotechnology, Antioch, CA
    (2007 – 2012) NIH Biodata Management & Analysis Study Section (BDMA)
    (2005 – 2007) European Union (EU) 6th Framework Grant Study Section
    (2001 – 2010) Scientific Advisory Board, Genstruct (Selventa), Cambridge, MA

    Editorial Boards
    Current: Cell, Cell Systems, Cell Reports, Scientific Data, PLoS Computational Biology, Molecular Systems Biology
    Previous: Bioinformatics (2006 - 2013)

    Collapse Research 
    Collapse Research Activities and Funding
    The Psychiatric Cell Map Initiative: Connecting Genomics, Subcellular Networks, and Higher Order Phenotypes
    NIH U01MH115747Sep 5, 2018 - Jun 30, 2023
    Role: Co-Principal Investigator
    Research Center for Cancer Systems Biology: Cancer Cell Map Initiative
    NIH U54CA209891May 11, 2017 - Apr 30, 2022
    Role: Co-Principal Investigator
    NDEx - the Network Data Exchange A Network Commons for Biologists
    NIH U24CA184427May 1, 2014 - Apr 30, 2022
    Role: Principal Investigator
    San Diego Center for Systems Biology: From Maps to Models
    NIH P50GM085764Sep 18, 2010 - May 31, 2019
    Role: Principal Investigator
    National Resource for Network Biology (NRNB)
    NIH P41GM103504Sep 13, 2010 - Apr 30, 2025
    Role: Principal Investigator
    Resource for Analysis, Vizualization, and Integration of Networks (RAVIN)
    NIH P41RR031228Sep 13, 2010 - Jun 30, 2015
    Role: Principal Investigator
    Massively parallel epigenomics: building new value with current resources
    NIH R21HG005252Feb 1, 2010 - Jan 31, 2013
    Role: Principal Investigator
    Comparative Analysis of Genetic Interaction Networks
    NIH R01GM084279Aug 1, 2008 - Feb 28, 2019
    Role: Principal Investigator
    A Systems Approach to Mapping the DNA Damage Response
    NIH R01ES014811Sep 26, 2005 - Aug 31, 2022
    Role: Principal Investigator
    Cytoscape: A Modeling Platform for Biomolecular Networks
    NIH R01HG009979Jun 1, 2004 - Aug 31, 2022
    Role: Principal Investigator
    Cytoscape: A Modeling Platform for Biomolecular Networks
    NIH R01GM070743Jun 1, 2004 - Aug 31, 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 Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex. 2021 07 05; 31(8):3752-3763. Lew BJ, Schantell MD, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. PMID: 33822880; PMCID: PMC8258439.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    2. Unveiling Complexity and Multipotentiality of Early Heart Fields. Circ Res. 2021 08 06; 129(4):474-487. Zhang Q, Carlin D, Zhu F, Cattaneo P, Ideker T, Evans SM, Bloomekatz J, Chi NC. PMID: 34162224; PMCID: PMC9308985.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    3. Mapping the multiscale structure of biological systems. Cell Syst. 2021 06 16; 12(6):622-635. Schaffer LV, Ideker T. PMID: 34139169; PMCID: PMC8245186.
      View in: PubMed   Mentions: 9     Fields:    
    4. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell. 2021 06 17; 81(12):2656-2668.e8. Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. PMID: 33930332; PMCID: PMC8043580.
      View in: PubMed   Mentions: 130     Fields:    Translation:HumansAnimalsCells
    5. Author Correction: A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2021 Mar; 21(3):212. Kuenzi BM, Ideker T. PMID: 33441978.
      View in: PubMed   Mentions:    Fields:    
    6. Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Nat Cancer. 2021 02; 2(2):233-244. Ma J, Fong SH, Luo Y, Bakkenist CJ, Shen JP, Mourragui S, Wessels LFA, Hafner M, Sharan R, Peng J, Ideker T. PMID: 34223192; PMCID: PMC8248912.
