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Phase IB/II Trial with Correlative Analyses of Doxorubicin plus Durvalumab Combination in Patients with Advanced Soft Tissue Sarcoma. Clin Cancer Res. 2026 Feb 06. Yun KH, Sim NS, Shin SJ, Lee YH, Baek W, Han YD, Park JW, Kim SK, Cho I, Jung I, Mesirov JP, Rha SY, Choi SH, Yoon HI, Kim SH, Kim HS. PMID: 41649866.
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igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. bioRxiv. 2025 Nov 10. Robinson JT, Thorvaldsdottir H, Mesirov JP. PMID: 41278691; PMCID: PMC12636309.
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Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing. bioRxiv. 2025 Oct 02. Eisemann T, Masihi MB, Tzaridis T, Pister V, Youm I, Chambers KR, Dutta A, Wenzel AT, Chin K, Pomeroy SL, Mesirov JP, Fraenkel E, Bagchi A, Chavez L, Wechsler-Reya RJ. PMID: 41256535; PMCID: PMC12621956.
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Extrachromosomal DNA associates with poor survival across a broad spectrum of childhood solid tumors. medRxiv. 2025 Aug 07. Chapman OS, Sridhar S, Chow EY, Kenkre R, Kirkland J, Dutta A, Wang S, Zhang W, Brown M, Luebeck J, Lo YY, Rodriguez-Fos E, Henssen AG, Okonechnikov K, Ghasemi DR, Pajtler KW, Kawauchi D, Bafna V, Paul M, Yip K, Mesirov JP, Chavez L. PMID: 40778132; PMCID: PMC12330472.
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A Systematic Review with a Demonstrative Case of KIT and DOG-1 Expressing Gastrointestinal Stromal Tumors Harboring ETV6-NTRK3 Fusions. Clin Cancer Res. 2025 May 15; 31(10):2056-2061. Ranjbarian T, Antkowiak M, Mallory RJ, Doherty TM, Hosseini M, Mesirov JP, Fanta PT, Sicklick JK. PMID: 39992648; PMCID: PMC12081180.
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Inactivation of Histone Chaperone HIRA Unmasks a Link Between Normal Embryonic Development of Melanoblasts and Maintenance of Adult Melanocyte Stem Cells. Aging Cell. 2025 Jul; 24(7):e70070. Jaber-Hijazi F, Arnold R, Swaminathan K, Gilroy K, Wenzel AT, Lagnado A, Kirschner K, Robertson N, Reid C, Fullarton N, Pawlikowski J, Rai TS, Baranyk I, Shi CH, Yip KY, Blyth K, Mesirov JP, Harris ML, Passos JF, Machesky LM, Adams PD. PMID: 40669469; PMCID: PMC12266762.
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MICAL2 Promotes Pancreatic Cancer Growth and Metastasis. Cancer Res. 2025 Mar 14; 85(6):1049-1063. Garg B, Khan S, Courelli AS, Panneerpandian P, Sheik Pran Babu D, Mose ES, Gulay KCM, Sharma S, Sood D, Wenzel AT, Martsinkovskiy A, Rajbhandari N, Patel J, Jaquish D, Esparza E, Jaque K, Aggarwal N, Lambies G, D'Ippolito A, Austgen K, Johnston B, Orlando DA, Jang GH, Gallinger S, Goodfellow E, Brodt P, Commisso C, Tamayo P, Mesirov JP, Tiriac H, Lowy AM. PMID: 39745352; PMCID: PMC11907191.
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Genomics to Notebook (g2nb): Extending the Electronic Notebook to Address the Challenges of Bioinformatics Analysis. J Bioinform Syst Biol. 2025; 8(1):1-7. Reich M, Tabor T, Liefeld T, Joshi J, Kim F, Huang E, Thorvaldsdottir H, Blankenberg D, Mesirov JP. PMID: 40191160; PMCID: PMC11970915.
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Transforming Cancer Research through Informatics. Cancer Discov. 2024 Oct 04; 14(10):1779-1782. Klemm JD, Singer DS, Mesirov JP. PMID: 39363746; PMCID: PMC11463720.
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Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. Bioinformatics. 2024 08 02; 40(8). Panda A, Suvakov M, Thorvaldsdottir H, Mesirov JP, Robinson JT, Abyzov A. PMID: 39018173; PMCID: PMC11303504.
