Panda A, Suvakov M, Thorvaldsdottir H, Mesirov JP, Robinson JT, Abyzov A. Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. Bioinformatics. 2024 Aug 2;40(8):btae453. doi: 10.1093/bioinformatics/btae453. PMID: 39018173; PMCID: PMC11303504.
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. MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis. bioRxiv [Preprint]. 2024 Jun 30:2024.06.26.600548. doi: 10.1101/2024.06.26.600548. PMID: 38979336; PMCID: PMC11230455.
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. Developmental basis of SHH medulloblastoma heterogeneity. Nat Commun. 2024 Jan 8;15(1):270. doi: 10.1038/s41467-023-44300-0. PMID: 38191555; PMCID: PMC10774283.
2023
Ma JY, Ting S, Tam B, Pham T, Reich M, Mesvirov J, Tamayo P, Kim W. Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies. bioRxiv [Preprint]. 2023 Nov 16:2023.11.14.567106. doi: 10.1101/2023.11.14.567106. PMID: 38014215; PMCID: PMC10680728.
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. 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 Dec;18(12):3690-3731. doi: 10.1038/s41596-023-00892-x. Epub 2023 Nov 21. PMID: 37989764; PMCID: PMC10961825.
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. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet. 2023 Dec;55(12):2189-2199. doi: 10.1038/s41588-023-01551-3. Epub 2023 Nov 9. PMID: 37945900; PMCID: PMC10703696.
Castanza AS, Recla JM, Eby D, Thorvaldsdóttir H, Bult CJ, Mesirov JP. Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods. 2023 Nov;20(11):1619-1620. doi: 10.1038/s41592-023-02014-7. PMID: 37704782.
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. The GPCR-Gαs-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Nat Immunol. 2023 Aug;24(8):1318-1330. doi: 10.1038/s41590-023-01529-7. Epub 2023 Jun 12. PMID: 37308665; PMCID: PMC10735169.
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. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun. 2023 May 12;14(1):2744. doi: 10.1038/s41467-023-38271-5. PMID: 37173324; PMCID: PMC10182072.
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. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun. 2023 Apr 21;14(1):2300. doi: 10.1038/s41467-023-38044-0. PMID: 37085539; PMCID: PMC10121654.
Reich M, Tabor T, Liefeld J, Joshi J, Kim F, Thorvaldsdottir H, Blankenberg D, Mesirov JP. Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. bioRxiv [Preprint]. 2023 Apr 6:2023.04.04.535621. doi: 10.1101/2023.04.04.535621. PMID: 37066251; PMCID: PMC10104038.
Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 2023 Jan 1;39(1):btac830. doi: 10.1093/bioinformatics/btac830. PMID: 36562559; PMCID: PMC9825295.
2022
Leskoske KL, Garcia-Mansfield K, Sharma R, Krishnan A, Rusert JM, Mesirov JP, Wechsler-Reya RJ, Pirrotte P. Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts. J Proteome Res. 2022 Sep 2;21(9):2124-2136. doi: 10.1021/acs.jproteome.2c00203. Epub 2022 Aug 17. PMID: 35977718 PMCID: PMC9442791
Wenzel AT, Champa D, Venkatesh H, Sun S, Tsai CY, Mesirov JP, Bui JD, Howell SB, Harismendy O. Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. NPJ Syst Biol Appl. 2022 Jun 17;8(1):20. doi: 10.1038/s41540-022-00230-z. PMID: 35715421 PMCID: PMC9206019
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. Lymphatic-preserving treatment sequencing with immune checkpoint inhibition unleashes cDC1-dependent antitumor immunity in HNSCC. Nat Comm. 2022 Jul 25;13(1):4298. doi: 10.1038/s41467-022-31941-w. PMID: 35879302 PMCID: PMC9314425
Do M, Wu CCN, Sonavane PR, Juarez EF, Adams SR, Ross J, Rodriguez YBA, Patel C, Mesirov JP, Carson DA, Advani SJ, Willert K. A FZD7-specific Antibody-Drug Conjugate Induces Ovarian Tumor Regression in Preclinical Models. Mol Cancer Ther. 2022;21(1):113-24. Epub 20211019. doi: 10.1158/1535-7163.MCT-21-0548. PubMed PMID: 34667113; PMCID: PMC8742765.
2021
Sharma AK, de la Torre J, NS IJ, 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. Location of Gastrointestinal Stromal Tumor (GIST) in the Stomach Predicts Tumor Mutation Profile and Drug Sensitivity. Clin Cancer Res. 2021. Epub 20210729. doi: 10.1158/1078-0432.CCR-21-1221. PubMed PMID: 34326133.
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. Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 2021;1(3). Epub 20210630. doi: 10.1016/j.crmeth.2021.100040. PubMed PMID: 34761247; PMCID: PMC8577426.
