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Results: 1 to 20 of 203

1.

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
2.

NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.

Xia Z, Wen J, Chang CC, Zhou X.

BMC Bioinformatics. 2011 May 16;12:162. doi: 10.1186/1471-2105-12-162.

PMID:
21575225
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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]
4.

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
5.

Identifying differentially spliced genes from two groups of RNA-seq samples.

Wang W, Qin Z, Feng Z, Wang X, Zhang X.

Gene. 2013 Apr 10;518(1):164-70. doi: 10.1016/j.gene.2012.11.045. Epub 2012 Dec 8.

PMID:
23228854
[PubMed - indexed for MEDLINE]
6.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

PMID:
20436464
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A robust method for transcript quantification with RNA-seq data.

Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J.

J Comput Biol. 2013 Mar;20(3):167-87. doi: 10.1089/cmb.2012.0230.

PMID:
23461570
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

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
10.

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
11.

Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.

Suo C, Calza S, Salim A, Pawitan Y.

Bioinformatics. 2014 Feb 15;30(4):506-13. doi: 10.1093/bioinformatics/btt704. Epub 2013 Dec 3.

PMID:
24307704
[PubMed - indexed for MEDLINE]
12.

IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly.

Li W, Feng J, Jiang T.

J Comput Biol. 2011 Nov;18(11):1693-707. doi: 10.1089/cmb.2011.0171. Epub 2011 Sep 27.

PMID:
21951053
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Brooks MJ, Rajasimha HK, Roger JE, Swaroop A.

Mol Vis. 2011;17:3034-54. Epub 2011 Nov 23.

PMID:
22162623
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Katz Y, Wang ET, Airoldi EM, Burge CB.

Nat Methods. 2010 Dec;7(12):1009-15. doi: 10.1038/nmeth.1528. Epub 2010 Nov 7.

PMID:
21057496
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.

Li W, Jiang T.

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.

PMID:
23060617
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.

Du J, Leng J, Habegger L, Sboner A, McDermott D, Gerstein M.

PLoS One. 2012;7(1):e29175. doi: 10.1371/journal.pone.0029175. Epub 2012 Jan 6.

PMID:
22238592
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.

Mezlini AM, Smith EJ, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M.

Genome Res. 2013 Mar;23(3):519-29. doi: 10.1101/gr.142232.112. Epub 2012 Nov 29.

PMID:
23204306
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.

PMID:
23734605
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.

Nariai N, Hirose O, Kojima K, Nagasaki M.

Bioinformatics. 2013 Sep 15;29(18):2292-9. doi: 10.1093/bioinformatics/btt381. Epub 2013 Jul 2.

PMID:
23821651
[PubMed - indexed for MEDLINE]

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