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Items: 1 to 20 of 178

1.

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.

2.

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads.

Chen HI, Liu Y, Zou Y, Lai Z, Sarkar D, Huang Y, Chen Y.

BMC Genomics. 2015;16 Suppl 7:S14. doi: 10.1186/1471-2164-16-S7-S14. Epub 2015 Jun 11.

3.

Power analysis and sample size estimation for RNA-Seq differential expression.

Ching T, Huang S, Garmire LX.

RNA. 2014 Nov;20(11):1684-96. doi: 10.1261/rna.046011.114. Epub 2014 Sep 22.

4.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

Zhang ZH, Jhaveri DJ, Marshall VM, Bauer DC, Edson J, Narayanan RK, Robinson GJ, Lundberg AE, Bartlett PF, Wray NR, Zhao QY.

PLoS One. 2014 Aug 13;9(8):e103207. doi: 10.1371/journal.pone.0103207. eCollection 2014.

5.

DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression.

George NI, Chang CW.

BMC Bioinformatics. 2014 Mar 31;15:92. doi: 10.1186/1471-2105-15-92.

6.

Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.

7.

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.

Li X, Brock GN, Rouchka EC, Cooper NGF, Wu D, O'Toole TE, Gill RS, Eteleeb AM, O'Brien L, Rai SN.

PLoS One. 2017 May 1;12(5):e0176185. doi: 10.1371/journal.pone.0176185. eCollection 2017.

8.

RNA-seq differential expression studies: more sequence or more replication?

Liu Y, Zhou J, White KP.

Bioinformatics. 2014 Feb 1;30(3):301-4. doi: 10.1093/bioinformatics/btt688. Epub 2013 Dec 6.

9.

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.

10.

Differential gene expression analysis using coexpression and RNA-Seq data.

Yang EW, Girke T, Jiang T.

Bioinformatics. 2013 Sep 1;29(17):2153-61. doi: 10.1093/bioinformatics/btt363. Epub 2013 Jun 21.

PMID:
23793751
11.

PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.

12.

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V, Wrobel N, Gharbi K, Simpson GG, Owen-Hughes T, Blaxter M, Barton GJ.

RNA. 2016 Jun;22(6):839-51. doi: 10.1261/rna.053959.115. Epub 2016 Mar 28. Erratum in: RNA. 2016 Oct;22(10):1641.

13.

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.

14.

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.

15.

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.

Lin Y, Golovnina K, Chen ZX, Lee HN, Negron YL, Sultana H, Oliver B, Harbison ST.

BMC Genomics. 2016 Jan 5;17:28. doi: 10.1186/s12864-015-2353-z.

16.

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.

17.

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

Finotello F, Di Camillo B.

Brief Funct Genomics. 2015 Mar;14(2):130-42. doi: 10.1093/bfgp/elu035. Epub 2014 Sep 18. Review.

PMID:
25240000
18.

Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates.

Al Seesi S, Tiagueu YT, Zelikovsky A, Măndoiu II.

BMC Genomics. 2014;15 Suppl 8:S2. doi: 10.1186/1471-2164-15-S8-S2. Epub 2014 Nov 13.

19.

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Glaus P, Honkela A, Rattray M.

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.

20.

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA.

PLoS One. 2013 Aug 19;8(8):e71745. doi: 10.1371/journal.pone.0071745. eCollection 2013.

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