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Items: 1 to 20 of 185

1.

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y.

Genome Res. 2008 Sep;18(9):1509-17. doi: 10.1101/gr.079558.108. Epub 2008 Jun 11.

2.

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.

Bottomly D, Walter NA, Hunter JE, Darakjian P, Kawane S, Buck KJ, Searles RP, Mooney M, McWeeney SK, Hitzemann R.

PLoS One. 2011 Mar 24;6(3):e17820. doi: 10.1371/journal.pone.0017820.

3.

Estimating accuracy of RNA-Seq and microarrays with proteomics.

Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P.

BMC Genomics. 2009 Apr 16;10:161. doi: 10.1186/1471-2164-10-161.

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.

5.

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.

6.

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.

Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG, Tong W, Shi L.

Chem Res Toxicol. 2011 Sep 19;24(9):1486-93. doi: 10.1021/tx200103b. Epub 2011 Aug 23.

PMID:
21834575
7.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP.

BMC Genomics. 2009 Nov 16;10:531. doi: 10.1186/1471-2164-10-531.

8.

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.

9.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

10.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

11.

Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.

Lahiry P, Lee LJ, Frey BJ, Rupar CA, Siu VM, Blencowe BJ, Hegele RA.

PLoS One. 2011;6(9):e25400. doi: 10.1371/journal.pone.0025400. Epub 2011 Sep 27.

12.

Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

Gavery MR, Roberts SB.

Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):94-9. doi: 10.1016/j.cbd.2011.12.003. Epub 2011 Dec 29.

PMID:
22244882
13.

Cross platform microarray analysis for robust identification of differentially expressed genes.

Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S5.

14.

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells.

Kloster MB, Bilgrau AE, Rodrigo-Domingo M, Bergkvist KS, Schmitz A, Sønderkær M, Bødker JS, Falgreen S, Nyegaard M, Johnsen HE, Nielsen KL, Dybkaer K, Bøgsted M.

BMC Genomics. 2012 Nov 5;13:596. doi: 10.1186/1471-2164-13-596.

15.

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.

Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, Etherington GJ, Sohn KH, MacLean D, Jones JD.

BMC Genomics. 2014 May 6;15:341. doi: 10.1186/1471-2164-15-341.

16.

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.

17.

Gene filtering in the analysis of Illumina microarray experiments.

Forcheh AC, Verbeke G, Kasim A, Lin D, Shkedy Z, Talloen W, Göhlmann HW, Clement L.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1710/1544-6115.1710.xml. doi: 10.2202/1544-6115.1710.

PMID:
22499694
18.

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.

19.

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates.

Wu Z, Jenkins BD, Rynearson TA, Dyhrman ST, Saito MA, Mercier M, Whitney LP.

BMC Bioinformatics. 2010 Nov 16;11:564. doi: 10.1186/1471-2105-11-564.

20.

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.

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