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Items: 1 to 20 of 59

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.

2.

Analysis of androgen and anti-androgen regulation of KLK-related peptidase 2, 3, and 4 alternative transcripts in prostate cancer.

Lai J, An J, Nelson CC, Lehman ML, Batra J, Clements JA.

Biol Chem. 2014 Sep;395(9):1127-32. doi: 10.1515/hsz-2014-0149.

PMID:
25153393
3.

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.

4.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.

Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD.

BMC Med Genomics. 2011 Jan 24;4:11. doi: 10.1186/1755-8794-4-11.

5.

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
6.

Gene Ontology based housekeeping gene selection for RNA-seq normalization.

Chen CM, Lu YL, Sio CP, Wu GC, Tzou WS, Pai TW.

Methods. 2014 Jun 1;67(3):354-63. doi: 10.1016/j.ymeth.2014.01.019. Epub 2014 Feb 18.

PMID:
24561167
7.

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
8.

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.

9.

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
10.

mRNA-Seq of single prostate cancer circulating tumor cells reveals recapitulation of gene expression and pathways found in prostate cancer.

Cann GM, Gulzar ZG, Cooper S, Li R, Luo S, Tat M, Stuart S, Schroth G, Srinivas S, Ronaghi M, Brooks JD, Talasaz AH.

PLoS One. 2012;7(11):e49144. doi: 10.1371/journal.pone.0049144. Epub 2012 Nov 7.

11.

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
12.

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
13.

Transcriptome profiling of the cancer and normal tissues from gastric cancer patients by deep sequencing.

Zhang FG, He ZY, Wang Q.

Tumour Biol. 2014 Aug;35(8):7423-7. doi: 10.1007/s13277-014-2003-0. Epub 2014 Apr 30.

PMID:
24777338
14.

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.

15.

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.

16.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

17.

Bias detection and correction in RNA-Sequencing data.

Zheng W, Chung LM, Zhao H.

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.

18.

A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond.

Lang BJ, Holton KM, Gong J, Calderwood SK.

Methods Mol Biol. 2018;1709:233-252. doi: 10.1007/978-1-4939-7477-1_18.

PMID:
29177664
19.

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.

20.

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

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