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MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis. bioRxiv. 2024 Jun 30. Garg B, Khan S, Babu DS, Mose E, Gulay K, Sharma S, Sood D, Wenzel AT, Martsinkovskiy A, Patel J, Jaquish D, Lambies G, D'Ippolito A, Austgen K, Johnston B, Orlando D, Jang GH, Gallinger S, Goodfellow E, Brodt P, Commisso C, Tamayo P, Mesirov JP, Tiriac H, Lowy AM. PMID: 38979336; PMCID: PMC11230455.
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Developmental basis of SHH medulloblastoma heterogeneity. Nat Commun. 2024 01 08; 15(1):270. Gold MP, Ong W, Masteller AM, Ghasemi DR, Galindo JA, Park NR, Huynh NC, Donde A, Pister V, Saurez RA, Vladoiu MC, Hwang GH, Eisemann T, Donovan LK, Walker AD, Benetatos J, Dufour C, Garzia L, Segal RA, Wechsler-Reya RJ, Mesirov JP, Korshunov A, Pajtler KW, Pomeroy SL, Ayrault O, Davidson SM, Cotter JA, Taylor MD, Fraenkel E. PMID: 38191555; PMCID: PMC10774283.
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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS. Nat Protoc. 2023 12; 18(12):3690-3731. Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. PMID: 37989764; PMCID: PMC10961825.
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Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies. bioRxiv. 2023 Nov 16. Ma JY, Ting S, Tam B, Pham T, Reich M, Mesirov J, Tamayo P, Kim W. PMID: 38014215; PMCID: PMC10680728.
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Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet. 2023 12; 55(12):2189-2199. Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. PMID: 37945900; PMCID: PMC10703696.
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Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods. 2023 11; 20(11):1619-1620. Castanza AS, Recla JM, Eby D, Thorvaldsdóttir H, Bult CJ, Mesirov JP. PMID: 37704782; PMCID: PMC11397807.
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The GPCR-Gαs-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Nat Immunol. 2023 08; 24(8):1318-1330. Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS. PMID: 37308665; PMCID: PMC10735169.
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Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun. 2023 05 12; 14(1):2744. Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. PMID: 37173324; PMCID: PMC10182072.
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3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun. 2023 04 21; 14(1):2300. Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. PMID: 37085539; PMCID: PMC10121654.
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Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. bioRxiv. 2023 Apr 06. Reich M, Tabor T, Liefeld J, Joshi J, Kim F, Thorvaldsdottir H, Blankenberg D, Mesirov JP. PMID: 37066251; PMCID: PMC10104038.
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igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 2023 01 01; 39(1). Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. PMID: 36562559; PMCID: PMC9825295.
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Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts. J Proteome Res. 2022 09 02; 21(9):2124-2136. Leskoske KL, Garcia-Mansfield K, Sharma R, Krishnan A, Rusert JM, Mesirov JP, Wechsler-Reya RJ, Pirrotte P. PMID: 35977718; PMCID: PMC9442791.
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Lymphatic-preserving treatment sequencing with immune checkpoint inhibition unleashes cDC1-dependent antitumor immunity in HNSCC. Nat Commun. 2022 07 25; 13(1):4298. Saddawi-Konefka R, O'Farrell A, Faraji F, Clubb L, Allevato MM, Jensen SM, Yung BS, Wang Z, Wu VH, Anang NA, Msari RA, Schokrpur S, Pietryga IF, Molinolo AA, Mesirov JP, Simon AB, Fox BA, Bui JD, Sharabi A, Cohen EEW, Califano JA, Gutkind JS. PMID: 35879302; PMCID: PMC9314425.
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Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. NPJ Syst Biol Appl. 2022 06 17; 8(1):20. Wenzel AT, Champa D, Venkatesh H, Sun S, Tsai CY, Mesirov JP, Bui JD, Howell SB, Harismendy O. PMID: 35715421; PMCID: PMC9206019.
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A FZD7-specific Antibody-Drug Conjugate Induces Ovarian Tumor Regression in Preclinical Models. Mol Cancer Ther. 2022 01; 21(1):113-124. Do M, Wu CCN, Sonavane PR, Juarez EF, Adams SR, Ross J, Rodriguez Y Baena A, Patel C, Mesirov JP, Carson DA, Advani SJ, Willert K. PMID: 34667113; PMCID: PMC8742765.
