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    Jill Mesirov

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0602
    CA La Jolla 92093
    Phone858-534-5096
    vCardDownload vCard

      Collapse Research 
      Collapse Research Activities and Funding
      The Integrative Genomics Viewer (IGV): visualization supporting cancer research
      NIH/NCI U24CA210004Sep 1, 2016 - Aug 31, 2021
      Role: Principal Investigator
      GenePattern Notebooks for Cancer Research
      NIH/NCI U24CA194107Apr 1, 2015 - Mar 31, 2020
      Role: Principal Investigator
      Embryonal Brain Tumor Networks
      NIH/NCI U01CA184898Jul 1, 2014 - May 31, 2019
      Role: Principal Investigator
      GenomeSpace: community web environment for analysis across diverse genomic tools
      NIH/NHGRI U41HG007517Mar 17, 2014 - Feb 28, 2018
      Role: Principal Investigator
      A next-generation Integrative Genomics Viewer for biomedical and cancer research.
      NIH/NCI R01CA157304Jul 1, 2012 - Apr 30, 2016
      Role: Principal Investigator
      MIT-Harvard Center of Cancer Nanotechnology Excellence
      NIH U54CA151884Sep 1, 2010 - Jul 31, 2015
      Role: Co-Investigator
      GenomeSpace: A community web environment for integrative genomic analysis
      NIH/NHGRI P01HG005062Sep 11, 2009 - Jun 30, 2014
      Role: Principal Investigator
      An Integrative Genomics Data Viewer to Support the TCGA Project
      NIH/NCI R21CA135827Sep 12, 2008 - Aug 31, 2011
      Role: Principal Investigator
      Knowledge-based Gene Expression Analysis for Biomedical and Cancer Research
      NIH/NCI R01CA121941Aug 1, 2006 - Apr 30, 2017
      Role: Principal Investigator
      Supporting Integrative Genomic Analysis Users with GenePattern
      NIH/NIGMS R01GM074024Jun 1, 2005 - Nov 30, 2019
      Role: Principal Investigator
      Broad Institute Center for Cancer Systems Biology
      NIH U54CA112962Sep 30, 2004 - Feb 28, 2015
      Role: Co-Investigator
      Genomic Analysis of Medulloblastomas
      NIH/NCI R01CA109467Aug 1, 2004 - May 31, 2016
      Role: Principal Investigator
      GenePattern: Methodologies and Software Tools.
      NIH/NCI R33CA097556Jul 1, 2002 - Jun 30, 2006
      Role: Principal Investigator
      NATIONAL BIOMEDICAL COMPUTATION RESOURCE
      NIH P41RR008605Apr 15, 1994 - Apr 30, 2014
      Role: Co-Investigator
      Cancer Center Support (Core) Grant
      NIH P30CA014051Sep 1, 1975 - Apr 30, 2020
      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.
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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 J, 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.
        View in: PubMed
      2. Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov J. The GenePattern Notebook Environment. Cell Syst. 2017 Aug 23; 5(2):149-151.e1. PMID: 28822753.
        View in: PubMed
      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 J, 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.
        View in: PubMed
      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.
        View in: PubMed
      5. Boulay G, Awad ME, Riggi N, Archer TC, Iyer S, Boonseng WE, Rossetti NE, Naigles B, Rengarajan S, Volorio A, Kim JC, Mesirov J, 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. Silterra J, Gillette MA, Lanaspa M, Pellé KG, Valim C, Ahmad R, Acácio S, Almendinger KD, Tan Y, Madrid L, Alonso PL, Carr SA, Wiegand RC, Bassat Q, Mesirov J, Milner DA, Wirth DF. Transcriptional categorization of the etiology of pneumonia syndrome in pediatric patients in malaria endemic areas. J Infect Dis. 2016 Nov 10. PMID: 27837008.
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      7. Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov J, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 Sep 27; 113(39):10750-8. PMID: 27638202.
        View in: PubMed
      8. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov J, Lander ES, Aiden EL. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst. 2016 Jul; 3(1):99-101. PMID: 27467250.
        View in: PubMed
      9. D'Antonio M, Tamayo P, Mesirov J, 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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      10. Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov J, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 19; 165(5):1267-79. PMID: 27180905.
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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 J, 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 J, 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. Valim C, Ahmad R, Lanaspa M, Tan Y, Acácio S, Gillette MA, Almendinger KD, Milner DA, Madrid L, Pellé K, Harezlak J, Silterra J, Alonso PL, Carr SA, Mesirov J, Wirth DF, Wiegand RC, Bassat Q. Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia. Am J Respir Crit Care Med. 2016 Feb 15; 193(4):448-59. PMID: 26469764.
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      14. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov J, 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 J, 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 J, 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. Papageorgiou A, Rapley J, Mesirov J, 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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      18. 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 J, 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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      19. Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov J. A genomic data viewer for iPad. Genome Biol. 2015; 16(1):46. PMID: 25723152.
