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    Pablo Tamayo

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0658
    CA La Jolla 92093
    Phone858-246-2385
    vCardDownload vCard

      Collapse Research 
      Collapse Research Activities and Funding
      Next-generation Functional Genetic Screening of Un-screenable Traits
      NIH/NHGRI R01HG009285Aug 25, 2017 - Jul 31, 2021
      Role: Co-Principal Investigator
      Molecular Signatures to Characterize the Oncogenic State of Individual Tumors
      NIH/NCI R01CA154480Jul 1, 2011 - Apr 30, 2016
      Role: Principal 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.
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      1. Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 Aug 23; 5(2):105-118.e9. PMID: 28837809.
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      2. Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP. The GenePattern Notebook Environment. Cell Syst. 2017 Aug 23; 5(2):149-151.e1. PMID: 28822753.
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      3. Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 Jul 27; 547(7664):453-457. PMID: 28678785.
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      4. Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA. Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 Sep; 7(9):973-983. PMID: 28515055.
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      5. Boulay G, Awad ME, Riggi N, Archer TC, Iyer S, Boonseng WE, Rossetti NE, Naigles B, Rengarajan S, Volorio A, Kim JC, Mesirov JP, Tamayo P, Pomeroy SL, Aryee MJ, Rivera MN. OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma. Cancer Discov. 2017 Feb 17. PMID: 28213356.
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      6. Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in ß-Catenin-Active Cancers. Cell Syst. 2016 Sep 28; 3(3):302-316.e4. PMID: 27684187.
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      7. Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell. 2016 Aug 8; 30(2):214-28. PMID: 27478040.
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      8. D'Antonio M, Tamayo P, Mesirov JP, Frazer KA. Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels. Cell Rep. 2016 Jul 19; 16(3):672-83. PMID: 27373164.
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      9. Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov. 2016 Jul; 6(7):714-26. PMID: 27147599.
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      10. Yard BD, Adams DJ, Chie EK, Tamayo P, Battaglia JS, Gopal P, Rogacki K, Pearson BE, Phillips J, Raymond DP, Pennell NA, Almeida F, Cheah JH, Clemons PA, Shamji A, Peacock CD, Schreiber SL, Hammerman PS, Abazeed ME. A genetic basis for the variation in the vulnerability of cancer to DNA damage. Nat Commun. 2016; 7:11428. PMID: 27109210.
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      11. Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P. Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 May; 34(5):539-46. PMID: 27088724.
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      12. Hanaford AR, Archer TC, Price A, Kahlert UD, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA, Dancík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees MG, Shamji A, Schreiber S, Fraenkel E, Pomeroy SL, Mesirov JP, Tamayo P, Eberhart CG, Raabe EH. DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets. Clin Cancer Res. 2016 Aug 1; 22(15):3903-14. PMID: 27012813.
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      13. Yu C, Mannan AM, Yvone GM, Ross KN, Zhang YL, Marton MA, Taylor BR, Crenshaw A, Gould JZ, Tamayo P, Weir BA, Tsherniak A, Wong B, Garraway LA, Shamji AF, Palmer MA, Foley MA, Winckler W, Schreiber SL, Kung AL, Golub TR. High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Nat Biotechnol. 2016 Apr; 34(4):419-23. PMID: 26928769.
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      14. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19; 44(1):194-206. PMID: 26795250.
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      15. Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015 Dec 23; 1(6):417-425. PMID: 26771021.
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      16. Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME. Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron. 2016 Jan 6; 89(1):100-12. PMID: 26711116.
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      17. Stewart ML, Tamayo P, Wilson AJ, Wang S, Chang YM, Kim JW, Khabele D, Shamji AF, Schreiber SL. KRAS Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine. Cancer Res. 2015 Jul 15; 75(14):2897-906. PMID: 25968887.
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      18. Papageorgiou A, Rapley J, Mesirov JP, Tamayo P, Avruch J. A Genome-Wide siRNA Screen in Mammalian Cells for Regulators of S6 Phosphorylation. PLoS One. 2015; 10(3):e0116096. PMID: 25790369.
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      19. Wilson FH, Johannessen CM, Piccioni F, Tamayo P, Kim JW, Van Allen EM, Corsello SM, Capelletti M, Calles A, Butaney M, Sharifnia T, Gabriel SB, Mesirov JP, Hahn WC, Engelman JA, Meyerson M, Root DE, Jänne PA, Garraway LA. A Functional Landscape of Resistance to ALK Inhibition in Lung Cancer. Cancer Cell. 2015 Mar 9; 27(3):397-408. PMID: 25759024.
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      20. Barbie TU, Alexe G, Aref AR, Li S, Zhu Z, Zhang X, Imamura Y, Thai TC, Huang Y, Bowden M, Herndon J, Cohoon TJ, Fleming T, Tamayo P, Mesirov JP, Ogino S, Wong KK, Ellis MJ, Hahn WC, Barbie DA, Gillanders WE. Targeting an IKBKE cytokine network impairs triple-negative breast cancer growth. J Clin Invest. 2014 Dec 1; 124(12):5411-23. PMID: 25365225.
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      21. Tamayo P, Montes C, Perez ME, Martin E, García-Talavera JR. A novel, fully automated, observer-independent program for semiquantifying striatal ¹²³I-FP-CIT uptake. Rev Esp Med Nucl Imagen Mol. 2015 Mar-Apr; 34(2):89-94. PMID: 25304848.
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      22. Cowley GS, Weir BA, Vazquez F, Tamayo P, Scott JA, Rusin S, East-Seletsky A, Ali LD, Gerath WF, Pantel SE, Lizotte PH, Jiang G, Hsiao J, Tsherniak A, Dwinell E, Aoyama S, Okamoto M, Harrington W, Gelfand E, Green TM, Tomko MJ, Gopal S, Wong TC, Li H, Howell S, Stransky N, Liefeld T, Jang D, Bistline J, Hill Meyers B, Armstrong SA, Anderson KC, Stegmaier K, Reich M, Pellman D, Boehm JS, Mesirov JP, Golub TR, Root DE, Hahn WC. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci Data. 2014; 1:140035. PMID: 25984343.
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      23. Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One. 2014; 9(7):e100334. PMID: 24983991.
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      24. Konieczkowski DJ, Johannessen CM, Abudayyeh O, Kim JW, Cooper ZA, Piris A, Frederick DT, Barzily-Rokni M, Straussman R, Haq R, Fisher DE, Mesirov JP, Hahn WC, Flaherty KT, Wargo JA, Tamayo P, Garraway LA. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 2014 Jul; 4(7):816-27. PMID: 24771846.
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      25. Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC, Reibel JB, Tamayo P, Godfrey JT, Qian ZR, Page AN, Maciag K, Chan EM, Silkworth W, Labowsky MT, Rozhansky L, Mesirov JP, Gillanders WE, Ogino S, Hacohen N, Gaudet S, Eck MJ, Engelman JA, Corcoran RB, Wong KK, Hahn WC, Barbie DA. Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Cancer Discov. 2014 Apr; 4(4):452-65. PMID: 24444711.
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      26. Li L, Shen C, Nakamura E, Ando K, Signoretti S, Beroukhim R, Cowley GS, Lizotte P, Liberzon E, Bair S, Root DE, Tamayo P, Tsherniak A, Cheng SC, Tabak B, Jacobsen A, Hakimi AA, Schultz N, Ciriello G, Sander C, Hsieh JJ, Kaelin WG. SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell. 2013 Dec 9; 24(6):738-50. PMID: 24332042.
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      27. Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN. Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol. 2014 Jan; 44(1):285-95. PMID: 24136404.
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      28. Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Integrative radiogenomic profiling of squamous cell lung cancer. Cancer Res. 2013 Oct 15; 73(20):6289-98. PMID: 23980093.
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      29. Hagerstrand D, Tong A, Schumacher SE, Ilic N, Shen RR, Cheung HW, Vazquez F, Shrestha Y, Kim SY, Giacomelli AO, Rosenbluh J, Schinzel AC, Spardy NA, Barbie DA, Mermel CH, Weir BA, Garraway LA, Tamayo P, Mesirov JP, Beroukhim R, Hahn WC. Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Cancer Discov. 2013 Sep; 3(9):1044-57. PMID: 23764425.
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      30. Raeder MB, Birkeland E, Trovik J, Krakstad C, Shehata S, Schumacher S, Zack TI, Krohn A, Werner HM, Moody SE, Wik E, Stefansson IM, Holst F, Oyan AM, Tamayo P, Mesirov JP, Kalland KH, Akslen LA, Simon R, Beroukhim R, Salvesen HB. Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. PLoS One. 2013; 8(2):e54873. PMID: 23393560.
