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Results: 1 to 20 of 62

1.

Gene ontology analysis for RNA-seq: accounting for selection bias.

Young MD, Wakefield MJ, Smyth GK, Oshlack A.

Genome Biol. 2010;11(2):R14. doi: 10.1186/gb-2010-11-2-r14. Epub 2010 Feb 4.

PMID:
20132535
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
21625565
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Uncovering the complexity of transcriptomes with RNA-Seq.

Costa V, Angelini C, De Feis I, Ciccodicola A.

J Biomed Biotechnol. 2010;2010:853916. doi: 10.1155/2010/853916. Epub 2010 Jun 27. Review.

PMID:
20625424
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.

Wang X, Cairns MJ.

BMC Bioinformatics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2105-14-S5-S16. Epub 2013 Apr 10.

PMID:
23734663
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Analysis of gene expression in prostate cancer epithelial and interstitial stromal cells using laser capture microdissection.

Gregg JL, Brown KE, Mintz EM, Piontkivska H, Fraizer GC.

BMC Cancer. 2010 Apr 28;10:165. doi: 10.1186/1471-2407-10-165.

PMID:
20426842
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC.

Bioinformatics. 2011 Jun 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.

PMID:
21478487
[PubMed - indexed for MEDLINE]
Free Article
7.

Identification of somatic mutations in human prostate cancer by RNA-Seq.

Xu X, Zhu K, Liu F, Wang Y, Shen J, Jin J, Wang Z, Chen L, Li J, Xu M.

Gene. 2013 May 1;519(2):343-7. doi: 10.1016/j.gene.2013.01.046. Epub 2013 Feb 19.

PMID:
23434521
[PubMed - indexed for MEDLINE]
8.

Comparative effects of DHEA and DHT on gene expression in human LNCaP prostate cancer cells.

Steele VE, Arnold JT, Lei H, Izmirlian G, Blackman MR.

Anticancer Res. 2006 Sep-Oct;26(5A):3205-15.

PMID:
17094431
[PubMed - indexed for MEDLINE]
Free Article
9.

Differentially expressed genes in the prostate cancer cell line LNCaP after exposure to androgen and anti-androgen.

Coutinho-Camillo CM, Salaorni S, Sarkis AS, Nagai MA.

Cancer Genet Cytogenet. 2006 Apr 15;166(2):130-8.

PMID:
16631469
[PubMed - indexed for MEDLINE]
10.

Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer.

Love HD, Booton SE, Boone BE, Breyer JP, Koyama T, Revelo MP, Shappell SB, Smith JR, Hayward SW.

PLoS One. 2009 Dec 21;4(12):e8384. doi: 10.1371/journal.pone.0008384.

PMID:
20027305
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Androgens down-regulate myosin light chain kinase in human prostate cancer cells.

Léveillé N, Fournier A, Labrie C.

J Steroid Biochem Mol Biol. 2009 Apr;114(3-5):174-9. doi: 10.1016/j.jsbmb.2009.02.002. Epub 2009 Feb 13.

PMID:
19429448
[PubMed - indexed for MEDLINE]
12.

Length bias correction in gene ontology enrichment analysis using logistic regression.

Mi G, Di Y, Emerson S, Cumbie JS, Chang JH.

PLoS One. 2012;7(10):e46128. doi: 10.1371/journal.pone.0046128. Epub 2012 Oct 2.

PMID:
23056249
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Differentially expressed genes in androgen-dependent and -independent prostate carcinomas.

Chang GT, Blok LJ, Steenbeek M, Veldscholte J, van Weerden WM, van Steenbrugge GJ, Brinkmann AO.

Cancer Res. 1997 Sep 15;57(18):4075-81.

PMID:
9307296
[PubMed - indexed for MEDLINE]
Free Article
14.

GREB1 is a novel androgen-regulated gene required for prostate cancer growth.

Rae JM, Johnson MD, Cordero KE, Scheys JO, Larios JM, Gottardis MM, Pienta KJ, Lippman ME.

Prostate. 2006 Jun 1;66(8):886-94.

PMID:
16496412
[PubMed - indexed for MEDLINE]
15.

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.

Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG, Tong W, Shi L.

Chem Res Toxicol. 2011 Sep 19;24(9):1486-93. doi: 10.1021/tx200103b. Epub 2011 Aug 23.

PMID:
21834575
[PubMed - indexed for MEDLINE]
16.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ.

BMC Genomics. 2006 Sep 29;7:246.

PMID:
17010196
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Endothelin-1 production by prostate cancer cell lines is up-regulated by factors involved in cancer progression and down-regulated by androgens.

Granchi S, Brocchi S, Bonaccorsi L, Baldi E, Vinci MC, Forti G, Serio M, Maggi M.

Prostate. 2001 Dec 1;49(4):267-77.

PMID:
11746273
[PubMed - indexed for MEDLINE]
18.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB.

Genome Biol. 2010;11(10):R104. doi: 10.1186/gb-2010-11-10-r104. Epub 2010 Oct 21.

PMID:
20964841
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.

PMID:
22345621
[PubMed - indexed for MEDLINE]
Free Article
20.

Novel expressed sequences identified in a model of androgen independent prostate cancer.

Quayle SN, Hare H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJ, Marra MA, Sadar MD.

BMC Genomics. 2007 Jan 26;8:32.

PMID:
17257419
[PubMed - indexed for MEDLINE]
Free PMC Article

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