      View in: PubMed   Mentions: 47     Fields:    Translation:Humans
    7. HiDeF: identifying persistent structures in multiscale 'omics data. Genome Biol. 2021 01 07; 22(1):21. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. PMID: 33413539; PMCID: PMC7789082.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    8. Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2021 Jan 04; 12(1):200. Vakirlis N, Acar O, Hsu B, Coelho NC, 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: 33398071; PMCID: PMC7782721.
      View in: PubMed   Mentions:    Fields:    
    9. Multiscale community detection in Cytoscape. PLoS Comput Biol. 2020 10; 16(10):e1008239. Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, Ideker T. PMID: 33095781; PMCID: PMC7584444.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    10. Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. Cancer Cell. 2020 11 09; 38(5):672-684.e6. Kuenzi BM, Park J, Fong SH, Sanchez KS, Lee J, Kreisberg JF, Ma J, Ideker T. PMID: 33096023; PMCID: PMC7737474.
      View in: PubMed   Mentions: 137     Fields:    Translation:HumansCells
    11. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521). Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, et al. PMID: 33060197; PMCID: PMC7808408.
      View in: PubMed   Mentions: 382     Fields:    Translation:HumansCells
    12. Identifying persistent structures in multiscale 'omics data. bioRxiv. 2020 Oct 03. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. PMID: 32587977; PMCID: PMC7310637.
      View in: PubMed   Mentions:
    13. Functional Landscape of SARS-CoV-2 Cellular Restriction. bioRxiv. 2020 Sep 30. Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. PMID: 33024967; PMCID: PMC7536870.
      View in: PubMed   Mentions:
    14. Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda). 2020 09 02; 10(9):2981-2988. Silva E, Michaca M, Munson B, Bean GJ, Jaeger PA, Licon K, Winzeler EA, Ideker T. PMID: 32732306; PMCID: PMC7466999.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    15. Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open. 2020 09 01; 3(9):e2015428. Proskovec AL, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. PMID: 32926115; PMCID: PMC7490648.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    16. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020 10; 39(40):6327-6339. Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. PMID: 32848210; PMCID: PMC7529583.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    17. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Syst. 2020 08 26; 11(2):176-185.e6. 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; PMCID: PMC7484147.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    18. A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. J Cell Sci. 2020 05 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; PMCID: PMC7325435.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    19. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, 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, 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-Ozturk 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; PMCID: PMC7431030.
      View in: PubMed   Mentions: 2478     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    20. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Ann Hum Genet. 2020 05; 84(3):214-220. Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. PMID: 32232836; PMCID: PMC7402360.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    21. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 27. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, 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, 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, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, 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; PMCID: PMC7239059.
      View in: PubMed   Mentions: 6  
    22. Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. Cereb Cortex. 2020 03 14; 30(3):1234-1243. Wiesman AI, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. PMID: 31504270; PMCID: PMC7132912.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    23. A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2020 04; 20(4):233-246. Kuenzi BM, Ideker T. PMID: 32066900; PMCID: PMC7224610.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    24. 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; PMCID: PMC7005711.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    25. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 01 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; PMCID: PMC7030789.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    26. The great hairball gambit. PLoS Genet. 2019 11; 15(11):e1008519. Flint J, Ideker T. PMID: 31770365; PMCID: PMC6910700.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    27. 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; PMCID: PMC6876109.
      View in: PubMed   Mentions: 359     Fields:    Translation:HumansAnimalsCells
    28. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 Oct 23; 9(4):414. Fong SH, Carlin DE, Ozturk K, 2018 UCSD Network Biology Class, Ideker T. PMID: 31647918.
      View in: PubMed   Mentions: 1     Fields:    
    29. 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; PMCID: PMC6728083.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    30. 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; PMCID: PMC6746583.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    31. 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; PMCID: PMC6816465.
      View in: PubMed   Mentions: 43     Fields:    Translation:Humans
    32. 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; PMCID: PMC6541594.
      View in: PubMed   Mentions: 1     Fields:    
    33. 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; PMCID: PMC6537421.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    34. 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; PMCID: PMC6554232.
