SwissRegulon: a database of genome-wide annotations of regulatory sites. - Mikhail Pachkov; Ionas Erb; Nacho Molina; Erik van Nimwegen (Nucleic Acids Res., 2007)

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. - Phil Arnold; Ionas Erb; Mikhail Pachkov; Nacho Molina; Erik van Nimwegen (Bioinform., 2012)

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. - Mikhail Pachkov; Piotr J. Balwierz; Phil Arnold; Evgeniy A. Ozonov; Erik van Nimwegen (Nucleic Acids Res., 2013)

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. - Saeed Omidi; Mihaela Zavolan; Mikhail Pachkov; Jeremie Breda; Severin Berger; Erik van Nimwegen (PLoS Comput. Biol., 2017)