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Items: 1 to 20 of 70

1.

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.

Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG Jr, Spardy N, Hahn WC, Hoshida Y, Ogino S, DePinho RA, Chin L, Garraway LA, Fuchs CS, Baselga J, Tabernero J, Gabriel S, Lander ES, Getz G, Meyerson M.

Nat Genet. 2011 Sep 4;43(10):964-968. doi: 10.1038/ng.936.

2.

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Kim D, Salzberg SL.

Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72.

3.

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1.

Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN.

Science. 2011 Aug 26;333(6046):1154-7. doi: 10.1126/science.1206923. Epub 2011 Jul 28.

4.

The mutational landscape of head and neck squamous cell carcinoma.

Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortés ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio RC, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR.

Science. 2011 Aug 26;333(6046):1157-60. doi: 10.1126/science.1208130. Epub 2011 Jul 28.

5.

Integrated genomic analyses of ovarian carcinoma.

Cancer Genome Atlas Research Network.

Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298.

6.

Unraveling the genetics of cancer: genome sequencing and beyond.

Wong KM, Hudson TJ, McPherson JD.

Annu Rev Genomics Hum Genet. 2011;12:407-30. doi: 10.1146/annurev-genom-082509-141532. Review.

PMID:
21639794
7.

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP.

PLoS Comput Biol. 2011 May;7(5):e1001138. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19.

8.

Computational methods for transcriptome annotation and quantification using RNA-seq.

Garber M, Grabherr MG, Guttman M, Trapnell C.

Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. Epub 2011 May 27. Review. Erratum in: Nat Methods. 2011 Jun;8(6):following 477.

PMID:
21623353
9.

A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia.

Klinakis A, Lobry C, Abdel-Wahab O, Oh P, Haeno H, Buonamici S, van De Walle I, Cathelin S, Trimarchi T, Araldi E, Liu C, Ibrahim S, Beran M, Zavadil J, Efstratiadis A, Taghon T, Michor F, Levine RL, Aifantis I.

Nature. 2011 May 12;473(7346):230-3. doi: 10.1038/nature09999.

10.

Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis.

Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C.

Nat Genet. 2011 Mar 6;43(4):306-8. doi: 10.1038/ng.778.

PMID:
21378989
11.

Notch1 and Notch2 have opposite prognostic effects on patients with colorectal cancer.

Chu D, Zhang Z, Zhou Y, Wang W, Li Y, Zhang H, Dong G, Zhao Q, Ji G.

Ann Oncol. 2011 Nov;22(11):2440-7. doi: 10.1093/annonc/mdq776. Epub 2011 Mar 4.

PMID:
21378202
12.

Hallmarks of cancer: the next generation.

Hanahan D, Weinberg RA.

Cell. 2011 Mar 4;144(5):646-74. doi: 10.1016/j.cell.2011.02.013. Review.

13.

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.

Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P, Johnson NA, Zhao Y, Telenius A, Neriah SB, McPherson A, Meissner B, Okoye UC, Diepstra A, van den Berg A, Sun M, Leung G, Jones SJ, Connors JM, Huntsman DG, Savage KJ, Rimsza LM, Horsman DE, Staudt LM, Steidl U, Marra MA, Gascoyne RD.

Nature. 2011 Mar 17;471(7338):377-81. doi: 10.1038/nature09754. Epub 2011 Mar 2.

14.

Genomic and epigenomic integration identifies a prognostic signature in colon cancer.

Yi JM, Dhir M, Van Neste L, Downing SR, Jeschke J, Glöckner SC, de Freitas Calmon M, Hooker CM, Funes JM, Boshoff C, Smits KM, van Engeland M, Weijenberg MP, Iacobuzio-Donahue CA, Herman JG, Schuebel KE, Baylin SB, Ahuja N.

Clin Cancer Res. 2011 Mar 15;17(6):1535-45. doi: 10.1158/1078-0432.CCR-10-2509. Epub 2011 Jan 28.

15.

RNA sequencing: advances, challenges and opportunities.

Ozsolak F, Milos PM.

Nat Rev Genet. 2011 Feb;12(2):87-98. doi: 10.1038/nrg2934. Epub 2010 Dec 30. Review.

16.

Exon array analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer.

Langer W, Sohler F, Leder G, Beckmann G, Seidel H, Gröne J, Hummel M, Sommer A.

BMC Genomics. 2010 Nov 30;11:676. doi: 10.1186/1471-2164-11-676.

17.

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Katz Y, Wang ET, Airoldi EM, Burge CB.

Nat Methods. 2010 Dec;7(12):1009-15. doi: 10.1038/nmeth.1528. Epub 2010 Nov 7.

18.

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged.

David CJ, Manley JL.

Genes Dev. 2010 Nov 1;24(21):2343-64. doi: 10.1101/gad.1973010. Review.

19.

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.

Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin PC, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA.

Genome Res. 2011 Jan;21(1):56-67. doi: 10.1101/gr.110684.110. Epub 2010 Oct 29.

20.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

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