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Items: 17

1.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA.

Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19.

2.

Mapping RNA-seq Reads with STAR.

Dobin A, Gingeras TR.

Curr Protoc Bioinformatics. 2015 Sep 3;51:11.14.1-19. doi: 10.1002/0471250953.bi1114s51. Review.

3.

Overview of available methods for diverse RNA-Seq data analyses.

Chen G, Wang C, Shi T.

Sci China Life Sci. 2011 Dec;54(12):1121-8. doi: 10.1007/s11427-011-4255-x. Epub 2012 Jan 7. Review.

PMID:
22227904
4.

A survey of best practices for RNA-seq data analysis.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Erratum in: Genome Biol. 2016;17(1):181.

5.

Computation for ChIP-seq and RNA-seq studies.

Pepke S, Wold B, Mortazavi A.

Nat Methods. 2009 Nov;6(11 Suppl):S22-32. doi: 10.1038/nmeth.1371. Review.

6.

[RNA-Seq and its applications: a new technology for transcriptomics].

Qi YX, Liu YB, Rong WH.

Yi Chuan. 2011 Nov;33(11):1191-202. Review. Chinese.

PMID:
22120074
7.

RNA-Seq: a revolutionary tool for transcriptomics.

Wang Z, Gerstein M, Snyder M.

Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Review.

8.

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.

Poplawski A, Marini F, Hess M, Zeller T, Mazur J, Binder H.

Brief Bioinform. 2016 Mar;17(2):213-23. doi: 10.1093/bib/bbv036. Epub 2015 Jun 23. Review.

PMID:
26108229
9.

Library construction for next-generation sequencing: overviews and challenges.

Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P.

Biotechniques. 2014 Feb 1;56(2):61-4, 66, 68, passim. doi: 10.2144/000114133. eCollection 2014. Review.

10.

Genome-guided transcriptome assembly in the age of next-generation sequencing.

Florea LD, Salzberg SL.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1234-40. Review.

11.

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.

Ding L, Rath E, Bai Y.

Curr Genomics. 2017 Jun;18(3):268-277. doi: 10.2174/1389202918666170215125048. Review.

PMID:
28659722
12.

A comprehensive overview and evaluation of circular RNA detection tools.

Zeng X, Lin W, Guo M, Zou Q.

PLoS Comput Biol. 2017 Jun 8;13(6):e1005420. doi: 10.1371/journal.pcbi.1005420. eCollection 2017 Jun. Review.

13.

Comprehensive molecular screening: from the RT-PCR to the RNA-seq.

Costa C, Giménez-Capitán A, Karachaliou N, Rosell R.

Transl Lung Cancer Res. 2013 Apr;2(2):87-91. doi: 10.3978/j.issn.2218-6751.2013.02.05. Review.

14.

High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants.

Brown JW, Calixto CP, Zhang R.

New Phytol. 2017 Jan;213(2):525-530. doi: 10.1111/nph.14208. Epub 2016 Sep 23. Review.

PMID:
27659901
15.

RNA sequencing: advances, challenges and opportunities.

Ozsolak F, Milos PM.

Nat Rev Genet. 2011 Feb;12(2):87-98. doi: 10.1038/nrg2934. Epub 2010 Dec 30. Review.

16.

Differential Expression Analysis for RNA-Seq: An Overview of Statistical Methods and Computational Software.

Huang HC, Niu Y, Qin LX.

Cancer Inform. 2015 Dec 13;14(Suppl 1):57-67. doi: 10.4137/CIN.S21631. eCollection 2015. Review.

17.

Single-cell RNA-sequencing of the brain.

Cuevas-Diaz Duran R, Wei H, Wu JQ.

Clin Transl Med. 2017 Dec;6(1):20. doi: 10.1186/s40169-017-0150-9. Epub 2017 Jun 8. Review.

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