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      31. Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013 Apr; 23(4):665-78. PMID: 23269662.
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      32. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan 2; 123(1):517-25. PMID: 23257362.
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      33. Quayle SN, Chheda MG, Shukla SA, Wiedemeyer R, Tamayo P, Dewan RW, Zhuang L, Huang-Hobbs E, Haidar S, Xiao Y, Ligon KL, Hahn WC, Chin L. Integrative functional genomics identifies RINT1 as a novel GBM oncogene. Neuro Oncol. 2012 Nov; 14(11):1325-31. PMID: 23074196.
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      34. Tamayo P, Steinhardt G, Liberzon A, Mesirov JP. The limitations of simple gene set enrichment analysis assuming gene independence. Stat Methods Med Res. 2016 Feb; 25(1):472-87. PMID: 23070592.
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      35. Ottoboni L, Keenan BT, Tamayo P, Kuchroo M, Mesirov JP, Buckle GJ, Khoury SJ, Hafler DA, Weiner HL, De Jager PL. An RNA profile identifies two subsets of multiple sclerosis patients differing in disease activity. Sci Transl Med. 2012 Sep 26; 4(153):153ra131. PMID: 23019656.
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      36. Ren Y, Cheung HW, von Maltzhan G, Agrawal A, Cowley GS, Weir BA, Boehm JS, Tamayo P, Karst AM, Liu JF, Hirsch MS, Mesirov JP, Drapkin R, Root DE, Lo J, Fogal V, Ruoslahti E, Hahn WC, Bhatia SN. Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4. Sci Transl Med. 2012 Aug 15; 4(147):147ra112. PMID: 22896676.
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      37. Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, Carneiro MO, Carter SL, Cibulskis K, Erlich RL, Greulich H, Lawrence MS, Lennon NJ, McKenna A, Meldrim J, Ramos AH, Ross MG, Russ C, Shefler E, Sivachenko A, Sogoloff B, Stojanov P, Tamayo P, Mesirov JP, Amani V, Teider N, Sengupta S, Francois JP, Northcott PA, Taylor MD, Yu F, Crabtree GR, Kautzman AG, Gabriel SB, Getz G, Jäger N, Jones DT, Lichter P, Pfister SM, Roberts TM, Meyerson M, Pomeroy SL, Cho YJ. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature. 2012 Aug 2; 488(7409):106-10. PMID: 22820256.
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      38. Tran PT, Shroff EH, Burns TF, Thiyagarajan S, Das ST, Zabuawala T, Chen J, Cho YJ, Luong R, Tamayo P, Salih T, Aziz K, Adam SJ, Vicent S, Nielsen CH, Withofs N, Sweet-Cordero A, Gambhir SS, Rudin CM, Felsher DW. Twist1 suppresses senescence programs and thereby accelerates and maintains mutant Kras-induced lung tumorigenesis. PLoS Genet. 2012; 8(5):e1002650. PMID: 22654667.
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      39. Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root DE, Garraway LA, Sabatini DM. MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma. Sci Signal. 2012; 5(224):rs4. PMID: 22589389.
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      40. McKenna ES, Tamayo P, Cho YJ, Tillman EJ, Mora-Blanco EL, Sansam CG, Koellhoffer EC, Pomeroy SL, Roberts CW. Epigenetic inactivation of the tumor suppressor BIN1 drives proliferation of SNF5-deficient tumors. Cell Cycle. 2012 May 15; 11(10):1956-65. PMID: 22544318.
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      41. Galili N, Tamayo P, Botvinnik OB, Mesirov JP, Brooks MR, Brown G, Raza A. Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome. J Hematol Oncol. 2012; 5:20. PMID: 22559819.
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      42. Cheung HW, Cowley GS, Weir BA, Boehm JS, Rusin S, Scott JA, East A, Ali LD, Lizotte PH, Wong TC, Jiang G, Hsiao J, Mermel CH, Getz G, Barretina J, Gopal S, Tamayo P, Gould J, Tsherniak A, Stransky N, Luo B, Ren Y, Drapkin R, Bhatia SN, Mesirov JP, Garraway LA, Meyerson M, Lander ES, Root DE, Hahn WC. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc Natl Acad Sci U S A. 2011 Jul 26; 108(30):12372-7. PMID: 21746896.
