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Items: 1 to 50 of 102

1.

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.

Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL.

Cell Syst. 2018 Feb 28;6(2):256-258.e1. doi: 10.1016/j.cels.2018.01.001. Epub 2018 Feb 7.

2.

Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2.

Hachigian LJ, Carmona V, Fenster RJ, Kulicke R, Heilbut A, Sittler A, Pereira de Almeida L, Mesirov JP, Gao F, Kolaczyk ED, Heiman M.

Cell Rep. 2017 Dec 5;21(10):2688-2695. doi: 10.1016/j.celrep.2017.11.018.

3.

Variant Review with the Integrative Genomics Viewer.

Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP.

Cancer Res. 2017 Nov 1;77(21):e31-e34. doi: 10.1158/0008-5472.CAN-17-0337.

PMID:
29092934
4.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

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.

Cell Syst. 2017 Aug 23;5(2):105-118.e9. doi: 10.1016/j.cels.2017.08.002.

PMID:
28837809
5.

The GenePattern Notebook Environment.

Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP.

Cell Syst. 2017 Aug 23;5(2):149-151.e1. doi: 10.1016/j.cels.2017.07.003. Epub 2017 Aug 16.

PMID:
28822753
6.

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway.

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.

Nature. 2017 Jul 27;547(7664):453-457. doi: 10.1038/nature23007. Epub 2017 Jul 5.

7.

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma.

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.

Cancer Discov. 2017 Mar;7(3):288-301. doi: 10.1158/2159-8290.CD-16-0844. Epub 2017 Feb 17.

8.

Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas.

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.

J Infect Dis. 2017 Jan 15;215(2):312-320. doi: 10.1093/infdis/jiw531.

PMID:
27837008
9.

Leveraging premalignant biology for immune-based cancer prevention.

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.

Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10750-8. doi: 10.1073/pnas.1608077113. Epub 2016 Sep 16.

10.

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL.

Cell Syst. 2016 Jul;3(1):99-101. doi: 10.1016/j.cels.2015.07.012.

11.

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels.

D'Antonio M, Tamayo P, Mesirov JP, Frazer KA.

Cell Rep. 2016 Jul 19;16(3):672-83. doi: 10.1016/j.celrep.2016.06.026. Epub 2016 Jun 30.

12.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

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.

Cell. 2016 May 19;165(5):1267-1279. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May 12.

13.

Characterizing genomic alterations in cancer by complementary functional associations.

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.

Nat Biotechnol. 2016 May;34(5):539-46. doi: 10.1038/nbt.3527. Epub 2016 Apr 18.

14.

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets.

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.

Clin Cancer Res. 2016 Aug 1;22(15):3903-14. doi: 10.1158/1078-0432.CCR-15-3011. Epub 2016 Mar 24.

15.

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN.

Immunity. 2016 Jan 19;44(1):194-206. doi: 10.1016/j.immuni.2015.12.006. Epub 2016 Jan 12.

16.

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

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.

Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18.

17.

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P.

Cell Syst. 2015 Dec 23;1(6):417-425.

18.

Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation.

Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME.

Neuron. 2016 Jan 6;89(1):100-12. doi: 10.1016/j.neuron.2015.11.030. Epub 2015 Dec 17.

19.

Constellation Map: Downstream visualization and interpretation of gene set enrichment results.

Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP.

F1000Res. 2015 Jun 24;4:167. doi: 10.12688/f1000research.6644.1. eCollection 2015.

20.

Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia.

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.

Am J Respir Crit Care Med. 2016 Feb 15;193(4):448-59. doi: 10.1164/rccm.201506-1100OC.

21.

A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation.

Papageorgiou A, Rapley J, Mesirov JP, Tamayo P, Avruch J.

PLoS One. 2015 Mar 19;10(3):e0116096. doi: 10.1371/journal.pone.0116096. eCollection 2015.

22.

A functional landscape of resistance to ALK inhibition in lung cancer.

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.

Cancer Cell. 2015 Mar 9;27(3):397-408. doi: 10.1016/j.ccell.2015.02.005.

23.

A genomic data viewer for iPad.

Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov JP.

Genome Biol. 2015 Feb 26;16:46. doi: 10.1186/s13059-015-0595-3.

24.

Quantitative visualization of alternative exon expression from RNA-seq data.

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB.

Bioinformatics. 2015 Jul 15;31(14):2400-2. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.

25.

Plasmodium falciparum gene expression measured directly from tissue during human infection.

Van Tyne D, Tan Y, Daily JP, Kamiza S, Seydel K, Taylor T, Mesirov JP, Wirth DF, Milner DA Jr.

Genome Med. 2014 Nov 29;6(11):110. doi: 10.1186/s13073-014-0110-6. eCollection 2014.

26.

Targeting an IKBKE cytokine network impairs triple-negative breast cancer growth.

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.

J Clin Invest. 2014 Dec;124(12):5411-23. doi: 10.1172/JCI75661. Epub 2014 Nov 3.

27.

Cytoscape: the network visualization tool for GenomeSpace workflows.

Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP.

Version 2. F1000Res. 2014 Jul 1 [revised 2014 Jan 1];3:151. doi: 10.12688/f1000research.4492.2. eCollection 2014.

28.

A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors.