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Location of Gastrointestinal Stromal Tumor (GIST) in the Stomach Predicts Tumor Mutation Profile and Drug Sensitivity. Clin Cancer Res. 2021 10 01; 27(19):5334-5342. Sharma AK, de la Torre J, IJzerman NS, Sutton TL, Zhao B, Khan TM, Banerjee S, Cui C, Nguyen V, Alkhuziem M, Snaebjornsson P, van Boven H, Bruining A, Tang CM, Yoon H, De la Fuente A, Kato S, Patel H, Heinrich MC, Corless CL, Horgan S, Burgoyne AM, Fanta P, Mesirov JP, Blakely AM, Davis JL, Mayo SC, van Houdt WJ, Steeghs N, Sicklick JK. PMID: 34326133; PMCID: PMC8799780.
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KITlow Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. Mol Cancer Ther. 2021 10; 20(10):2035-2048. Banerjee S, Yoon H, Ting S, Tang CM, Yebra M, Wenzel AT, Yeerna H, Mesirov JP, Wechsler-Reya RJ, Tamayo P, Sicklick JK. PMID: 34376580; PMCID: PMC8492542.
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PTEN deficiency leads to proteasome addiction: a novel vulnerability in glioblastoma. Neuro Oncol. 2021 07 01; 23(7):1072-1086. Benitez JA, Finlay D, Castanza A, Parisian AD, Ma J, Longobardi C, Campos A, Vadla R, Izurieta A, Scerra G, Koga T, Long T, Chavez L, Mesirov JP, Vuori K, Furnari F. PMID: 33428749; PMCID: PMC8661409.
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Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 2021 07 26; 1(3). Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. PMID: 34761247; PMCID: PMC8577426.
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A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells. STAR Protoc. 2021 06 18; 2(2):100561. Chen K, Ozturk K, Liefeld T, Reich M, Mesirov JP, Carter H, Fraley SI. PMID: 34095869; PMCID: PMC8165572.
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TORC1/2 kinase inhibition depletes glutathione and synergizes with carboplatin to suppress the growth of MYC-driven medulloblastoma. Cancer Lett. 2021 04 28; 504:137-145. Maynard RE, Poore B, Hanaford AR, Pham K, James M, Alt J, Park Y, Slusher BS, Tamayo P, Mesirov J, Archer TC, Pomeroy SL, Eberhart CG, Raabe EH. PMID: 33571541; PMCID: PMC9195565.
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Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res. 2020 12 01; 80(23):5393-5407. Rusert JM, Juarez EF, Brabetz S, Jensen J, Garancher A, Chau LQ, Tacheva-Grigorova SK, Wahab S, Udaka YT, Finlay D, Seker-Cin H, Reardon B, Gröbner S, Serrano J, Ecker J, Qi L, Kogiso M, Du Y, Baxter PA, Henderson JJ, Berens ME, Vuori K, Milde T, Cho YJ, Li XN, Olson JM, Reyes I, Snuderl M, Wong TC, Dimmock DP, Nahas SA, Malicki D, Crawford JR, Levy ML, Van Allen EM, Pfister SM, Tamayo P, Kool M, Mesirov JP, Wechsler-Reya RJ. PMID: 33046443; PMCID: PMC7718387.
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Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. JCO Clin Cancer Inform. 2020 05; 4:421-435. Gevaert O, Nabian M, Bakr S, Everaert C, Shinde J, Manukyan A, Liefeld T, Tabor T, Xu J, Lupberger J, Haas BJ, Baumert TF, Hernaez M, Reich M, Quintana FJ, Uhlmann EJ, Krichevsky AM, Mesirov JP, Carey V, Pochet N. PMID: 32383980; PMCID: PMC7265792.
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Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression. Proc Natl Acad Sci U S A. 2019 12 03; 116(49):24881-24891. Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. PMID: 31754034; PMCID: PMC6900511.
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Biallelic loss of GNAS in a patient with pediatric medulloblastoma. Cold Spring Harb Mol Case Stud. 2019 10; 5(5). Tokita MJ, Nahas S, Briggs B, Malicki DM, Mesirov JP, Reyes IAC, Farnaes L, Levy ML, Kingsmore SF, Dimmock D, Crawford JR, Wechsler-Reya RJ. PMID: 31624069; PMCID: PMC6824258.
