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Items: 1 to 20 of 111


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.


Empirical Bayes screening of many p-values with applications to microarray studies.

Datta S, Datta S.

Bioinformatics. 2005 May 1;21(9):1987-94. Epub 2005 Feb 2.


Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach.

Li D, Le Pape MA, Parikh NI, Chen WX, Dye TD.

PLoS One. 2013 Nov 27;8(11):e80099. doi: 10.1371/journal.pone.0080099. eCollection 2013.


Bayesian mixture model based clustering of replicated microarray data.

Medvedovic M, Yeung KY, Bumgarner RE.

Bioinformatics. 2004 May 22;20(8):1222-32. Epub 2004 Feb 10.


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.


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.


NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.

Bi Y, Davuluri RV.

BMC Bioinformatics. 2013 Aug 27;14:262. doi: 10.1186/1471-2105-14-262.


Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.

McCarthy DJ, Chen Y, Smyth GK.

Nucleic Acids Res. 2012 May;40(10):4288-97. doi: 10.1093/nar/gks042. Epub 2012 Jan 28.


Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.

't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT.

Nucleic Acids Res. 2008 Dec;36(21):e141. doi: 10.1093/nar/gkn705. Epub 2008 Oct 15.


Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.


Validation of differential gene expression algorithms: application comparing fold-change estimation to hypothesis testing.

Yanofsky CM, Bickel DR.

BMC Bioinformatics. 2010 Jan 28;11:63. doi: 10.1186/1471-2105-11-63.


BADGE: a novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data.

Gu J, Wang X, Halakivi-Clarke L, Clarke R, Xuan J.

BMC Bioinformatics. 2014;15 Suppl 9:S6. doi: 10.1186/1471-2105-15-S9-S6. Epub 2014 Sep 10.


GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y.

Bioinformatics. 2012 Nov 1;28(21):2782-8. doi: 10.1093/bioinformatics/bts515. Epub 2012 Aug 24.


Flexible empirical Bayes models for differential gene expression.

Lo K, Gottardo R.

Bioinformatics. 2007 Feb 1;23(3):328-35. Epub 2006 Nov 30.


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.


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.


Bayesian infinite mixture model based clustering of gene expression profiles.

Medvedovic M, Sivaganesan S.

Bioinformatics. 2002 Sep;18(9):1194-206.


Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL, Ohno-Machado L, Hovig E, Kuo WP.

BMC Genomics. 2007 Jun 7;8:153.


An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments.

Datta S, Satten GA, Benos DJ, Xia J, Heslin MJ, Datta S.

Bioinformatics. 2004 Jan 22;20(2):235-42.

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