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Jill Mesirov

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

    Collapse Research 
    Collapse Research Activities and Funding
    Supporting and evolving Gene Set Enrichment Analysis and the Molecular Signatures Database for cancer research
    NIH/NCI U24CA220341May 1, 2018 - Apr 30, 2023
    Role: Principal Investigator
    A Rational Systematic Approach to Find Combinations of Pharmacologic and Immune Therapies that Target Identifiable Oncogenic States
    NIH/NCI U01CA217885Sep 12, 2017 - Jul 31, 2022
    Role: Co-Principal Investigator
    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, 2020
    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. Archer TC, Ehrenberger T, Mundt F, Gold MP, Krug K, Mah CK, Mahoney EL, Daniel CJ, LeNail A, Ramamoorthy D, Mertins P, Mani DR, Zhang H, Gillette MA, Clauser K, Noble M, Tang LC, Pierre-François J, Silterra J, Jensen J, Tamayo P, Korshunov A, Pfister SM, Kool M, Northcott PA, Sears RC, Lipton JO, Carr SA, Mesirov JP, Pomeroy SL, Fraenkel E. Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2018 Sep 10; 34(3):396-410.e8. PMID: 30205044.
      View in: PubMed
    2. Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. GeNets: a unified web platform for network-based genomic analyses. Nat Methods. 2018 Jun 18. PMID: 29915188.
      View in: PubMed
    3. Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst. 2018 Feb 28; 6(2):256-258.e1. PMID: 29428417.
      View in: PubMed
    4. Hachigian LJ, Carmona V, Fenster RJ, Kulicke R, Heilbut A, Sittler A, Pereira de Almeida L, Mesirov JP, Gao F, Kolaczyk ED, Heiman M. Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2. Cell Rep. 2017 Dec 05; 21(10):2688-2695. PMID: 29212017.
      View in: PubMed
    5. Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant Review with the Integrative Genomics Viewer. Cancer Res. 2017 11 01; 77(21):e31-e34. PMID: 29092934.
      View in: PubMed
    6. 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.
      View in: PubMed
    7. 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.
      View in: PubMed
    8. 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 07 27; 547(7664):453-457. PMID: 28678785.
      View in: PubMed
    9. Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017; 6:784. PMID: 29487738.
      View in: PubMed
    10. 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 09; 7(9):973-983. PMID: 28515055.
      View in: PubMed
    11. 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 03; 7(3):288-301. PMID: 28213356.
      View in: PubMed
    12. 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 JP, Milner DA, Wirth DF. Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis. 2017 Jan 15; 215(2):312-320. PMID: 27837008.
      View in: PubMed
    13. Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 09 27; 113(39):10750-8. PMID: 27638202.
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    14. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, 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
    15. 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 07 19; 16(3):672-83. PMID: 27373164; PMCID: PMC4972030.
    16. Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 19; 165(5):1267-1279. PMID: 27180905.
      View in: PubMed
    17. 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 05; 34(5):539-46. PMID: 27088724.
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    18. 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 01; 22(15):3903-14. PMID: 27012813.
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    19. 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 JP, 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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    20. Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar; 13(3):245-247. PMID: 26780094; PMCID: PMC4767623.
    21. 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.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. 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 06; 89(1):100-12. PMID: 26711116; PMCID: PMC4707072 [Available on 01/06/17].
    24. Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res. 2015; 4:167. PMID: 26594333; PMCID: PMC4648224.
    25. 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; PMCID: PMC4366019.
    26. 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 09; 27(3):397-408. PMID: 25759024; PMCID: PMC4398996.
    27. Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov JP. A genomic data viewer for iPad. Genome Biol. 2015 Feb 26; 16:46. PMID: 25723152; PMCID: PMC4342165.
    28. Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. 2015 Jul 15; 31(14):2400-2. PMID: 25617416; PMCID: PMC4542614.
    29. Van Tyne D, Tan Y, Daily JP, Kamiza S, Seydel K, Taylor T, Mesirov JP, Wirth DF, Milner DA. Plasmodium falciparum gene expression measured directly from tissue during human infection. Genome Med. 2014; 6(11):110. PMID: 25520756; PMCID: PMC4269068.
    30. 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; 124(12):5411-23. PMID: 25365225; PMCID: PMC4348940.
    31. 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, 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; PMCID: PMC4432652.
    32. Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014; 3:151. PMID: 25165537.
      View in: PubMed
    33. 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; PMCID: PMC4077578.
    34. 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; PMCID: PMC4154497.
    35. Heiman M, Heilbut A, Francardo V, Kulicke R, Fenster RJ, Kolaczyk ED, Mesirov JP, 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; PMCID: PMC3970487.
    36. 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; PMCID: PMC3980023.
    37. 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; PMCID: PMC3973429.
    38. Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov JP. Compression of structured high-throughput sequencing data. PLoS One. 2013; 8(11):e79871. PMID: 24260313; PMCID: PMC3832420.
    39. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, 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 Oct 17; 11:220. PMID: 24228635; PMCID: PMC3852338.
    40. McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, 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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    41. 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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    42. Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR. GenePattern flow cytometry suite. Source Code Biol Med. 2013 Jul 03; 8(1):14. PMID: 23822732; PMCID: PMC3717030.
    43. 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; PMCID: PMC3770815.
    44. 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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    45. 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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    46. 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; PMCID: PMC3613583.
    47. 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; 123(1):517-25. PMID: 23257362.
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    48. 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 JP, 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; PMCID: PMC3530160.
    49. 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; PMCID: PMC3758419 [Available on 02/01/17].
    50. 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; PMCID: PMC3753678.