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Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2019 01; 565(7738):E5-E6. 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. PMID: 30559381.
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Precision Medicine: Improving health through high-resolution analysis of personal data. Pac Symp Biocomput. 2019; 24:220-223. Brenner SE, Bulyk M, Crawford DC, Mesirov JP, Morgan AA, Radivojac P. PMID: 30864324; PMCID: PMC6526370.
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A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics. 2019 03; 18(3):576-593. Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR. PMID: 30563849; PMCID: PMC6398202.
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An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays. F1000Res. 2018; 7. Mah CK, Mesirov JP, Chavez L. PMID: 31105932; PMCID: PMC6498745.
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Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2018 09 10; 34(3):396-410.e8. 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. PMID: 30205044; PMCID: PMC6372116.
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An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data. F1000Res. 2018; 7:1306. Mah CK, Wenzel AT, Juarez EF, Tabor T, Reich MM, Mesirov JP. PMID: 31316748; PMCID: PMC6611141.
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GeNets: a unified web platform for network-based genomic analyses. Nat Methods. 2018 07; 15(7):543-546. 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. PMID: 29915188; PMCID: PMC6450090.
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Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst. 2018 Feb 28; 6(2):256-258.e1. Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. PMID: 29428417; PMCID: PMC6047755.
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Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2. Cell Rep. 2017 Dec 05; 21(10):2688-2695. Hachigian LJ, Carmona V, Fenster RJ, Kulicke R, Heilbut A, Sittler A, Pereira de Almeida L, Mesirov JP, Gao F, Kolaczyk ED, Heiman M. PMID: 29212017.
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Variant Review with the Integrative Genomics Viewer. Cancer Res. 2017 11 01; 77(21):e31-e34. Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. PMID: 29092934; PMCID: PMC5678989.
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Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 08 23; 5(2):105-118.e9. 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. PMID: 28837809; PMCID: PMC5639711.
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The GenePattern Notebook Environment. Cell Syst. 2017 08 23; 5(2):149-151.e1. Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP. PMID: 28822753; PMCID: PMC5572818.
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Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 07 27; 547(7664):453-457. 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. PMID: 28678785; PMCID: PMC5667900.
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A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017; 6:784. Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. PMID: 29487738; PMCID: PMC5806050.
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Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 09; 7(9):973-983. 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. PMID: 28515055; PMCID: PMC5836784.
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OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma. Cancer Discov. 2017 03; 7(3):288-301. 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. PMID: 28213356; PMCID: PMC5340587.
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Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis. 2017 01 15; 215(2):312-320. 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. PMID: 27837008; PMCID: PMC6392473.
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Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 09 27; 113(39):10750-8. Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. PMID: 27638202; PMCID: PMC5047191.
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst. 2016 07; 3(1):99-101. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. PMID: 27467250; PMCID: PMC5596920.
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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. D'Antonio M, Tamayo P, Mesirov JP, Frazer KA. PMID: 27373164; PMCID: PMC4972030.
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RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 19; 165(5):1267-1279. 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. PMID: 27180905; PMCID: PMC5029792.
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Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46. 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. PMID: 27088724; PMCID: PMC4868596.
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DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets. Clin Cancer Res. 2016 08 01; 22(15):3903-14. 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. PMID: 27012813; PMCID: PMC5055054.
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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. 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. PMID: 26469764; PMCID: PMC5440057.
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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar; 13(3):245-247. Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. PMID: 26780094; PMCID: PMC4767623.
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Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19; 44(1):194-206. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. PMID: 26795250; PMCID: PMC5330663.
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The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015 Dec 23; 1(6):417-425. Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. PMID: 26771021; PMCID: PMC4707969.
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Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron. 2016 Jan 06; 89(1):100-12. Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME. PMID: 26711116; PMCID: PMC4707072.
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Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res. 2015; 4:167. Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. PMID: 26594333; PMCID: PMC4648224.
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A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation. PLoS One. 2015; 10(3):e0116096. Papageorgiou A, Rapley J, Mesirov JP, Tamayo P, Avruch J. PMID: 25790369; PMCID: PMC4366019.
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A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar 09; 27(3):397-408. 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. PMID: 25759024; PMCID: PMC4398996.
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A genomic data viewer for iPad. Genome Biol. 2015 Feb 26; 16:46. Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov JP. PMID: 25723152; PMCID: PMC4342165.
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Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. 2015 Jul 15; 31(14):2400-2. Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. PMID: 25617416; PMCID: PMC4542614.
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Plasmodium falciparum gene expression measured directly from tissue during human infection. Genome Med. 2014; 6(11):110. Van Tyne D, Tan Y, Daily JP, Kamiza S, Seydel K, Taylor T, Mesirov JP, Wirth DF, Milner DA. PMID: 25520756; PMCID: PMC4269068.
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Targeting an IKBKE cytokine network impairs triple-negative breast cancer growth. J Clin Invest. 2014 Dec; 124(12):5411-23. 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. PMID: 25365225; PMCID: PMC4348940.
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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. 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. PMID: 25984343; PMCID: PMC4432652.
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Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014; 3:151. Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. PMID: 25165537; PMCID: PMC4133763.
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Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One. 2014; 9(7):e100334. 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. PMID: 24983991; PMCID: PMC4077578.
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A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 2014 Jul; 4(7):816-27. 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. PMID: 24771846; PMCID: PMC4154497.
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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. Heiman M, Heilbut A, Francardo V, Kulicke R, Fenster RJ, Kolaczyk ED, Mesirov JP, Surmeier DJ, Cenci MA, Greengard P. PMID: 24599591; PMCID: PMC3970487.
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Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Cancer Discov. 2014 Apr; 4(4):452-65. 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. PMID: 24444711; PMCID: PMC3980023.
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Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol. 2014 Jan; 44(1):285-95. Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN. PMID: 24136404; PMCID: PMC3973429.
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Compression of structured high-throughput sequencing data. PLoS One. 2013; 8(11):e79871. Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov JP. PMID: 24260313; PMCID: PMC3832420.
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Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration. BMC Med. 2013 Oct 17; 11:220. 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. PMID: 24228635; PMCID: PMC3852338.
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Criteria for the use of omics-based predictors in clinical trials. Nature. 2013 Oct 17; 502(7471):317-20. 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. PMID: 24132288; PMCID: PMC4180668.
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Integrative radiogenomic profiling of squamous cell lung cancer. Cancer Res. 2013 Oct 15; 73(20):6289-98. 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. PMID: 23980093; PMCID: PMC3856255.
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GenePattern flow cytometry suite. Source Code Biol Med. 2013 Jul 03; 8(1):14. 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. PMID: 23822732; PMCID: PMC3717030.
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Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Cancer Discov. 2013 Sep; 3(9):1044-57. 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. PMID: 23764425; PMCID: PMC3770815.
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Reproducibility: In praise of open research measures. Nature. 2013 Jun 13; 498(7453):170. 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. PMID: 23765483.
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Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. PLoS One. 2013; 8(2):e54873. 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. PMID: 23393560; PMCID: PMC3564856.
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ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013 Apr; 23(4):665-78. 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. PMID: 23269662; PMCID: PMC3613583.
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Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25. 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, Cancer Genome Atlas Research Network. PMID: 23257362; PMCID: PMC3533304.
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β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell. 2012 Dec 21; 151(7):1457-73. 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. PMID: 23245941; PMCID: PMC3530160.
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The limitations of simple gene set enrichment analysis assuming gene independence. Stat Methods Med Res. 2016 Feb; 25(1):472-87. Tamayo P, Steinhardt G, Liberzon A, Mesirov JP. PMID: 23070592; PMCID: PMC3758419.
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An RNA profile identifies two subsets of multiple sclerosis patients differing in disease activity. Sci Transl Med. 2012 Sep 26; 4(153):153ra131. Ottoboni L, Keenan BT, Tamayo P, Kuchroo M, Mesirov JP, Buckle GJ, Khoury SJ, Hafler DA, Weiner HL, De Jager PL. PMID: 23019656; PMCID: PMC3753678.
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Cancer vulnerabilities unveiled by genomic loss. Cell. 2012 Aug 17; 150(4):842-54. 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. PMID: 22901813; PMCID: PMC3429351.
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Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4. Sci Transl Med. 2012 Aug 15; 4(147):147ra112. 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. PMID: 22896676; PMCID: PMC3633234.
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Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature. 2012 Aug 02; 488(7409):106-10. 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. PMID: 22820256; PMCID: PMC3413789.
