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Results: 1 to 20 of 99

1.

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF.

Genome Biol. 2014 Feb 10;15(2):R34. doi: 10.1186/gb-2014-15-2-r34.

PMID:
24512684
[PubMed - in process]
Free PMC Article
2.

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

Otto C, Stadler PF, Hoffmann S.

Bioinformatics. 2014 Jul 1;30(13):1837-43. doi: 10.1093/bioinformatics/btu146. Epub 2014 Mar 13.

PMID:
24626854
[PubMed - in process]
3.

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
4.

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
5.

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
6.

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
7.

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF.

Bioinformatics. 2011 Jul 15;27(14):1894-900. doi: 10.1093/bioinformatics/btr314. Epub 2011 May 26.

PMID:
21622663
[PubMed - indexed for MEDLINE]
Free 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.

PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.

PMID:
23557086
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.

Gulledge AA, Vora H, Patel K, Loraine AE.

Methods Mol Biol. 2014;1158:123-37. doi: 10.1007/978-1-4939-0700-7_8.

PMID:
24792048
[PubMed - in process]
Free PMC Article
11.

TrueSight: a new algorithm for splice junction detection using RNA-seq.

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J.

Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18.

PMID:
23254332
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

Au KF, Jiang H, Lin L, Xing Y, Wong WH.

Nucleic Acids Res. 2010 Aug;38(14):4570-8. doi: 10.1093/nar/gkq211. Epub 2010 Apr 5.

PMID:
20371516
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.

PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11.

PMID:
19750212
[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.

SplicingCompass: differential splicing detection using RNA-seq data.

Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R.

Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.

PMID:
23449093
[PubMed - indexed for MEDLINE]
Free Article
16.

High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates.

Matsumoto J, Dewar K, Wasserscheid J, Wiley GB, Macmil SL, Roe BA, Zeller RW, Satou Y, Hastings KE.

Genome Res. 2010 May;20(5):636-45. doi: 10.1101/gr.100271.109. Epub 2010 Mar 8.

PMID:
20212022
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

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
19.

Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.

Srinivasan S, Patil AH, Verma M, Bingham JL, Srivatsan R.

J Clin Bioinforma. 2012 Nov 26;2(1):21. doi: 10.1186/2043-9113-2-21.

PMID:
23181285
[PubMed]
Free PMC Article
20.

Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene.

Khare P, Mortimer SI, Cleto CL, Okamura K, Suzuki Y, Kusakabe T, Nakai K, Meedel TH, Hastings KE.

Nucleic Acids Res. 2011 Apr;39(7):2638-48. doi: 10.1093/nar/gkq1151. Epub 2010 Nov 24.

PMID:
21109525
[PubMed - indexed for MEDLINE]
Free PMC Article

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