Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. - Frank Johannes; René Wardenaar; Maria Colomé-Tatché; Florence Mousson; Petra de Graaf; Michal Mokry; Victor Guryev; H. Th. Marc Timmers; Edwin Cuppen; Ritsert C. Jansen (Bioinform., 2010)

MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. - Michael Seifert; Sandra Cortijo; Maria Colomé-Tatché; Frank Johannes; François Roudier; Vincent Colot (Bioinform., 2012)

histoneHMM: Differential analysis of histone modifications with broad genomic footprints. - Matthias Heinig; Maria Colomé-Tatché; Aaron Taudt; Carola Rintisch; Sebastian Schafer; Michal Pravenec; Norbert Hübner; Martin Vingron; Frank Johannes (BMC Bioinform., 2015)

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. - David Porubsky; Ashley D. Sanders; Aaron Taudt; Maria Colomé-Tatché; Peter M. Lansdorp; Victor Guryev (Bioinform., 2020)

EpiScanpy: integrated single-cell epigenomic analysis. - Anna Danese; Maria L. Richter; Kridsadakorn Chaichoompu; David S. Fischer; Fabian J. Theis; Maria Colomé-Tatché (Zenodo, 2020)