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      20. Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov J, Airoldi EM, Burge CB. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. 2015 Jul 15; 31(14):2400-2. PMID: 25617416.
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      21. Van Tyne D, Tan Y, Daily JP, Kamiza S, Seydel K, Taylor T, Mesirov J, Wirth DF, Milner DA. Plasmodium falciparum gene expression measured directly from tissue during human infection. Genome Med. 2014; 6(11):110. PMID: 25520756.
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      22. 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 J, 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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      23. 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 J, 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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      24. Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov J. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014; 3:151. PMID: 25165537.
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      25. 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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      26. Konieczkowski DJ, Johannessen CM, Abudayyeh O, Kim JW, Cooper ZA, Piris A, Frederick DT, Barzily-Rokni M, Straussman R, Haq R, Fisher DE, Mesirov J, 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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      27. Heiman M, Heilbut A, Francardo V, Kulicke R, Fenster RJ, Kolaczyk ED, Mesirov J, Surmeier DJ, Cenci MA, Greengard P. Molecular adaptations of striatal spiny projection neurons during levodopa-induced dyskinesia. Proc Natl Acad Sci U S A. 2014 Mar 25; 111(12):4578-83. PMID: 24599591.
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      28. 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 J, 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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      29. Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov J, 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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      30. Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov J. Compression of structured high-throughput sequencing data. PLoS One. 2013; 8(11):e79871. PMID: 24260313.
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      31. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov J, Polley MY, Kim KY, Tricoli JV, Taylor JM, Shuman DJ, Simon RM, Doroshow JH, Conley BA. Criteria for the use of omics-based predictors in clinical trials. Nature. 2013 Oct 17; 502(7471):317-20. PMID: 24132288.
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      32. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov J, Polley MY, Kim KY, Tricoli JV, Taylor JM, Shuman DJ, Simon RM, Doroshow JH, Conley BA. Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration. BMC Med. 2013; 11:220. PMID: 24228635.
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      33. Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov J, 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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      34. Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov J, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR. GenePattern flow cytometry suite. Source Code Biol Med. 2013; 8(1):14. PMID: 23822732.
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      35. Kolker E, Altintas I, Bourne P, Faris J, Fox G, Frishman D, Geraci C, Hancock W, Lin B, Lancet D, Lisitsa A, Knight R, Martens L, Mesirov J, Özdemir V, Schultes E, Smith T, Snyder M, Srivastava S, Toppo S, Wilmes P. Reproducibility: In praise of open research measures. Nature. 2013 Jun 13; 498(7453):170. PMID: 23765483.
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      36. 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 J, 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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      37. 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 J, 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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      38. 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 J. 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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      39. 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 J, 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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      40. Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov J, Beroukhim R, Kuo CJ, Goessling W, Hahn WC. ß-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell. 2012 Dec 21; 151(7):1457-73. PMID: 23245941.
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      41. Tamayo P, Steinhardt G, Liberzon A, Mesirov J. 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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      42. Ottoboni L, Keenan BT, Tamayo P, Kuchroo M, Mesirov J, 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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      43. Nijhawan D, Zack TI, Ren Y, Strickland MR, Lamothe R, Schumacher SE, Tsherniak A, Besche HC, Rosenbluh J, Shehata S, Cowley GS, Weir BA, Goldberg AL, Mesirov J, Root DE, Bhatia SN, Beroukhim R, Hahn WC. Cancer vulnerabilities unveiled by genomic loss. Cell. 2012 Aug 17; 150(4):842-54. PMID: 22901813.
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      44. Ren Y, Cheung HW, von Maltzhan G, Agrawal A, Cowley GS, Weir BA, Boehm JS, Tamayo P, Karst AM, Liu JF, Hirsch MS, Mesirov J, 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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      45. 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 J, 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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      46. Milner DA, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov J. Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. PLoS One. 2012; 7(7):e40739. PMID: 22815802.
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      47. Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov J, Ge SX. AraPath: a knowledgebase for pathway analysis in Arabidopsis. Bioinformatics. 2012 Sep 1; 28(17):2291-2. PMID: 22760305.
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      48. Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov J, 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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      49. Galili N, Tamayo P, Botvinnik OB, Mesirov J, 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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      50. Thorvaldsdóttir H, Robinson JT, Mesirov J. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013 Mar; 14(2):178-92. PMID: 22517427.
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      51. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov J, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012 Mar 29; 483(7391):603-7. PMID: 22460905.
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      52. 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 J, 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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      53. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov J. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011 Jun 15; 27(12):1739-40. PMID: 21546393.
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      54. 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 J. 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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      55. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov J. Integrative genomics viewer. Nat Biotechnol. 2011 Jan; 29(1):24-6. PMID: 21221095.
