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Results: 1 to 20 of 97

1.

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.

Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, Yu Y, Zhu D, Nickerson ML, Wan S, Liao X, Zhu X, Peng S, Li Y, Wang J, Guo G.

Genome Biol. 2013 Feb 14;14(2):R12. doi: 10.1186/gb-2013-14-2-r12.

PMID:
23409703
[PubMed - in process]
Free PMC Article
2.

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
3.

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362. Epub 2011 May 27.

PMID:
21622959
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data.

Huang S, Zhang J, Li R, Zhang W, He Z, Lam TW, Peng Z, Yiu SM.

Front Genet. 2011 Jul 7;2:46. doi: 10.3389/fgene.2011.00046. eCollection 2011.

PMID:
22303342
[PubMed]
Free PMC Article
6.

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Li Y, Zhao DY, Greenblatt JF, Zhang Z.

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.

PMID:
23455476
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W.

Bioinformatics. 2011 Jul 15;27(14):1922-8. doi: 10.1093/bioinformatics/btr310. Epub 2011 May 18.

PMID:
21593131
[PubMed - indexed for MEDLINE]
Free Article
9.

Recurrent read-through fusion transcripts in breast cancer.

Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM.

Breast Cancer Res Treat. 2014 Jul;146(2):287-97. doi: 10.1007/s10549-014-3019-2. Epub 2014 Jun 15.

PMID:
24929677
[PubMed - in process]
Free PMC Article
10.

RVboost: RNA-Seq variants prioritization using a boosting method.

Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW.

Bioinformatics. 2014 Aug 27. pii: btu577. [Epub ahead of print]

PMID:
25170027
[PubMed - as supplied by publisher]
Free Article
11.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.

PMID:
24209455
[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.

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A.

Cancer Prev Res (Phila). 2011 Jun;4(6):803-17. doi: 10.1158/1940-6207.CAPR-11-0212.

PMID:
21636547
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

PRADA: pipeline for RNA sequencing data analysis.

Torres-García W, Zheng S, Sivachenko A, Vegesna R, Wang Q, Yao R, Berger MF, Weinstein JN, Getz G, Verhaak RG.

Bioinformatics. 2014 Aug 1;30(15):2224-6. doi: 10.1093/bioinformatics/btu169. Epub 2014 Apr 1.

PMID:
24695405
[PubMed - in process]
15.

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.

Sheynkman GM, Shortreed MR, Frey BL, Smith LM.

Mol Cell Proteomics. 2013 Aug;12(8):2341-53. doi: 10.1074/mcp.O113.028142. Epub 2013 Apr 29.

PMID:
23629695
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, Slagboom PE, Ye K.

Bioinformatics. 2012 Feb 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.

PMID:
22219203
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.

PMID:
24130305
[PubMed - indexed for MEDLINE]
19.

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.

Li Y, Chien J, Smith DI, Ma J.

Bioinformatics. 2011 Jun 15;27(12):1708-10. doi: 10.1093/bioinformatics/btr265. Epub 2011 May 5.

PMID:
21546395
[PubMed - indexed for MEDLINE]
Free Article
20.

FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.

Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH.

PLoS One. 2012;7(6):e39987. doi: 10.1371/journal.pone.0039987. Epub 2012 Jun 27.

PMID:
22761941
[PubMed - indexed for MEDLINE]
Free PMC Article

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