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Results: 1 to 20 of 100

1.

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
2.

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.

PMID:
21036922
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.

Ha KC, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros MB, Mitsopoulos C, Hakas J, Kozarewa I, Fenwick K, Lord CJ, Ashworth A, Vincent-Salomon A, Basik M, Reis-Filho JS, Majewski J, Foulkes WD.

BMC Med Genomics. 2011 Oct 27;4:75. doi: 10.1186/1755-8794-4-75.

PMID:
22032724
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
21261984
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.

Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A.

Bioinformatics. 2012 Dec 15;28(24):3232-9. doi: 10.1093/bioinformatics/bts617. Epub 2012 Oct 23.

PMID:
23093608
[PubMed - indexed for MEDLINE]
Free Article
6.

Chimeric transcript discovery by paired-end transcriptome sequencing.

Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8. doi: 10.1073/pnas.0904720106. Epub 2009 Jul 10.

PMID:
19592507
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
21625565
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.

Sakarya O, Breu H, Radovich M, Chen Y, Wang YN, Barbacioru C, Utiramerur S, Whitley PP, Brockman JP, Vatta P, Zhang Z, Popescu L, Muller MW, Kudlingar V, Garg N, Li CY, Kong BS, Bodeau JP, Nutter RC, Gu J, Bramlett KS, Ichikawa JK, Hyland FC, Siddiqui AS.

PLoS Comput Biol. 2012;8(4):e1002464. doi: 10.1371/journal.pcbi.1002464. Epub 2012 Apr 5.

PMID:
22496636
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.

Abate F, Acquaviva A, Paciello G, Foti C, Ficarra E, Ferrarini A, Delledonne M, Iacobucci I, Soverini S, Martinelli G, Macii E.

Bioinformatics. 2012 Aug 15;28(16):2114-21. doi: 10.1093/bioinformatics/bts334. Epub 2012 Jun 17.

PMID:
22711792
[PubMed - indexed for MEDLINE]
Free Article
10.

Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumägi A, Kallioniemi O.

PLoS One. 2012;7(10):e48745. doi: 10.1371/journal.pone.0048745. Epub 2012 Oct 31.

PMID:
23119097
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.

Bioinformatics. 2011 Apr 15;27(8):1068-75. doi: 10.1093/bioinformatics/btr085. Epub 2011 Feb 16.

PMID:
21330288
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.

Wu J, Zhang W, Huang S, He Z, Cheng Y, Wang J, Lam TW, Peng Z, Yiu SM.

Bioinformatics. 2013 Dec 1;29(23):2971-8. doi: 10.1093/bioinformatics/btt522. Epub 2013 Oct 11.

PMID:
24123671
[PubMed - indexed for MEDLINE]
13.

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.

Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Gerstein MB, Rubin MA.

Neoplasia. 2009 Aug;11(8):804-11.

PMID:
19649210
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.

Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Bernardi LR, Albertini A, Lee C, Mattick JS, Zucchi I, De Bellis G.

BMC Genomics. 2009 Apr 20;10:163. doi: 10.1186/1471-2164-10-163.

PMID:
19379481
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
21835007
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Chimeric transcript generated by cis-splicing of adjacent genes regulates prostate cancer cell proliferation.

Zhang Y, Gong M, Yuan H, Park HG, Frierson HF, Li H.

Cancer Discov. 2012 Jul;2(7):598-607. doi: 10.1158/2159-8290.CD-12-0042. Epub 2012 Jun 19.

PMID:
22719019
[PubMed - indexed for MEDLINE]
17.

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

Wang XS, Prensner JR, Chen G, Cao Q, Han B, Dhanasekaran SM, Ponnala R, Cao X, Varambally S, Thomas DG, Giordano TJ, Beer DG, Palanisamy N, Sartor MA, Omenn GS, Chinnaiyan AM.

Nat Biotechnol. 2009 Nov;27(11):1005-11. doi: 10.1038/nbt.1584. Epub 2009 Nov 1.

PMID:
19881495
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
19.

Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Chen YT, Scanlan MJ, Venditti CA, Chua R, Theiler G, Stevenson BJ, Iseli C, Gure AO, Vasicek T, Strausberg RL, Jongeneel CV, Old LJ, Simpson AJ.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7940-5. Epub 2005 May 19.

PMID:
15905330
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Liu C, Ma J, Chang CJ, Zhou X.

BMC Bioinformatics. 2013 Jun 15;14:193. doi: 10.1186/1471-2105-14-193.

PMID:
23768108
[PubMed - indexed for MEDLINE]
Free PMC Article

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