Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD and Irizarry RA (2014). “Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.” Bioinformatics, 30(10), pp. 1363–1369. doi: 10.1093/bioinformatics/btu049.

Maksimovic J, Gordon L and Oshlack A (2012). “SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips.” Genome Biology, 13(6), pp. R44. doi: 10.1186/gb-2012-13-6-r44.

Fortin J, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM and Hansen KD (2014). “Functional normalization of 450k methylation array data improves replication in large cancer studies.” Genome Biology, 15(12), pp. 503. doi: 10.1186/s13059-014-0503-2.

Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW and Siegmund KD (2013). “Low-level processing of Illumina Infinium DNA Methylation BeadArrays.” Nucleic Acids Research, 41(7), pp. e90. doi: 10.1093/nar/gkt090.

Fortin J and Hansen KD (2015). “Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.” Genome Biology, 16, pp. 180. doi: 10.1186/s13059-015-0741-y.

Fortin J and Hansen KD (2016). “'Gap hunting' to identify multimodal distributions of DNA methylation.” bioRxiv. doi: 10.1101/059659.

Fortin J, Triche TJ and Hansen KD (2016). “Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array.” bioRxiv. doi: 10.1101/065490.