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.

Cancer Discov. 2014 Jul;4(7):816-27. doi: 10.1158/2159-8290.CD-13-0424. Epub 2014 Apr 25.

29.

Molecular adaptations of striatal spiny projection neurons during levodopa-induced dyskinesia.

Heiman M, Heilbut A, Francardo V, Kulicke R, Fenster RJ, Kolaczyk ED, Mesirov JP, Surmeier DJ, Cenci MA, Greengard P.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4578-83. doi: 10.1073/pnas.1401819111. Epub 2014 Mar 5.

30.

Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit.

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.

Cancer Discov. 2014 Apr;4(4):452-65. doi: 10.1158/2159-8290.CD-13-0646. Epub 2014 Jan 20.

31.

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies.

Cowley GS, Weir BA, Vazquez F, Tamayo P, Scott JA, Rusin S, East-Seletsky A, Ali LD, Gerath WF, Pantel SE, Lizotte PH, Jiang G, Hsiao J, Tsherniak A, Dwinell E, Aoyama S, Okamoto M, Harrington W, Gelfand E, Green TM, Tomko MJ, Gopal S, Wong TC, Li H, Howell S, Stransky N, Liefeld T, Jang D, Bistline J, Hill Meyers B, Armstrong SA, Anderson KC, Stegmaier K, Reich M, Pellman D, Boehm JS, Mesirov JP, Golub TR, Root DE, Hahn WC.

Sci Data. 2014 Sep 30;1:140035. doi: 10.1038/sdata.2014.35. eCollection 2014. Erratum in: Sci Data. 2014;1:140044. Wong, Terrence C [corrected to Wong, Terence C].

32.

Compression of structured high-throughput sequencing data.

Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov JP.

PLoS One. 2013 Nov 18;8(11):e79871. doi: 10.1371/journal.pone.0079871. eCollection 2013.

33.

Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration.

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.

BMC Med. 2013 Oct 17;11:220. doi: 10.1186/1741-7015-11-220.

34.

Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response.

Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN.

Eur J Immunol. 2014 Jan;44(1):285-95. doi: 10.1002/eji.201343657. Epub 2013 Nov 29.

35.

Criteria for the use of omics-based predictors in clinical trials.

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.

Nature. 2013 Oct 17;502(7471):317-20. doi: 10.1038/nature12564.

36.

Integrative radiogenomic profiling of squamous cell lung cancer.

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.

Cancer Res. 2013 Oct 15;73(20):6289-98. doi: 10.1158/0008-5472.CAN-13-1616. Epub 2013 Aug 26.

37.

GenePattern flow cytometry suite.

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.

Source Code Biol Med. 2013 Jul 3;8(1):14. doi: 10.1186/1751-0473-8-14.

38.

Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers.

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.

Cancer Discov. 2013 Sep;3(9):1044-57. doi: 10.1158/2159-8290.CD-12-0592. Epub 2013 Jun 13.

39.

Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers.

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.

PLoS One. 2013;8(2):e54873. doi: 10.1371/journal.pone.0054873. Epub 2013 Feb 5.

40.

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.

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.

Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112. Epub 2012 Dec 26.

41.

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma.

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.

J Clin Invest. 2013 Jan;123(1):517-25. doi: 10.1172/JCI65833. Epub 2012 Dec 21.

42.

β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis.

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.

Cell. 2012 Dec 21;151(7):1457-73. doi: 10.1016/j.cell.2012.11.026. Epub 2012 Dec 13. Erratum in: Cell. 2013 Mar 28;153(1):267-70.

43.

The limitations of simple gene set enrichment analysis assuming gene independence.

Tamayo P, Steinhardt G, Liberzon A, Mesirov JP.

Stat Methods Med Res. 2016 Feb;25(1):472-87. doi: 10.1177/0962280212460441. Epub 2012 Oct 14.

44.

An RNA profile identifies two subsets of multiple sclerosis patients differing in disease activity.

Ottoboni L, Keenan BT, Tamayo P, Kuchroo M, Mesirov JP, Buckle GJ, Khoury SJ, Hafler DA, Weiner HL, De Jager PL.

Sci Transl Med. 2012 Sep 26;4(153):153ra131.

45.

Cancer vulnerabilities unveiled by genomic loss.

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.

Cell. 2012 Aug 17;150(4):842-54. doi: 10.1016/j.cell.2012.07.023.

46.

Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4.

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.

Sci Transl Med. 2012 Aug 15;4(147):147ra112. doi: 10.1126/scitranslmed.3003778.

47.

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.

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.

Nature. 2012 Aug 2;488(7409):106-10. doi: 10.1038/nature11329.

48.

Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters.

Milner DA Jr, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP.

PLoS One. 2012;7(7):e40739. doi: 10.1371/journal.pone.0040739. Epub 2012 Jul 18.

49.

AraPath: a knowledgebase for pathway analysis in Arabidopsis.

Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX.

Bioinformatics. 2012 Sep 1;28(17):2291-2. doi: 10.1093/bioinformatics/bts421. Epub 2012 Jul 3.

50.

MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma.

Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root DE, Garraway LA, Sabatini DM.

Sci Signal. 2012 May 15;5(224):rs4. doi: 10.1126/scisignal.2002612.

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