      View in: PubMed   Mentions: 15  
    35. 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; PMCID: PMC6522544.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    36. Transcriptional responses to DNA damage. DNA Repair (Amst). 2019 07; 79:40-49. Silva E, Ideker T. PMID: 31102970; PMCID: PMC6570417.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    37. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 04 24; 8(4):275-280. Fong SH, Carlin DE, Ozturk K, 2018 UCSD Network Biology Class, Ideker T. PMID: 31022372; PMCID: PMC6764759.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    38. 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; PMCID: PMC6711371.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansAnimalsCells
    39. 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; PMCID: PMC7042149.
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    40. Classifying tumors by supervised network propagation. Bioinformatics. 2019 07; 35(14):2528. Zhang W, Ma J, Ideker T. PMID: 30726869; PMCID: PMC6612840.
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    41. 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; PMCID: PMC7423300.
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    42. A Blueprint for Systems Biology. Clin Chem. 2019 02; 65(2):342-344. Ideker T, Hood L. PMID: 30593465.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    43. 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; PMCID: PMC6265471.
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    44. 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; PMCID: PMC6175900.
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    45. 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; PMCID: PMC6520108.
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    46. 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; PMCID: PMC6138910.
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    47. 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; PMCID: PMC6375299.
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    48. 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; PMCID: PMC6084608.
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    49. Genomic Landscape of Appendiceal Neoplasms. JCO Precis Oncol. 2018; 2. Ang CS, Shen JP, Hardy-Abeloos CJ, Huang JK, Ross JS, Miller VA, Jacobs MT, Chen IL, Xu D, Ali SM, Baumgartner J, Lowy A, Fanta P, Ideker T, Millis SZ, Harismendy O. PMID: 32913983; PMCID: PMC7446344.
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    50. 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; PMCID: PMC6247911.
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    51. Classifying tumors by supervised network propagation. Bioinformatics. 2018 07 01; 34(13):i484-i493. Zhang W, Ma J, Ideker T. PMID: 29949979; PMCID: PMC6022559.
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    52. 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; PMCID: PMC6013757.
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    53. 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; PMCID: PMC6097899.
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    54. 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; PMCID: PMC6483071.
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    55. 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; PMCID: PMC6030464.
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    56. 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; PMCID: PMC5893414.
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    57. 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; PMCID: PMC5920724.
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    58. 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; PMCID: PMC5882547.
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    59. 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.
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    60. 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; PMCID: PMC5819357.
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    61. 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; PMCID: PMC6248454.
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    62. 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; PMCID: PMC6049073.
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    63. 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; PMCID: PMC5777277.
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    64. 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; PMCID: PMC5806628.
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    65. Correcting CRISPR for copy number. Nat Genet. 2017 Nov 29; 49(12):1674-1675. Shen JP, Ideker T. PMID: 29186130.
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    66. 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; PMCID: PMC5679399.
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    67. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun. 2017 11 01; 8(1):1238. Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. PMID: 29089570; PMCID: PMC5663702.
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    68. 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; PMCID: PMC5711564.
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    69. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct; 13(10):e1005771. Ideker T, Nussinov R. PMID: 29023447; PMCID: PMC5638228.
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    70. 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; PMCID: PMC5638226.
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    71. 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; PMCID: PMC5467262.
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    72. 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.
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    73. 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; PMCID: PMC5806050.
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    74. 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; PMCID: PMC5529073.
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    75. 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; PMCID: PMC5584685.
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    76. 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; PMCID: PMC5933448.
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    77. 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; PMCID: PMC5371228.
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    78. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 2017 03 28; 18(1):58. Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD. PMID: 28351383; PMCID: PMC5370462.
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    79. 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; PMCID: PMC5449203.
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    80. 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; PMCID: PMC5462515.
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    81. 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; PMCID: PMC5460679.
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    82. 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; PMCID: PMC5439305.
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    83. 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; PMCID: PMC5070958.
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    84. 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; PMCID: PMC5047191.
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    85. 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; PMCID: PMC5209245.
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    86. 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; PMCID: PMC4947162.
