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)

Regulation of transcription reactivation dynamics exiting mitosis. - Sergio Sarnataro; Andrea Riba; Nacho Molina (PLoS Comput. Biol., 2021)