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Benner, P.; Vingron, M.: ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. Journal of Computational Biology 27 (4), pp. 442 - 457 (2020)

Ramisch, A.; Heinrich, V.; Glaser, L. V.; Fuchs, A.; Yang, X.; Benner, P.; Schöpflin, R.; Li, N.; Kinkley, S.; Römer-Hillmann, A. et al.; Longinotto, J.; Heyne, S.; Czepukojc, B.; Kessler, S. M.; Kiemer, A. K.; Cadenas, C.; Arrigoni, L.; Gasparoni, N.; Manke, T.; Pap, T.; Pospisilik, A.; Hengstler, J.; Walter, J.; Meijsing, S.; Chung, H.-R.; Vingron, M.: CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biology: Biology for the Post-Genomic Era 20, 20:227 (2019)

Zehnder, T.; Benner, P.; Vingron, M.: Predicting enhancers in mammalian genomes using supervised hidden Markov models. BMC Bioinformatics 20, 157 (2019)

Schöne, S.; Bothe, A. M.; Einfeldt, E.; Borschiwer, M.; Benner, P. F.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genetics 14 (11), e1007793 (2018)