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Items: 1 to 20 of 327

1.

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.

2.

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.

3.

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.

4.

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R.

PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. doi: 10.1371/journal.pcbi.1004465. eCollection 2015 Dec.

5.

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.

6.

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads.

Warnke JD, Ali HH.

BMC Bioinformatics. 2013;14 Suppl 11:S7. doi: 10.1186/1471-2105-14-S11-S7. Epub 2013 Nov 4.

7.

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads.

Nariai N, Kojima K, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Nagasaki M.

BMC Genomics. 2014;15 Suppl 10:S5. doi: 10.1186/1471-2164-15-S10-S5. Epub 2014 Dec 12.

8.

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.

9.

Accurate inference of isoforms from multiple sample RNA-Seq data.

Tasnim M, Ma S, Yang EW, Jiang T, Li W.

BMC Genomics. 2015;16 Suppl 2:S15. doi: 10.1186/1471-2164-16-S2-S15. Epub 2015 Jan 21.

10.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Patro R, Mount SM, Kingsford C.

Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.

11.

SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.

Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C.

Genomics. 2013 Nov-Dec;102(5-6):507-14. doi: 10.1016/j.ygeno.2013.10.003. Epub 2013 Oct 23.

12.

Grape RNA-Seq analysis pipeline environment.

Knowles DG, Röder M, Merkel A, Guigó R.

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.

13.

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.

14.

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.

15.

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A.

BMC Genomics. 2014;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.

16.

Computational approaches for isoform detection and estimation: good and bad news.

Angelini C, De Canditiis D, De Feis I.

BMC Bioinformatics. 2014 May 9;15:135. doi: 10.1186/1471-2105-15-135.

17.

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.

18.

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.

Liu X, Shi X, Chen C, Zhang L.

BMC Bioinformatics. 2015 Oct 16;16:332. doi: 10.1186/s12859-015-0750-6.

19.

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.

20.

RNA-Seq for transcriptome analysis in non-model plants.

Garg R, Jain M.

Methods Mol Biol. 2013;1069:43-58. doi: 10.1007/978-1-62703-613-9_4.

PMID:
23996307
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