Robinson MD, Kahraman A, Law CW, Lindsay H, Nowicka M, Weber LM, Zhou X. Statistical methods for detecting differentially methylated loci and regions. Front Genet. 2014 Sep 16;5:324. doi: 10.3389/fgene.2014.00324. PMID: 25278959; PMCID: PMC4165320.
Abraham G, Kowalczyk A, Loi S, Haviv I, Zobel J. Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics. 2010 May 25;11:277. doi: 10.1186/1471-2105-11-277. PMID: 20500821; PMCID: PMC2895626.
Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Stat Methods Med Res. 2009 Dec;18(6):565-75. doi: 10.1177/0962280209351908. Erratum in: Stat Methods Med Res. 2011 Oct;20(5):571. PMID: 20048385; PMCID: PMC3134237.
Jung AY, Smulders Y, Verhoef P, Kok FJ, Blom H, Kok RM, Kampman E, Durga J. No effect of folic acid supplementation on global DNA methylation in men and women with moderately elevated homocysteine. PLoS One. 2011;6(9):e24976. doi: 10.1371/journal.pone.0024976. Epub 2011 Sep 23. PMID: 21966393; PMCID: PMC3179474.
Gevaert O. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics. 2015 Jun 1;31(11):1839-41. doi: 10.1093/bioinformatics/btv020. Epub 2015 Jan 20. PMID: 25609794; PMCID: PMC4443673.
Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics. 2014 Aug 15;30(16):2360-6. doi: 10.1093/bioinformatics/btu316. Epub 2014 May 2. PMID: 2
Korotkevich G, Sukhov V, Budin N, Shpak B, Artyomov MN, Sergushichev A. Fast gene set enrichment analysis. bioRxiv 060012; doi: https://doi.org/10.1101/060012
Robinson MD, Kahraman A, Law CW, Lindsay H, Nowicka M, Weber LM, Zhou X. Statistical methods for detecting differentially methylated loci and regions. Front Genet. 2014 Sep 16;5:324. doi: 10.3389/fgene.2014.00324. PMID: 25278959; PMCID: PMC4165320.
Abraham G, Kowalczyk A, Loi S, Haviv I, Zobel J. Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics. 2010 May 25;11:277. doi: 10.1186/1471-2105-11-277. PMID: 20500821; PMCID: PMC2895626.
Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Stat Methods Med Res. 2009 Dec;18(6):565-75. doi: 10.1177/0962280209351908. Erratum in: Stat Methods Med Res. 2011 Oct;20(5):571. PMID: 20048385; PMCID: PMC3134237.
Jung AY, Smulders Y, Verhoef P, Kok FJ, Blom H, Kok RM, Kampman E, Durga J. No effect of folic acid supplementation on global DNA methylation in men and women with moderately elevated homocysteine. PLoS One. 2011;6(9):e24976. doi: 10.1371/journal.pone.0024976. Epub 2011 Sep 23. PMID: 21966393; PMCID: PMC3179474.
Gevaert O. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics. 2015 Jun 1;31(11):1839-41. doi: 10.1093/bioinformatics/btv020. Epub 2015 Jan 20. PMID: 25609794; PMCID: PMC4443673.
Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics. 2014 Aug 15;30(16):2360-6. doi: 10.1093/bioinformatics/btu316. Epub 2014 May 2. PMID: 2
Korotkevich G, Sukhov V, Budin N, Shpak B, Artyomov MN, Sergushichev A. Fast gene set enrichment analysis. bioRxiv 060012; doi: https://doi.org/10.1101/060012