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Items: 1 to 20 of 215

1.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

PMID:
21697122
2.

Updating RNA-Seq analyses after re-annotation.

Roberts A, Schaeffer L, Pachter L.

Bioinformatics. 2013 Jul 1;29(13):1631-7. doi: 10.1093/bioinformatics/btt197. Epub 2013 May 14.

3.

Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A.

In Silico Biol. 2011-2012;11(5-6):251-61. doi: 10.3233/ISB-2012-0459.

PMID:
23202426
4.

wapRNA: a web-based application for the processing of RNA sequences.

Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S, Hu S.

Bioinformatics. 2011 Nov 1;27(21):3076-7. doi: 10.1093/bioinformatics/btr504. Epub 2011 Sep 6.

PMID:
21896507
5.

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences.

Bao E, Jiang T, Girke T.

Bioinformatics. 2013 May 15;29(10):1250-9. doi: 10.1093/bioinformatics/btt127. Epub 2013 Mar 14.

PMID:
23493323
6.

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

Watanabe KA, Homayouni A, Tufano T, Lopez J, Ringler P, Rushton P, Shen QJ.

DNA Res. 2015 Oct;22(5):319-29. doi: 10.1093/dnares/dsv015. Epub 2015 Sep 3.

7.

ECgene: genome annotation for alternative splicing.

Kim P, Kim N, Lee Y, Kim B, Shin Y, Lee S.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D75-9.

8.

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.

9.

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

Testa AC, Hane JK, Ellwood SR, Oliver RP.

BMC Genomics. 2015 Mar 11;16:170. doi: 10.1186/s12864-015-1344-4.

10.

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.

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.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Schulz MH, Zerbino DR, Vingron M, Birney E.

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

13.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

14.

RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K.

BMC Genomics. 2011 Nov 2;12:540. doi: 10.1186/1471-2164-12-540.

15.

FX: an RNA-Seq analysis tool on the cloud.

Hong D, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.

Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17.

PMID:
22257667
16.

Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

Kalume DE, Peri S, Reddy R, Zhong J, Okulate M, Kumar N, Pandey A.

BMC Genomics. 2005 Sep 19;6:128.

17.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

PMID:
19855105
18.

[Transcriptomes for serial analysis of gene expression].

Marti J, Piquemal D, Manchon L, Commes T.

J Soc Biol. 2002;196(4):303-7. Review. French.

PMID:
12645300
19.

RNA-eXpress annotates novel transcript features in RNA-seq data.

Forster SC, Finkel AM, Gould JA, Hertzog PJ.

Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.

20.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

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