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. TORC1/2 kinase inhibition depletes glutathione and synergizes with carboplatin to suppress the growth of MYC-driven medulloblastoma. Cancer Lett. 2021;504:137-45. Epub 20210208. doi: 10.1016/j.canlet.2021.02.001. PubMed PMID: 33571541.
Chen K, Ozturk K, Liefeld T, Reich M, Mesirov JP, Carter H, Fraley SI. A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells. STAR Protoc. 2021;2(2):100561. Epub 20210525. doi: 10.1016/j.xpro.2021.100561. PubMed PMID: 34095869; PMCID: PMC8165572.
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. Pten Deficiency Leads To Proteasome Addiction, A Novel Vulnerability In Glioblastoma. Neuro-oncology. 2021. Epub 2021/01/12. doi: 10.1093/neuonc/noab001. PubMed PMID: 33428749.
2020
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, Grobner 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. Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer research. 2020;80(23):5393-407. Epub 2020/10/14. doi: 10.1158/0008-5472.CAN-20-1655. PubMed PMID: 33046443; PMCID: PMC7718387.
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. Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. JCO clinical cancer informatics. 2020;4:421-35. Epub 2020/05/10. doi: 10.1200/CCI.19.00125. PubMed PMID: 32383980; PMCID: PMC7265792.
Wu VH, Wenzel A, Yung B, Wang Z, Mesirov JP, Gutkind JS. Illuminating the onco-GPCRome: targeting the prostaglandin receptor-Gαs signaling axis as a novel immune checkpoint in cancer. The Journal of Immunology. 2020;204(1 Supplement):165.37-.37
2019
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. Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression. Proc Natl Acad Sci U S A. 2019 Dec 3;116(49):24881-24891. doi: 10.1073/pnas.1912033116. Epub 2019 Nov 21. PubMed PMID: 31754034; PubMed Central PMCID: PMC6900511.
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. Biallelic loss of GNAS in a patient with pediatric medulloblastoma. Cold Spring Harb Mol Case Stud. 2019 Oct;5(5). doi: 10.1101/mcs.a004572. Print 2019 Oct. PubMed PMID: 31624069; PubMed Central PMCID: PMC6824258.
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. A Curated Resource for Phosphosite-specific Signature
Analysis. Mol Cell Proteomics. 2019 Mar;18(3):576-593. doi:
10.1074/mcp.TIR118.000943. Epub 2018 Dec 18. PubMed PMID: 30563849; PubMed
Central PMCID: PMC6398202.
Brenner SE, Bulyk M, Crawford DC, Mesirov JP, Morgan AA, Radivojac P. Precision Medicine: Improving health through
high-resolution analysis of personal data. Pac Symp Biocomput. 2019;24:220-223. PubMed PMID: 30864324;
NIHMSID:NIHMS1024185.M
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 Jr, 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. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2019 Jan;565(7738):E5-E6. doi: 10.1038/s41586-018-0722-x. PubMed PMID: 30559381.
2018
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. A curated resource for phosphosite-specific signature
analysis. Mol Cell Proteomics. 2018 Dec 18. pii: mcp.TIR118.000943. doi: 10.1074/mcp.TIR118.000943. [Epub ahead of
print] PubMed PMID: 30563849.
Mah CK, Tabor T and Mesirov JP. An accessible, interactive GenePattern Notebook for analysis and exploration of
single-cell transcriptomic data [version 1; referees: 2 approved with reservations]. F1000Research 2018, 7:1306
(https://doi.org/10.12688/f1000research.15830.1)
Carlin DE, Kim F, Ideker T and Mesirov JP. A unified GenomeSpace recipe to identify essential genes and associated
subnetworks from Genome-Scale CRISPR-Cas9 knockout screens [version 1; referees: awaiting peer review]. F1000Research
2018, 7:1636
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. doi:
10.1016/j.ccell.2018.08.004. PubMed PMID: 30205044.
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. Nature methods. 2018; 15(7):543-546. PubMed PMID: 29915188
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 systems. 2018; 6(2):256-258.e1. NIHMSID: NIHMS949176 PubMed PMID:29428417, PMCID: PMC6047755
2017
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 5;21(10):2688-2695. doi:
10.1016/j.celrep.2017.11.018. PubMed PMID: 29212017.
Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant Review with
the Integrative Genomics Viewer. Cancer Res. 2017 Nov 1;77(21):e31-e34. doi: 10.1158/0008-5472.CAN-17-0337.
PubMed PMID: 29092934; PubMed Central PMCID: PMC5678989.
Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson
BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW,
Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov
J, Tamayo P, Rubin MA, Powell IJ, Garraway LA. Exome Sequencing of African-American Prostate Cancer
Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 Sep;7(9):973-983. doi:
10.1158/2159-8290.CD-16-0960. Epub 2017 May 17. PubMed PMID: 28515055.
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. doi: 10.1016/j.cels.2017.08.002. PubMed PMID: 28837809.
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. doi: 10.1016/j.cels.2017.07.003. Epub 2017
Aug 16. PubMed PMID: 28822753; PubMed Central PMCID: PMC5572818.
Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B,Kaffenberger SD, Eaton JK,
Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV,
Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA,
Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF,
Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid
peroxidase pathway. Nature. 2017 Jul 27;547(7664):453-457. doi: 10.1038/nature23007. Epub 2017 Jul 5.
PubMed PMID: 28678785.
Carlin D, Kosnicki K, Garamszegi S et al. A multi-tool recipe to identify regions of protein-DNA
binding and their influence on associated gene expression. F1000Research 2017, 6:784 (doi:
10.12688/f1000research.11616.1)
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 Mar;7(3):288-301.
doi: 10.1158/2159-8290.CD-16-0844. Epub 2017 Feb 17. PubMed PMID: 28213356; PubMed Central PMCID:
PMC5340587.
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 Jr, 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. doi: 10.1093/infdis/jiw531. PubMed PMID: 27837008.
2016
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 Sep 27;113(39):10750-8. doi: 10.1073/pnas.1608077113. Epub 2016 Sep 16.
PubMed PMID: 27638202; PubMed Central PMCID: PMC5047191.
Hanaford AR, Archer TC, Price A, Kahlert UD, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA,
Dančík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees MG, Shamji A, Schreiber S, Fraenkel E, Pomeroy
SL, Mesirov JP, Tamayo P, Eberhart CG, Raabe EH. DiSCoVERing Innovative Therapies for Rare Tumors:
Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic
Targets. Clin Cancer Res. 2016 Aug 1;22(15):3903-14. Doi: 10.1158/1078-0432.CCR-15-3011. Epub 2016 Mar 24.
PubMed PMID: 27012813; PubMed Central PMCID: PMC5055054.
D'Antonio M, Tamayo P, Mesirov JP, Frazer KA. Kataegis Expression Signature in Breast Cancer Is
Associated with Late Onset, Better Prognosis, and Higher HER2 Levels. Cell Rep. 2016 Jul 19;16(3):672-83.
doi: 10.1016/j.celrep.2016.06.026. Epub 2016 Jun 30. PubMed PMID: 27373164; PubMed Central PMCID:
PMC4972030.
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.
doi: 10.1016/j.cels.2015.07.012. PubMed PMID: 27467250; PubMed Central PMCID: PMC5596920.
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. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May
12. PubMed PMID: 27180905; PubMed Central PMCID: PMC5029792.
Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D,
Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M,
Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R,
Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P.
Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016
May;34(5):539-46. doi: 10.1038/nbt.3527. Epub 2016 Apr 18. PubMed PMID: 27088724; PubMed Central PMCID:
PMC4868596.
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. doi:
10.1038/nmeth.3732. Epub 2016 Jan 18. PubMed PMID: 26780094; PubMed Central PMCID: PMC4767623.
Valim C, Ahmad R, Lanaspa M, Tan Y, Acácio S, Gillette MA, Almendinger KD, Milner DA Jr, 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. doi: 10.1164/rccm.201506-1100OC. PubMed PMID: 26469764; PubMed Central
PMCID: PMC5440057.
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. doi: 10.1016/j.immuni.2015.12.006. Epub 2016 Jan 12.
PubMed PMID: 26795250; PubMed Central PMCID: PMC5330663.
Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME. Role of Tet1/3 Genes
and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron. 2016 Jan 6;89(1):100-12. doi:
10.1016/j.neuron.2015.11.030. Epub 2015 Dec 17. PubMed PMID: 26711116; PubMed Central PMCID: PMC4707072.
2015
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. PubMed
PMID: 26771021; PubMed Central PMCID: PMC4707969.
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. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.
PubMed PMID: 25617416; PubMed Central PMCID: PMC4542614.
Wilson FH, Johannessen CM, Piccioni F, Tamayo P, Kim JW, Van Allen EM, Corsello SM, Capelletti M, Calles A,
Butaney M, Sharifnia T, Gabriel SB, Mesirov JP, Hahn WC, Engelman JA, Meyerson M, Root DE, Jänne PA,
Garraway LA. A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar
9;27(3):397-408. doi: 10.1016/j.ccell.2015.02.005. PubMed PMID: 25759024; PubMed Central PMCID: PMC4398996.
Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov JP. A genomic data viewer for iPad.
Genome Biol. 2015 Feb 26;16:46. doi: 10.1186/s13059-015-0595-3. PubMed PMID: 25723152; PubMed Central
PMCID: PMC4342165.
Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. Constellation Map: Downstream visualization and
interpretation of gene set enrichment results. F1000Res. 2015 Jun 24;4:167. doi:
10.12688/f1000research.6644.1. eCollection 2015. PubMed PMID: 26594333; PubMed Central PMCID: PMC4648224.
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 Mar 19;10(3):e0116096. doi:
10.1371/journal.pone.0116096. eCollection 2015. PubMed PMID: 25790369; PubMed Central PMCID: PMC4366019.