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Results: 1 to 20 of 170

1.

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
2.

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.

PMID:
21385036
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.

PMID:
24130305
[PubMed - indexed for MEDLINE]
4.

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
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.

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
7.

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
8.

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
9.

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.

Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S2. doi: 10.1186/1471-2105-12-S14-S2.

PMID:
22373417
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data.

Duan J, Xia C, Zhao G, Jia J, Kong X.

BMC Genomics. 2012 Aug 14;13:392. doi: 10.1186/1471-2164-13-392.

PMID:
22891638
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

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
13.

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
14.

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G.

Bioinformatics. 2013 Oct 15;29(20):2529-38. doi: 10.1093/bioinformatics/btt442. Epub 2013 Aug 25.

PMID:
23980025
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.

PMID:
24209455
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq.

Lu B, Zeng Z, Shi T.

Sci China Life Sci. 2013 Feb;56(2):143-55. doi: 10.1007/s11427-013-4442-z. Epub 2013 Feb 8.

PMID:
23393030
[PubMed - indexed for MEDLINE]
19.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

PMID:
21572440
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A novel min-cost flow method for estimating transcript expression with RNA-Seq.

Tomescu AI, Kuosmanen A, Rizzi R, Mäkinen V.

BMC Bioinformatics. 2013;14 Suppl 5:S15. doi: 10.1186/1471-2105-14-S5-S15. Epub 2013 Apr 10.

PMID:
23734627
[PubMed - indexed for MEDLINE]
Free PMC Article

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