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Items: 1 to 20 of 54

1.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983.

2.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Erratum in: Nat Protoc. 2014 Oct;9(10):2513.

3.

Transcriptomic landscape of breast cancers through mRNA sequencing.

Eswaran J, Cyanam D, Mudvari P, Reddy SD, Pakala SB, Nair SS, Florea L, Fuqua SA, Godbole S, Kumar R.

Sci Rep. 2012;2:264. doi: 10.1038/srep00264. Epub 2012 Feb 14.

4.

BRCA1 testing should be offered to individuals with triple-negative breast cancer diagnosed below 50 years.

Robertson L, Hanson H, Seal S, Warren-Perry M, Hughes D, Howell I, Turnbull C, Houlston R, Shanley S, Butler S, Evans DG, Ross G, Eccles D, Tutt A, Rahman N; TNT Trial TMG; BCSC (UK).

Br J Cancer. 2012 Mar 13;106(6):1234-8. doi: 10.1038/bjc.2012.31. Epub 2012 Feb 14.

5.

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.

Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y.

Nucleic Acids Res. 2012 Apr;40(8):e61. doi: 10.1093/nar/gkr1291. Epub 2012 Jan 20.

6.

Progression of ductal carcinoma in situ to invasive breast cancer is associated with gene expression programs of EMT and myoepithelia.

Knudsen ES, Ertel A, Davicioni E, Kline J, Schwartz GF, Witkiewicz AK.

Breast Cancer Res Treat. 2012 Jun;133(3):1009-24. doi: 10.1007/s10549-011-1894-3. Epub 2011 Dec 2.

PMID:
22134623
7.

Splicing programs and cancer.

Germann S, Gratadou L, Dutertre M, Auboeuf D.

J Nucleic Acids. 2012;2012:269570. doi: 10.1155/2012/269570. Epub 2011 Oct 24.

8.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

9.

Alternative splicings on p53, BRCA1 and PTEN genes involved in breast cancer.

Okumura N, Yoshida H, Kitagishi Y, Nishimura Y, Matsuda S.

Biochem Biophys Res Commun. 2011 Sep 30;413(3):395-9. doi: 10.1016/j.bbrc.2011.08.098. Epub 2011 Aug 27. Review.

PMID:
21893034
10.

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype.

Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB, Gertler FB.

PLoS Genet. 2011 Aug;7(8):e1002218. doi: 10.1371/journal.pgen.1002218. Epub 2011 Aug 18.

11.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

12.

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
13.

Changes in aromatase (CYP19) gene promoter usage in non-small cell lung cancer.

Demura M, Demura Y, Ameshima S, Ishizaki T, Sasaki M, Miyamori I, Yamagishi M, Takeda Y, Bulun SE.

Lung Cancer. 2011 Sep;73(3):289-93. doi: 10.1016/j.lungcan.2011.01.003. Epub 2011 Feb 12.

14.

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts.

Ferreira EN, Rangel MC, Galante PF, de Souza JE, Molina GC, de Souza SJ, Carraro DM.

BMC Genomics. 2010 Dec 22;11 Suppl 5:S4. doi: 10.1186/1471-2164-11-S5-S4.

15.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS.

Genome Res. 2010 Dec;20(12):1730-9. doi: 10.1101/gr.108217.110. Epub 2010 Nov 2.

16.

Expression of tenascin-C and its isoforms in the breast.

Guttery DS, Shaw JA, Lloyd K, Pringle JH, Walker RA.

Cancer Metastasis Rev. 2010 Dec;29(4):595-606. doi: 10.1007/s10555-010-9249-9. Review.

PMID:
20814719
17.

Adducins regulate remodeling of apical junctions in human epithelial cells.

Naydenov NG, Ivanov AI.

Mol Biol Cell. 2010 Oct 15;21(20):3506-17. doi: 10.1091/mbc.E10-03-0259. Epub 2010 Sep 1.

18.

Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities.

Bemmo A, Dias C, Rose AA, Russo C, Siegel P, Majewski J.

PLoS One. 2010 Aug 6;5(8):e11981. doi: 10.1371/journal.pone.0011981.

19.

Alternative splicing and breast cancer.

Dutertre M, Vagner S, Auboeuf D.

RNA Biol. 2010 Jul-Aug;7(4):403-11. Epub 2010 Jul 1. Review.

PMID:
20622514
20.

Exon-level microarray analyses identify alternative splicing programs in breast cancer.

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW.

Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6.

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