Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 137

1.

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S, Lewin A.

Genome Biol. 2011;12(2):R13. doi: 10.1186/gb-2011-12-2-r13. Epub 2011 Feb 10.

PMID:
21310039
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
24307704
[PubMed - indexed for MEDLINE]
3.

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
4.

Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.

Pandey RV, Franssen SU, Futschik A, Schlötterer C.

Mol Ecol Resour. 2013 Jul;13(4):740-5. doi: 10.1111/1755-0998.12110. Epub 2013 Apr 25.

PMID:
23615333
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.

Ma X, Zhang X.

BMC Bioinformatics. 2013 Jul 10;14:220. doi: 10.1186/1471-2105-14-220.

PMID:
23837734
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
24161398
[PubMed - indexed for MEDLINE]
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.

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
10.

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]
11.

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.

Seok J, Xu W, Jiang H, Davis RW, Xiao W.

PLoS One. 2012;7(2):e31440. doi: 10.1371/journal.pone.0031440. Epub 2012 Feb 1.

PMID:
22312447
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

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
14.

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
15.

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
16.

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
17.

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

Schulz MH, Zerbino DR, Vingron M, Birney E.

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

PMID:
22368243
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
19.

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
20.

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

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk