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Results: 1 to 20 of 76

1.

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.

Genome Biol. 2013;14(9):R95.

PMID:
24020486
[PubMed - in process]
Free PMC Article
2.

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

Bullard JH, Purdom E, Hansen KD, Dudoit S.

BMC Bioinformatics. 2010 Feb 18;11:94. doi: 10.1186/1471-2105-11-94.

PMID:
20167110
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.

Wu H, Wang C, Wu Z.

Biostatistics. 2013 Apr;14(2):232-43. doi: 10.1093/biostatistics/kxs033. Epub 2012 Sep 22.

PMID:
23001152
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
5.

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.

Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB.

Microbiome. 2014 May 5;2:15. doi: 10.1186/2049-2618-2-15. eCollection 2014.

PMID:
24910773
[PubMed]
Free PMC Article
6.

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.

SEQC/MAQC-III Consortium; SEQC/MAQC-III Consortium.

Nat Biotechnol. 2014 Sep;32(9):903-14. doi: 10.1038/nbt.2957. Epub 2014 Aug 24.

PMID:
25150838
[PubMed - in process]
7.

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.

Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ.

BMC Genomics. 2010 May 5;11:282. doi: 10.1186/1471-2164-11-282.

PMID:
20444259
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Differential expression in RNA-seq: a matter of depth.

Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A.

Genome Res. 2011 Dec;21(12):2213-23. doi: 10.1101/gr.124321.111. Epub 2011 Sep 8.

PMID:
21903743
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A comparison of methods for differential expression analysis of RNA-seq data.

Soneson C, Delorenzi M.

BMC Bioinformatics. 2013 Mar 9;14:91. doi: 10.1186/1471-2105-14-91.

PMID:
23497356
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.

PMID:
21685096
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.

PMID:
22345621
[PubMed - indexed for MEDLINE]
Free Article
12.

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J.

Nucleic Acids Res. 2012 Nov 1;40(20):10084-97. doi: 10.1093/nar/gks804. Epub 2012 Sep 10.

PMID:
22965124
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.

Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, Chen R, Zhou H.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S5. doi: 10.1186/1471-2105-12-S10-S5.

PMID:
22165852
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.

Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, Jaffrézic F; French StatOmique Consortium.

Brief Bioinform. 2013 Nov;14(6):671-83. doi: 10.1093/bib/bbs046. Epub 2012 Sep 17.

PMID:
22988256
[PubMed - indexed for MEDLINE]
15.

ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

McKinney BA, White BC, Grill DE, Li PW, Kennedy RB, Poland GA, Oberg AL.

PLoS One. 2013 Dec 10;8(12):e81527. doi: 10.1371/journal.pone.0081527. eCollection 2013.

PMID:
24339943
[PubMed - in process]
Free PMC Article
16.

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
17.

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.

Robles JA, Qureshi SE, Stephen SJ, Wilson SR, Burden CJ, Taylor JM.

BMC Genomics. 2012 Sep 17;13:484. doi: 10.1186/1471-2164-13-484.

PMID:
22985019
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.

Paşaniuc B, Zaitlen N, Halperin E.

J Comput Biol. 2011 Mar;18(3):459-68. doi: 10.1089/cmb.2010.0259.

PMID:
21385047
[PubMed - indexed for MEDLINE]
19.

Comparison of software packages for detecting differential expression in RNA-seq studies.

Seyednasrollah F, Laiho A, Elo LL.

Brief Bioinform. 2013 Dec 2. [Epub ahead of print]

PMID:
24300110
[PubMed - as supplied by publisher]
20.

Phylogenomic distance method for analyzing transcriptome evolution based on RNA-seq data.

Gu X, Zou Y, Huang W, Shen L, Arendsee Z, Su Z.

Genome Biol Evol. 2013;5(9):1746-53. doi: 10.1093/gbe/evt121.

PMID:
23940099
[PubMed - indexed for MEDLINE]
Free PMC Article

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