Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. - James H. Bullard; Elizabeth Purdom; Kasper D. Hansen; Sandrine Dudoit (BMC Bioinform., 2010)

illuminaio: An open source IDAT parsing tool for Illumina microarrays. - Mike L. Smith; Keith A. Baggerly; Henrik Bengtsson; Matthew E. Ritchie; Kasper D. Hansen (F1000Research, 2013)

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. - Martin J. Aryee; Andrew E. Jaffe; Héctor Corrada Bravo; Christine Ladd-Acosta; Andrew P. Feinberg; Kasper D. Hansen; Rafael A. Irizarry (Bioinform., 2014)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. - Abhinav Nellore; Christopher Wilks; Kasper D. Hansen; Jeffrey T. Leek; Ben Langmead (Bioinform., 2016)

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. - Jean-Philippe Fortin; Timothy Triche; Kasper D. Hansen (Bioinform., 2017)

Addressing the mean-correlation relationship in co-expression analysis. - Yi Wang 097; Stephanie C. Hicks; Kasper D. Hansen (PLoS Comput. Biol., 2022)

Removing unwanted variation between samples in Hi-C experiments. - Kipper Fletez-Brant; Yunjiang Qiu; David U. Gorkin; Ming Hu; Kasper D. Hansen (Briefings Bioinform., 2024)