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Results: 1 to 20 of 159

1.

The bench scientist's guide to statistical analysis of RNA-Seq data.

Yendrek CR, Ainsworth EA, Thimmapuram J.

BMC Res Notes. 2012 Sep 14;5:506. doi: 10.1186/1756-0500-5-506.

PMID:
22980220
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
3.

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.

PMID:
21824971
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.

Raghavachari N, Barb J, Yang Y, Liu P, Woodhouse K, Levy D, O'Donnell CJ, Munson PJ, Kato GJ.

BMC Med Genomics. 2012 Jun 29;5:28. doi: 10.1186/1755-8794-5-28.

PMID:
22747986
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.

Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR.

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.

PMID:
23965047
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.

Black MB, Parks BB, Pluta L, Chu TM, Allen BC, Wolfinger RD, Thomas RS.

Toxicol Sci. 2014 Feb;137(2):385-403. doi: 10.1093/toxsci/kft249. Epub 2013 Nov 5.

PMID:
24194394
[PubMed - indexed for MEDLINE]
7.

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data.

Kvam VM, Liu P, Si Y.

Am J Bot. 2012 Feb;99(2):248-56. doi: 10.3732/ajb.1100340. Epub 2012 Jan 20. Review.

PMID:
22268221
[PubMed - indexed for MEDLINE]
Free Article
8.

A model based criterion for gene expression calls using RNA-seq data.

Wagner GP, Kin K, Lynch VJ.

Theory Biosci. 2013 Sep;132(3):159-64. doi: 10.1007/s12064-013-0178-3. Epub 2013 Apr 25.

PMID:
23615947
[PubMed - indexed for MEDLINE]
9.

Identifying differentially spliced genes from two groups of RNA-seq samples.

Wang W, Qin Z, Feng Z, Wang X, Zhang X.

Gene. 2013 Apr 10;518(1):164-70. doi: 10.1016/j.gene.2012.11.045. Epub 2012 Dec 8.

PMID:
23228854
[PubMed - indexed for MEDLINE]
10.

RNA-seq analysis of transcriptomes in thrombin-treated and control human pulmonary microvascular endothelial cells.

Cheranova D, Gibson M, Chaudhary S, Zhang LQ, Heruth DP, Grigoryev DN, Ye SQ.

J Vis Exp. 2013 Feb 13;(72). pii: 4393. doi: 10.3791/4393.

PMID:
23426025
[PubMed - indexed for MEDLINE]
11.

Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencing.

Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R.

BMC Med Genet. 2009 Dec 31;10:149. doi: 10.1186/1471-2350-10-149.

PMID:
20043850
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.

Wan L, Sun F.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Sep-Oct;9(5):1281-92.

PMID:
22641709
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A.

Cancer Prev Res (Phila). 2011 Jun;4(6):803-17. doi: 10.1158/1940-6207.CAPR-11-0212.

PMID:
21636547
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq.

Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP.

PLoS One. 2011;6(10):e26426. doi: 10.1371/journal.pone.0026426. Epub 2011 Oct 19. Erratum in: PLoS One. 2011;6(11). doi: 10.1371/annotation/e5ef7afc-7e81-4053-8670-1bb3402f63fd.

PMID:
22039485
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering.

Sîrbu A, Kerr G, Crane M, Ruskin HJ.

PLoS One. 2012;7(12):e50986. doi: 10.1371/journal.pone.0050986. Epub 2012 Dec 10.

PMID:
23251411
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data.

Tonner P, Srinivasasainagendra V, Zhang S, Zhi D.

BMC Genomics. 2012 Aug 21;13:412. doi: 10.1186/1471-2164-13-412.

PMID:
22908858
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.

Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, Xu Z, Liu H.

BMC Bioinformatics. 2012 Dec 13;13:331. doi: 10.1186/1471-2105-13-331.

PMID:
23237380
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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
20.

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

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