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      43. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011 Jun 15; 27(12):1739-40. PMID: 21546393.
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      44. Tamayo P, Cho YJ, Tsherniak A, Greulich H, Ambrogio L, Schouten-van Meeteren N, Zhou T, Buxton A, Kool M, Meyerson M, Pomeroy SL, Mesirov JP. Predicting relapse in patients with medulloblastoma by integrating evidence from clinical and genomic features. J Clin Oncol. 2011 Apr 10; 29(11):1415-23. PMID: 21357789.
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      45. Cho YJ, Tsherniak A, Tamayo P, Santagata S, Ligon A, Greulich H, Berhoukim R, Amani V, Goumnerova L, Eberhart CG, Lau CC, Olson JM, Gilbertson RJ, Gajjar A, Delattre O, Kool M, Ligon K, Meyerson M, Mesirov JP, Pomeroy SL. Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J Clin Oncol. 2011 Apr 10; 29(11):1424-30. PMID: 21098324.
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      46. Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PT, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CW, Dorsch M. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33. PMID: 21076395.
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      47. Wolfer A, Wittner BS, Irimia D, Flavin RJ, Lupien M, Gunawardane RN, Meyer CA, Lightcap ES, Tamayo P, Mesirov JP, Liu XS, Shioda T, Toner M, Loda M, Brown M, Brugge JS, Ramaswamy S. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703. PMID: 20133671.
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      48. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010 Jan 19; 17(1):98-110. PMID: 20129251.
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      49. Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P, Meylan E, Scholl C, Fröhling S, Chan EM, Sos ML, Michel K, Mermel C, Silver SJ, Weir BA, Reiling JH, Sheng Q, Gupta PB, Wadlow RC, Le H, Hoersch S, Wittner BS, Ramaswamy S, Livingston DM, Sabatini DM, Meyerson M, Thomas RK, Lander ES, Mesirov JP, Root DE, Gilliland DG, Jacks T, Hahn WC. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009 Nov 5; 462(7269):108-12. PMID: 19847166.
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      50. Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Jr UR, Marie SK, Dahl O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer DG, Rustgi AK, Meyerson M. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet. 2009 Nov; 41(11):1238-42. PMID: 19801978.
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      51. Scholl C, Fröhling S, Dunn IF, Schinzel AC, Barbie DA, Kim SY, Silver SJ, Tamayo P, Wadlow RC, Ramaswamy S, Döhner K, Bullinger L, Sandy P, Boehm JS, Root DE, Jacks T, Hahn WC, Gilliland DG. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell. 2009 May 29; 137(5):821-34. PMID: 19490892.
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      52. Pyne S, Hu X, Wang K, Rossin E, Lin TI, Maier LM, Baecher-Allan C, McLachlan GJ, Tamayo P, Hafler DA, De Jager PL, Mesirov JP. Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci U S A. 2009 May 26; 106(21):8519-24. PMID: 19443687.
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      53. Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature. 2008 Sep 25; 455(7212):547-51. PMID: 18794900.
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      54. De Jager PL, Rossin E, Pyne S, Tamayo P, Ottoboni L, Viglietta V, Weiner M, Soler D, Izmailova E, Faron-Yowe L, O'Brien C, Freeman S, Granados S, Parker A, Roubenoff R, Mesirov JP, Khoury SJ, Hafler DA, Weiner HL. Cytometric profiling in multiple sclerosis uncovers patient population structure and a reduction of CD8low cells. Brain. 2008 Jul; 131(Pt 7):1701-11. PMID: 18567923.
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      55. Ebert BL, Galili N, Tamayo P, Bosco J, Mak R, Pretz J, Tanguturi S, Ladd-Acosta C, Stone R, Golub TR, Raza A. An erythroid differentiation signature predicts response to lenalidomide in myelodysplastic syndrome. PLoS Med. 2008 Feb; 5(2):e35. PMID: 18271621.
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      56. Ebert BL, Pretz J, Bosco J, Chang CY, Tamayo P, Galili N, Raza A, Root DE, Attar E, Ellis SR, Golub TR. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature. 2008 Jan 17; 451(7176):335-9. PMID: 18202658.
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      57. Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir O, Wypij D, Levasseur K, Thomas E, Tamayo P, Dong C, Zhou Y, Lander ES, Ndiaye D, Wirth D, Winzeler EA, Mesirov JP, Regev A. Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature. 2007 Dec 13; 450(7172):1091-5. PMID: 18046333.
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      58. Hoshida Y, Brunet JP, Tamayo P, Golub TR, Mesirov JP. Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One. 2007; 2(11):e1195. PMID: 18030330.
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      59. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G. High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res. 2007 Nov 15; 67(22):10669-76. PMID: 18006808.
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      60. Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G. Portraits of breast cancer progression. BMC Bioinformatics. 2007; 8:291. PMID: 17683614.
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      61. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007 Dec 1; 23(23):3251-3. PMID: 17644558.
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      62. Tamayo P, Scanfeld D, Ebert BL, Gillette MA, Roberts CW, Mesirov JP. Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc Natl Acad Sci U S A. 2007 Apr 3; 104(14):5959-64. PMID: 17389406.
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      63. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, Delisi C, Bhanot G. Breast cancer stratification from analysis of micro-array data of micro-dissected specimens. Genome Inform. 2007; 18:130-40. PMID: 18546481.
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      64. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet. 2006 May; 38(5):500-1. PMID: 16642009.
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      65. Isakoff MS, Sansam CG, Tamayo P, Subramanian A, Evans JA, Fillmore CM, Wang X, Biegel JA, Pomeroy SL, Mesirov JP, Roberts CW. Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation. Proc Natl Acad Sci U S A. 2005 Dec 6; 102(49):17745-50. PMID: 16301525.
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      66. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25; 102(43):15545-50. PMID: 16199517.
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      67. Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP. GeneCruiser: a web service for the annotation of microarray data. Bioinformatics. 2005 Sep 15; 21(18):3681-2. PMID: 16030072.
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      68. Brunet JP, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A. 2004 Mar 23; 101(12):4164-9. PMID: 15016911.
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      69. Reich M, Ohm K, Angelo M, Tamayo P, Mesirov JP. GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics. 2004 Jul 22; 20(11):1797-8. PMID: 14988123.
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      70. Fernandez-Teijeiro A, Betensky RA, Sturla LM, Kim JY, Tamayo P, Pomeroy SL. Combining gene expression profiles and clinical parameters for risk stratification in medulloblastomas. J Clin Oncol. 2004 Mar 15; 22(6):994-8. PMID: 14970184.
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      71. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003 Jul; 34(3):267-73. PMID: 12808457.
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      72. Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, Ladd C, Pohl U, Hartmann C, McLaughlin ME, Batchelor TT, Black PM, von Deimling A, Pomeroy SL, Golub TR, Louis DN. Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res. 2003 Apr 1; 63(7):1602-7. PMID: 12670911.
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      73. Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub TR, Mesirov JP. Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol. 2003; 10(2):119-42. PMID: 12804087.
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      74. Antipova AA, Tamayo P, Golub TR. A strategy for oligonucleotide microarray probe reduction. Genome Biol. 2002; 3(12):RESEARCH0073. PMID: 12537562.
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      75. Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell. 2002 Mar; 1(2):203-9. PMID: 12086878.
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      76. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002 Jan 24; 415(6870):436-42. PMID: 11807556.
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      77. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. 2002 Jan; 8(1):68-74. PMID: 11786909.
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      78. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A. 2001 Dec 18; 98(26):15149-54. PMID: 11742071.
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      79. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A. 2001 Sep 11; 98(19):10787-92. PMID: 11553813.
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      80. Ellisen LW, Palmer RE, Maki RG, Truong VB, Tamayo P, Oliner JD, Haber DA. Cascades of transcriptional induction during human lymphocyte activation. Eur J Cell Biol. 2001 May; 80(5):321-8. PMID: 11432721.
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      81. Yeang CH, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, Reich M, Lander E, Mesirov J, Golub T. Molecular classification of multiple tumor types. Bioinformatics. 2001; 17 Suppl 1:S316-22. PMID: 11473023.
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      82. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):12182-6. PMID: 11027309.
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      83. Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, Golub TR. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci U S A. 2000 Mar 28; 97(7):3260-5. PMID: 10737792.
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      84. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999 Oct 15; 286(5439):531-7. PMID: 10521349.
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      85. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999 Mar 16; 96(6):2907-12. PMID: 10077610.
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