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Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. PLoS One. 2012; 7(7):e40739. Milner DA, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP. PMID: 22815802; PMCID: PMC3399889.
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AraPath: a knowledgebase for pathway analysis in Arabidopsis. Bioinformatics. 2012 Sep 01; 28(17):2291-2. Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX. PMID: 22760305; PMCID: PMC3426845.
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MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma. Sci Signal. 2012 May 15; 5(224):rs4. Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root DE, Garraway LA, Sabatini DM. PMID: 22589389; PMCID: PMC3498828.
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Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome. J Hematol Oncol. 2012 May 06; 5:20. Galili N, Tamayo P, Botvinnik OB, Mesirov JP, Brooks MR, Brown G, Raza A. PMID: 22559819; PMCID: PMC3407785.
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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013 Mar; 14(2):178-92. Thorvaldsdóttir H, Robinson JT, Mesirov JP. PMID: 22517427; PMCID: PMC3603213.
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012 Mar 28; 483(7391):603-7. 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. PMID: 22460905; PMCID: PMC3320027.
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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. 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. PMID: 21746896; PMCID: PMC3145679.
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Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011 Jun 15; 27(12):1739-40. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. PMID: 21546393; PMCID: PMC3106198.
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Predicting relapse in patients with medulloblastoma by integrating evidence from clinical and genomic features. J Clin Oncol. 2011 Apr 10; 29(11):1415-23. 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. PMID: 21357789; PMCID: PMC3082982.
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Integrative genomics viewer. Nat Biotechnol. 2011 Jan; 29(1):24-6. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. PMID: 21221095; PMCID: PMC3346182.
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Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J Clin Oncol. 2011 Apr 10; 29(11):1424-30. 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. PMID: 21098324; PMCID: PMC3082983.
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Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33. 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. PMID: 21076395; PMCID: PMC3859448.
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MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703. 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. PMID: 20133671; PMCID: PMC2840447.
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Computer science. Accessible reproducible research. Science. 2010 Jan 22; 327(5964):415-6. Mesirov JP. PMID: 20093459; PMCID: PMC3878063.
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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. 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, Cancer Genome Atlas Research Network. PMID: 20129251; PMCID: PMC2818769.
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Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009 Nov 05; 462(7269):108-12. 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. PMID: 19847166; PMCID: PMC2783335.
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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. Wirth D, Daily J, Winzeler E, Mesirov JP, Regev A. PMID: 19570993; PMCID: PMC2708753.
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Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci U S A. 2009 May 26; 106(21):8519-24. 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. PMID: 19443687; PMCID: PMC2682540.
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Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009 Feb; 27(2):190-8. Fusaro VA, Mani DR, Mesirov JP, Carr SA. PMID: 19169245; PMCID: PMC2753399.
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ISMB 2008 Toronto. PLoS Comput Biol. 2008 Jun 27; 4(6):e1000094. Linial M, Mesirov JP, Morrison McKay BJ, Rost B. PMID: 18584023; PMCID: PMC2427177.
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Cytometric profiling in multiple sclerosis uncovers patient population structure and a reduction of CD8low cells. Brain. 2008 Jul; 131(Pt 7):1701-11. 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. PMID: 18567923; PMCID: PMC2730047.
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Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells. Cancer Res. 2008 Jun 01; 68(11):4331-9. Mishra PJ, Mishra PJ, Humeniuk R, Medina DJ, Alexe G, Mesirov JP, Ganesan S, Glod JW, Banerjee D. PMID: 18519693; PMCID: PMC2725025.
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Using GenePattern for gene expression analysis. Curr Protoc Bioinformatics. 2008 Jun; Chapter 7:7.12.1-7.12.39. Kuehn H, Liberzon A, Reich M, Mesirov JP. PMID: 18551415; PMCID: PMC3893799.
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Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. Mol Cancer Res. 2008 May; 6(5):760-9. Xu L, Shen SS, Hoshida Y, Subramanian A, Ross K, Brunet JP, Wagner SN, Ramaswamy S, Mesirov JP, Hynes RO. PMID: 18505921; PMCID: PMC2756991.
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Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature. 2007 Dec 13; 450(7172):1091-5. 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. PMID: 18046333.
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Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One. 2007 Nov 21; 2(11):e1195. Hoshida Y, Brunet JP, Tamayo P, Golub TR, Mesirov JP. PMID: 18030330; PMCID: PMC2065909.
