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Results: 1 to 20 of 86

1.

Modeling non-uniformity in short-read rates in RNA-Seq data.

Li J, Jiang H, Wong WH.

Genome Biol. 2010;11(5):R50. doi: 10.1186/gb-2010-11-5-r50. Epub 2010 May 11.

PMID:
20459815
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.

Wang X, Wu Z, Zhang X.

J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:177-92.

PMID:
21155027
[PubMed - indexed for MEDLINE]
3.

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. Epub 2008 May 30.

PMID:
18516045
[PubMed - indexed for MEDLINE]
4.

Towards reliable isoform quantification using RNA-SEQ data.

Howard BE, Heber S.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6. doi: 10.1186/1471-2105-11-S3-S6.

PMID:
20438653
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. doi: 10.1073/pnas.1113972108. Epub 2011 Dec 1.

PMID:
22135461
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.

Wu Z, Wang X, Zhang X.

Bioinformatics. 2011 Feb 15;27(4):502-8. doi: 10.1093/bioinformatics/btq696. Epub 2010 Dec 17.

PMID:
21169371
[PubMed - indexed for MEDLINE]
Free Article
7.

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.

Srivastava S, Chen L.

Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670. Epub 2010 Jul 29.

PMID:
20671027
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Richard H, Schulz MH, Sultan M, N├╝rnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML.

Nucleic Acids Res. 2010 Jun;38(10):e112. doi: 10.1093/nar/gkq041. Epub 2010 Feb 11.

PMID:
20150413
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.

Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.

PMID:
20022975
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Statistical inferences for isoform expression in RNA-Seq.

Jiang H, Wong WH.

Bioinformatics. 2009 Apr 15;25(8):1026-32. doi: 10.1093/bioinformatics/btp113. Epub 2009 Feb 25.

PMID:
19244387
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.

Hu Y, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M.

Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20.

PMID:
24362841
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

PMID:
18990248
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching.

Rehrauer H, Opitz L, Tan G, Sieverling L, Schlapbach R.

BMC Bioinformatics. 2013 Dec 24;14:370. doi: 10.1186/1471-2105-14-370.

PMID:
24365034
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Bias detection and correction in RNA-Sequencing data.

Zheng W, Chung LM, Zhao H.

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.

PMID:
21771300
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.

Kim H, Bi Y, Pal S, Gupta R, Davuluri RV.

BMC Bioinformatics. 2011 Jul 27;12:305. doi: 10.1186/1471-2105-12-305.

PMID:
21794104
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U.

Genome Biol. 2010;11(3):R34. doi: 10.1186/gb-2010-11-3-r34. Epub 2010 Mar 17.

PMID:
20236510
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.

Wu H, Wang C, Wu Z.

Biostatistics. 2013 Apr;14(2):232-43. doi: 10.1093/biostatistics/kxs033. Epub 2012 Sep 22.

PMID:
23001152
[PubMed - indexed for MEDLINE]
Free PMC Article
18.
19.

Reducing bias in RNA sequencing data: a novel approach to compute counts.

Finotello F, Lavezzo E, Bianco L, Barzon L, Mazzon P, Fontana P, Toppo S, Di Camillo B.

BMC Bioinformatics. 2014;15 Suppl 1:S7. doi: 10.1186/1471-2105-15-S1-S7. Epub 2014 Jan 10.

PMID:
24564404
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Finding the common structure shared by two homologous RNAs.

Perriquet O, Touzet H, Dauchet M.

Bioinformatics. 2003 Jan;19(1):108-16.

PMID:
12499300
[PubMed - indexed for MEDLINE]
Free Article

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