    51. 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 JP, Root DE, Bhatia SN, Beroukhim R, Hahn WC. Cancer vulnerabilities unveiled by genomic loss. Cell. 2012 Aug 17; 150(4):842-54. PMID: 22901813; PMCID: PMC3429351.
    52. 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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    53. 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 02; 488(7409):106-10. PMID: 22820256; PMCID: PMC3413789.
    54. Milner DA, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP. 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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    55. Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX. AraPath: a knowledgebase for pathway analysis in Arabidopsis. Bioinformatics. 2012 Sep 01; 28(17):2291-2. PMID: 22760305.
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    56. 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 May 15; 5(224):rs4. PMID: 22589389.
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    57. 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 May 06; 5:20. PMID: 22559819.
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    58. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013 Mar; 14(2):178-92. PMID: 22517427; PMCID: PMC3603213.
    59. 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 JP, 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 28; 483(7391):603-7. PMID: 22460905; PMCID: PMC3320027.
    60. 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; PMCID: PMC3145679.
    61. 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; PMCID: PMC3106198.
    62. 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; PMCID: PMC3082982.
    63. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011 Jan; 29(1):24-6. PMID: 21221095; PMCID: PMC3346182.
    64. 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; PMCID: PMC3082983.
    65. 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; PMCID: PMC3859448.
    66. 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; PMCID: PMC2840447.
    67. Mesirov JP. Computer science. Accessible reproducible research. Science. 2010 Jan 22; 327(5964):415-6. PMID: 20093459; PMCID: PMC3878063.
    68. 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; PMCID: PMC2818769.
    69. 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 05; 462(7269):108-12. PMID: 19847166; PMCID: PMC2783335.
    70. Wirth D, Daily J, Winzeler E, Mesirov JP, Regev A. In vivo profiles in malaria are consistent with a novel physiological state. Proc Natl Acad Sci U S A. 2009 Jul 07; 106(27):E70; author reply E71-2. PMID: 19570993; PMCID: PMC2708753.
    71. 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; PMCID: PMC2682540.
    72. Fusaro VA, Mani DR, Mesirov JP, Carr SA. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009 Feb; 27(2):190-8. PMID: 19169245; PMCID: PMC2753399.
    73. Linial M, Mesirov JP, Morrison McKay BJ, Rost B. ISMB 2008 Toronto. PLoS Comput Biol. 2008 Jun 27; 4(6):e1000094. PMID: 18584023; PMCID: PMC2427177.
    74. 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; PMCID: PMC2730047.
    75. Mishra PJ, Mishra PJ, Humeniuk R, Medina DJ, Alexe G, Mesirov JP, Ganesan S, Glod JW, Banerjee D. Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells. Cancer Res. 2008 Jun 01; 68(11):4331-9. PMID: 18519693; PMCID: PMC2725025.
    76. Kuehn H, Liberzon A, Reich M, Mesirov JP. Using GenePattern for gene expression analysis. Curr Protoc Bioinformatics. 2008 Jun; Chapter 7:Unit 7.12. PMID: 18551415; PMCID: PMC3893799.
    77. Xu L, Shen SS, Hoshida Y, Subramanian A, Ross K, Brunet JP, Wagner SN, Ramaswamy S, Mesirov JP, 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; PMCID: PMC2756991.
    78. 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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    79. Hoshida Y, Brunet JP, Tamayo P, Golub TR, Mesirov JP. Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One. 2007 Nov 21; 2(11):e1195. PMID: 18030330; PMCID: PMC2065909.
    80. 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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    81. 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 JP, 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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    82. Getz G, Höfling H, Mesirov JP, 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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    83. Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G. Portraits of breast cancer progression. BMC Bioinformatics. 2007 Aug 06; 8:291. PMID: 17683614; PMCID: PMC1978212.
    84. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007 Dec 01; 23(23):3251-3. PMID: 17644558.
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    85. 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 03; 104(14):5959-64. PMID: 17389406; PMCID: PMC1838404.
    86. 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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    87. Engels R, Yu T, Burge C, Mesirov JP, DeCaprio D, Galagan JE. Combo: a whole genome comparative browser. Bioinformatics. 2006 Jul 15; 22(14):1782-3. PMID: 16709588.
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    88. Gould J, Getz G, Monti S, Reich M, Mesirov JP. Comparative gene marker selection suite. Bioinformatics. 2006 Aug 01; 22(15):1924-5. PMID: 16709585.
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    89. 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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    90. 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 06; 102(49):17745-50. PMID: 16301525; PMCID: PMC1308926.
    91. 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; PMCID: PMC1239896.
    92. Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, 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; PMCID: PMC1182225.
    93. 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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    94. 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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    95. 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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    96. Mikkelsen TS, Galagan JE, Mesirov JP. Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics. 2005 Feb 15; 21(4):464-70. PMID: 15374867.
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    97. 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; PMCID: PMC384712.
    98. 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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    99. 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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    100. 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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    101. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003 Jan; 13(1):91-6. PMID: 12529310; PMCID: PMC430950.
    102. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. PMID: 12466850.
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    103. 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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    104. 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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    105. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002 Jan; 12(1):177-89. PMID: 11779843; PMCID: PMC155255.
    106. 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; PMCID: PMC64998.
    107. 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; PMCID: PMC58553.
    108. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921. PMID: 11237011.
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    109. 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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    110. Batzoglou S, Pachter L, Mesirov JP, 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; PMCID: PMC310911.
    111. 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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    112. 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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    113. 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; PMCID: PMC15868.
    114. Zhang X, Mesirov JP, Waltz DL. Hybrid system for protein secondary structure prediction. J Mol Biol. 1992 Jun 20; 225(4):1049-63. PMID: 1613789.
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