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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. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G. PMID: 18006808.
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Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet. 2007 Nov; 39(11):1321-8. 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. PMID: 17906626.
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Comment on "The consensus coding sequences of human breast and colorectal cancers". Science. 2007 Sep 14; 317(5844):1500. Getz G, Höfling H, Mesirov JP, Golub TR, Meyerson M, Tibshirani R, Lander ES. PMID: 17872428.
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Portraits of breast cancer progression. BMC Bioinformatics. 2007 Aug 06; 8:291. Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G. PMID: 17683614; PMCID: PMC1978212.
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GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007 Dec 01; 23(23):3251-3. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. PMID: 17644558.
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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. Tamayo P, Scanfeld D, Ebert BL, Gillette MA, Roberts CW, Mesirov JP. PMID: 17389406; PMCID: PMC1838404.
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Breast cancer stratification from analysis of micro-array data of micro-dissected specimens. Genome Inform. 2007; 18:130-40. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, Delisi C, Bhanot G. PMID: 18546481.
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Combo: a whole genome comparative browser. Bioinformatics. 2006 Jul 15; 22(14):1782-3. Engels R, Yu T, Burge C, Mesirov JP, DeCaprio D, Galagan JE. PMID: 16709588.
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Comparative gene marker selection suite. Bioinformatics. 2006 Aug 01; 22(15):1924-5. Gould J, Getz G, Monti S, Reich M, Mesirov JP. PMID: 16709585.
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GenePattern 2.0. Nat Genet. 2006 May; 38(5):500-1. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. PMID: 16642009.
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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. Isakoff MS, Sansam CG, Tamayo P, Subramanian A, Evans JA, Fillmore CM, Wang X, Biegel JA, Pomeroy SL, Mesirov JP, Roberts CW. PMID: 16301525; PMCID: PMC1308926.
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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. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. PMID: 16199517; PMCID: PMC1239896.
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Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 2005 Aug; 15(8):1127-35. 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. PMID: 16077012; PMCID: PMC1182225.
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GeneCruiser: a web service for the annotation of microarray data. Bioinformatics. 2005 Sep 15; 21(18):3681-2. Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP. PMID: 16030072.
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An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet. 2005 Jan; 37(1):48-55. Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T. PMID: 15608639.
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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004 Oct 21; 431(7011):946-57. 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. PMID: 15496914.
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Improving genome annotations using phylogenetic profile anomaly detection. Bioinformatics. 2005 Feb 15; 21(4):464-70. Mikkelsen TS, Galagan JE, Mesirov JP. PMID: 15374867.
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GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics. 2004 Jul 22; 20(11):1797-8. Reich M, Ohm K, Angelo M, Tamayo P, Mesirov JP. PMID: 14988123.
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PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003 Jul; 34(3):267-73. 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. PMID: 12808457.
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Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol. 2003; 10(2):119-42. Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub TR, Mesirov JP. PMID: 12804087.
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Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003 Jan; 13(1):91-6. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. PMID: 12529310; PMCID: PMC430950.
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Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. PMID: 12466850.
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Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002 Jan 24; 415(6870):436-42. 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. PMID: 11807556.
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Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. 2002 Jan; 8(1):68-74. 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. PMID: 11786909.
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ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002 Jan; 12(1):177-89. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. PMID: 11779843; PMCID: PMC155255.
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Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A. 2001 Dec 18; 98(26):15149-54. 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. PMID: 11742071; PMCID: PMC64998.
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Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921. 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, International Human Genome Sequencing Consortium. PMID: 11237011.
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Molecular classification of multiple tumor types. Bioinformatics. 2001; 17 Suppl 1:S316-22. Yeang CH, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, Reich M, Lander E, Mesirov J, Golub T. PMID: 11473023.
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Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000 Jul; 10(7):950-8. Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. PMID: 10899144; PMCID: PMC310911.
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Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Res. 1999 Dec; 9(12):1163-74. Batzoglou S, Berger B, Mesirov J, Lander ES. PMID: 10613838.
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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. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. PMID: 10077610; PMCID: PMC15868.
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Hybrid system for protein secondary structure prediction. J Mol Biol. 1992 Jun 20; 225(4):1049-63. Zhang X, Mesirov JP, Waltz DL. PMID: 1613789.
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