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      56. 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 J, 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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      57. 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 J, 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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      61. 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 J, 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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      62. Wirth D, Daily J, Winzeler E, Mesirov J, Regev A. In vivo profiles in malaria are consistent with a novel physiological state. Proc Natl Acad Sci U S A. 2009 Jul 7; 106(27):E70; author reply E71-2. PMID: 19570993.
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      63. 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 J. 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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      64. Fusaro VA, Mani DR, Mesirov J, Carr SA. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009 Feb; 27(2):190-8. PMID: 19169245.
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      66. 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 J, 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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      67. Kuehn H, Liberzon A, Reich M, Mesirov J. Using GenePattern for gene expression analysis. Curr Protoc Bioinformatics. 2008 Jun; Chapter 7:Unit 7.12. PMID: 18551415.
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      68. Mishra PJ, Mishra PJ, Humeniuk R, Medina DJ, Alexe G, Mesirov J, Ganesan S, Glod JW, Banerjee D. Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells. Cancer Res. 2008 Jun 1; 68(11):4331-9. PMID: 18519693.
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      69. Xu L, Shen SS, Hoshida Y, Subramanian A, Ross K, Brunet JP, Wagner SN, Ramaswamy S, Mesirov J, Hynes RO. Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. Mol Cancer Res. 2008 May; 6(5):760-9. PMID: 18505921.
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      70. 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 J, 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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      71. Hoshida Y, Brunet JP, Tamayo P, Golub TR, Mesirov J. Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One. 2007; 2(11):e1195. PMID: 18030330.
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      72. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov J, 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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      73. Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ, Comstock KE, Keller ET, Mesirov J, von Euler H, Kämpe O, Hedhammar A, Lander ES, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet. 2007 Nov; 39(11):1321-8. PMID: 17906626.
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      74. Getz G, Höfling H, Mesirov J, Golub TR, Meyerson M, Tibshirani R, Lander ES. Comment on "The consensus coding sequences of human breast and colorectal cancers". Science. 2007 Sep 14; 317(5844):1500. PMID: 17872428.
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      75. Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov J, Ganesan S, DeLisi C, Bhanot G. Portraits of breast cancer progression. BMC Bioinformatics. 2007; 8:291. PMID: 17683614.
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      76. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov J. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007 Dec 1; 23(23):3251-3. PMID: 17644558.
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      77. Tamayo P, Scanfeld D, Ebert BL, Gillette MA, Roberts CW, Mesirov J. 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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      78. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov J, 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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      79. Gould J, Getz G, Monti S, Reich M, Mesirov J. Comparative gene marker selection suite. Bioinformatics. 2006 Aug 1; 22(15):1924-5. PMID: 16709585.
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      80. Engels R, Yu T, Burge C, Mesirov J, DeCaprio D, Galagan JE. Combo: a whole genome comparative browser. Bioinformatics. 2006 Jul 15; 22(14):1782-3. PMID: 16709588.
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      81. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov J. GenePattern 2.0. Nat Genet. 2006 May; 38(5):500-1. PMID: 16642009.
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      82. Isakoff MS, Sansam CG, Tamayo P, Subramanian A, Evans JA, Fillmore CM, Wang X, Biegel JA, Pomeroy SL, Mesirov J, 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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      83. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov J. 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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      84. Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov J, Satoh N, Satou Y, Nusbaum C, Birren B, Galagan JE, Lander ES. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 2005 Aug; 15(8):1127-35. PMID: 16077012.
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      85. Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov J. GeneCruiser: a web service for the annotation of microarray data. Bioinformatics. 2005 Sep 15; 21(18):3681-2. PMID: 16030072.
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      86. Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet. 2005 Jan; 37(1):48-55. PMID: 15608639.
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      87. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigó R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quétier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004 Oct 21; 431(7011):946-57. PMID: 15496914.
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      88. Mikkelsen TS, Galagan JE, Mesirov J. Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics. 2005 Feb 15; 21(4):464-70. PMID: 15374867.
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      89. Brunet JP, Tamayo P, Golub TR, Mesirov J. 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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      90. Reich M, Ohm K, Angelo M, Tamayo P, Mesirov J. GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics. 2004 Jul 22; 20(11):1797-8. PMID: 14988123.
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      91. 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 J, 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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      92. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov J, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003 Jan; 13(1):91-6. PMID: 12529310.
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      93. Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub TR, Mesirov J. Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol. 2003; 10(2):119-42. PMID: 12804087.
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      94. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5; 420(6915):520-62. PMID: 12466850.
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      95. 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 J, 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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      96. 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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      97. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov J, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002 Jan; 12(1):177-89. PMID: 11779843.
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      98. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov J, 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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      99. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov J, 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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      101. 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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      102. Batzoglou S, Pachter L, Mesirov J, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000 Jul; 10(7):950-8. PMID: 10899144.
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      103. Batzoglou S, Berger B, Mesirov J, Lander ES. Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Res. 1999 Dec; 9(12):1163-74. PMID: 10613838.
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      104. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov J, 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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      105. 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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