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)

Multiple sequence alignment modeling: methods and applications. - Maria Chatzou; Cedrik Magis; Jia-Ming Chang; Carsten Kemena; Giovanni Bussotti; Ionas Erb; Cédric Notredame (Briefings Bioinform., 2016)

How should we measure proportionality on relative gene expression data? - Ionas Erb; Cédric Notredame (Theory Biosci., 2016)

Understanding sequencing data as compositions: an outlook and review. - Thomas P. Quinn; Ionas Erb; Mark F. Richardson; Tamsyn M. Crowley (Bioinform., 2018)

Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. - Jose Espinosa-Carrasco; Antonio Hermoso Pulido; Ionas Erb; Mara Dierssen; Julia V. Ponomarenko; Cédric Notredame (Nucleic Acids Res., 2019)

Highly significant improvement of protein sequence alignments with AlphaFold2. - Athanasios Baltzis; Leila Mansouri; Suzanne Jin; Björn E. Langer; Ionas Erb; Cédric Notredame (Bioinform., 2022)