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Results: 1 to 20 of 100

1.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.

PMID:
23618408
[PubMed - in process]
Free PMC Article
2.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

PMID:
19289445
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

HSA: a heuristic splice alignment tool.

Bu J, Chi X, Jin Z.

BMC Syst Biol. 2013;7 Suppl 2:S10. doi: 10.1186/1752-0509-7-S2-S10. Epub 2013 Dec 17.

PMID:
24564867
[PubMed - in process]
Free PMC Article
4.

STAR: ultrafast universal RNA-seq aligner.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.

Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

PMID:
23104886
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.

Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W.

Bioinformatics. 2013 Jul 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216.

PMID:
23812996
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

RNA-Seq read alignments with PALMapper.

Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708
[PubMed - indexed for MEDLINE]
7.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.

PMID:
18689821
[PubMed - indexed for MEDLINE]
Free Article
8.

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.

Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.

PMID:
20802226
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Supersplat--spliced RNA-seq alignment.

Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC.

Bioinformatics. 2010 Jun 15;26(12):1500-5. doi: 10.1093/bioinformatics/btq206. Epub 2010 Apr 21.

PMID:
20410051
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

SPA: a probabilistic algorithm for spliced alignment.

van Nimwegen E, Paul N, Sheridan R, Zavolan M.

PLoS Genet. 2006 Apr;2(4):e24. Epub 2006 Apr 28.

PMID:
16683023
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SRmapper: a fast and sensitive genome-hashing alignment tool.

Gontarz PM, Berger J, Wong CF.

Bioinformatics. 2013 Feb 1;29(3):316-21. doi: 10.1093/bioinformatics/bts712. Epub 2012 Dec 24.

PMID:
23267171
[PubMed - indexed for MEDLINE]
Free Article
13.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA.

Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.

PMID:
21775302
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.

Nucleic Acids Res. 2013 May 1;41(10):5149-63. doi: 10.1093/nar/gkt216. Epub 2013 Apr 9.

PMID:
23571760
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN.

BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323.

PMID:
21816040
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Comparing reference-based RNA-Seq mapping methods for non-human primate data.

Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE.

BMC Genomics. 2014 Jul 7;15:570. doi: 10.1186/1471-2164-15-570.

PMID:
25001289
[PubMed - in process]
Free PMC 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.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

PMID:
21653520
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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

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