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Items: 1 to 20 of 457

1.

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.

2.

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.

3.

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.

4.

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
5.

Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.

6.

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.

7.

Inference of isoforms from short sequence reads.

Feng J, Li W, Jiang T.

J Comput Biol. 2011 Mar;18(3):305-21. doi: 10.1089/cmb.2010.0243.

8.

Differential gene expression analysis using coexpression and RNA-Seq data.

Yang EW, Girke T, Jiang T.

Bioinformatics. 2013 Sep 1;29(17):2153-61. doi: 10.1093/bioinformatics/btt363. Epub 2013 Jun 21.

PMID:
23793751
9.

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.

10.

CIDANE: comprehensive isoform discovery and abundance estimation.

Canzar S, Andreotti S, Weese D, Reinert K, Klau GW.

Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0.

11.

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

Mangul S, Caciula A, Al Seesi S, Brinza D, MÓ‘ndoiu I, Zelikovsky A.

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

12.

Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model.

Wang Z, Wang J, Wu C, Deng M.

J Bioinform Comput Biol. 2015 Dec;13(6):1542001. doi: 10.1142/S0219720015420019. Epub 2015 Aug 11.

PMID:
26388142
13.

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.

14.

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.

Hu M, Zhu Y, Taylor JM, Liu JS, Qin ZS.

Bioinformatics. 2012 Jan 1;28(1):63-8. doi: 10.1093/bioinformatics/btr616. Epub 2011 Nov 8.

15.

smallWig: parallel compression of RNA-seq WIG files.

Wang Z, Weissman T, Milenkovic O.

Bioinformatics. 2016 Jan 15;32(2):173-80. doi: 10.1093/bioinformatics/btv561. Epub 2015 Sep 30.

PMID:
26424856
16.

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.

17.

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.

18.

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

Lee S, Seo CH, Alver BH, Lee S, Park PJ.

BMC Bioinformatics. 2015 Sep 3;16:278. doi: 10.1186/s12859-015-0704-z.

19.

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
20.

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.

Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X.

PLoS Comput Biol. 2016 Feb 19;12(2):e1004772. doi: 10.1371/journal.pcbi.1004772. eCollection 2016 Feb.

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