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Items: 1 to 20 of 341

1.

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
2.

Next generation sequencing of microbial transcriptomes: challenges and opportunities.

van Vliet AH.

FEMS Microbiol Lett. 2010 Jan;302(1):1-7. doi: 10.1111/j.1574-6968.2009.01767.x. Epub 2009 Aug 21. Review.

3.

Rat toxicogenomic study reveals analytical consistency across microarray platforms.

Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L.

Nat Biotechnol. 2006 Sep;24(9):1162-9.

PMID:
17061323
4.

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.

5.

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.

Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S, Zhu W, Davidson NO, Denoya P, Li E.

BMC Bioinformatics. 2013;14 Suppl 9:S1. doi: 10.1186/1471-2105-14-S9-S1. Epub 2013 Jun 28.

6.

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
7.

RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.

van Delft J, Gaj S, Lienhard M, Albrecht MW, Kirpiy A, Brauers K, Claessen S, Lizarraga D, Lehrach H, Herwig R, Kleinjans J.

Toxicol Sci. 2012 Dec;130(2):427-39. doi: 10.1093/toxsci/kfs250. Epub 2012 Aug 13.

PMID:
22889811
8.

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
9.

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.

10.

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.

Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, Thompson KL.

BMC Genomics. 2008 Jun 12;9:285. doi: 10.1186/1471-2164-9-285.

11.

RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing.

Wilhelm BT, Landry JR.

Methods. 2009 Jul;48(3):249-57. doi: 10.1016/j.ymeth.2009.03.016. Epub 2009 Mar 29.

PMID:
19336255
12.

Optimization of an animal test protocol for toxicogenomics studies (ii); a cross-laboratory gene expression analysis.

Sumida K, Saito K, Oeda K, Otsuka M, Tsujimura K, Miyaura H, Sekijima M, Nakayama K, Kawano Y, Kawakami Y, Asamoto M, Shirai T.

J Toxicol Sci. 2007 Feb;32(1):33-45.

13.

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR.

BMC Genomics. 2006 Mar 21;7:59.

14.

Toxicogenomics in the assessment of immunotoxicity.

Baken KA, Vandebriel RJ, Pennings JL, Kleinjans JC, van Loveren H.

Methods. 2007 Jan;41(1):132-41. Review.

PMID:
17161310
15.

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.

16.

Optimization of an animal test protocol for toxicogenomics studies (I); requirement study of a protocol.

Sumida K, Saito K, Oeda K, Otsuka M, Tsujimura K, Miyaura H, Sekijima M, Nakayama K, Kawano Y, Kawakami Y, Asamoto M, Shirai T.

J Toxicol Sci. 2007 Feb;32(1):19-32.

17.

RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice.

Nault R, Fader KA, Zacharewski T.

BMC Genomics. 2015 May 10;16:373. doi: 10.1186/s12864-015-1527-z.

18.

Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats.

Chen T, Guo L, Zhang L, Shi L, Fang H, Sun Y, Fuscoe JC, Mei N.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S20.

19.

Power of deep sequencing and agilent microarray for gene expression profiling study.

Feng L, Liu H, Liu Y, Lu Z, Guo G, Guo S, Zheng H, Gao Y, Cheng S, Wang J, Zhang K, Zhang Y.

Mol Biotechnol. 2010 Jun;45(2):101-10. doi: 10.1007/s12033-010-9249-6.

PMID:
20432071
20.

Methods for evaluating gene expression from Affymetrix microarray datasets.

Jiang N, Leach LJ, Hu X, Potokina E, Jia T, Druka A, Waugh R, Kearsey MJ, Luo ZW.

BMC Bioinformatics. 2008 Jun 17;9:284. doi: 10.1186/1471-2105-9-284.

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