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    87. 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; PMCID: PMC4877764.
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    88. 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; PMCID: PMC4845325.
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    89. 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; PMCID: PMC4995115.
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    90. 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; PMCID: PMC5579720.
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    91. 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; PMCID: PMC4772745.
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    92. 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; PMCID: PMC4767623.
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    93. 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; PMCID: PMC4764585.
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    94. 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; PMCID: PMC4640835.
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    95. 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; PMCID: PMC4742139.
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    96. 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; PMCID: PMC4649937.
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    97. 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; PMCID: PMC5706558.
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    98. 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; PMCID: PMC4841003.
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    99. Molecular networks in context. Nat Biotechnol. 2015 Jul; 33(7):720-1. Gross AM, Ideker T. PMID: 26154012.
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    100. 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; PMCID: PMC4510171.
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    101. 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; PMCID: PMC4477441.
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    102. 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; PMCID: PMC5359018.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    103. Transcriptional repression of IFNβ1 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; PMCID: PMC4558399.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    104. 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; PMCID: PMC4427339.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    105. 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; PMCID: PMC4590607.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    106. 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; PMCID: PMC4373083.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimalsCells
    107. 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; PMCID: PMC5706562.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    108. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. Cancer Genome Atlas Research Network. PMID: 25417114; PMCID: PMC4243044.
      View in: PubMed   Mentions: 1314     Fields:    Translation:Humans
    109. 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; PMCID: PMC4256704.
      View in: PubMed   Mentions: 119     Fields:    Translation:HumansCellsPHPublic Health
    110. 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; PMCID: PMC4469264.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    111. 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; PMCID: PMC4146706.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    112. 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; PMCID: PMC4121818.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    113. 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; PMCID: PMC4288400.
      View in: PubMed   Mentions: 7     Fields:    
    114. 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; PMCID: PMC4133763.
      View in: PubMed   Mentions: 108     Fields:    
    115. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 2014; 3:143. Ono K, Demchak B, Ideker T. PMID: 25520778; PMCID: PMC4264639.
      View in: PubMed   Mentions: 23     Fields:    
    116. 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; PMCID: PMC4058954.
      View in: PubMed   Mentions: 44     Fields:    Translation:Animals
    117. 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; PMCID: PMC4016004.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    118. 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; PMCID: PMC4000195.
      View in: PubMed   Mentions: 68     Fields:    Translation:AnimalsCells
    119. 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; PMCID: PMC4154484.
      View in: PubMed   Mentions: 18     Fields:    
    120. 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; PMCID: PMC4157572.
      View in: PubMed   Mentions: 260     Fields:    Translation:HumansAnimalsCells
    121. 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; PMCID: PMC3897414.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    122. 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; PMCID: PMC4136507.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    123. 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; PMCID: PMC3965056.
      View in: PubMed   Mentions: 8     Fields:    
    124. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. Carter H, Hofree M, Ideker T. PMID: 24238873; PMCID: PMC3866044.
      View in: PubMed   Mentions: 65     Fields:    Translation:Humans
    125. 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; PMCID: PMC4075427.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    126. 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; PMCID: PMC3810086.
      View in: PubMed   Mentions: 282     Fields:    Translation:Humans
    127. 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; PMCID: PMC3940161.
      View in: PubMed   Mentions: 236     Fields:    Translation:Humans
    128. 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; PMCID: PMC3866081.
      View in: PubMed   Mentions: 391     Fields:    Translation:Humans
    129. 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; PMCID: PMC3855057.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    130. 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; PMCID: PMC3679525.
      View in: PubMed   Mentions: 196     Fields:    Translation:AnimalsCells
    131. 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; PMCID: PMC3696746.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    132. 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; PMCID: PMC4142215.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    133. 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; PMCID: PMC3730102.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    134. 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; PMCID: PMC3649990.
      View in: PubMed   Mentions: 46     Fields:    Translation:Humans
    135. 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; PMCID: PMC3563736.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    136. 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; PMCID: PMC3633480.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    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; PMCID: PMC3102020.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansCells
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