MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. - Matthias Lienhard; Christina Grimm; Markus Morkel; Ralf Herwig; Lukas Chavez (Bioinform., 2014)

Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data. - Matthias Lienhard; Lukas Chavez (Statistical Genomics, 2016)

Computational Analysis of Genome-wide Methylation Enrichment Experiments (Computergestützte Analyse genomweiter Methylierungsanreicherungsexperimente) - Matthias Lienhard (2017)

A bioinformatics workflow to detect genes with DNA methylation alterations: a case study of analyzing MeDIP-seq data in cardiac microtissue exposed to epirubicin. - Nhan Nguyen; Matthias Lienhard; Ralf Herwig; Jos Kleinjans; Danyel Jennen (ICBBB, 2022)