MaBoSS 2.0: an environment for stochastic Boolean modeling. - Gautier Stoll; Barthélémy Caron; Eric Viara; Aurélien Dugourd; Andrei Yu. Zinovyev; Aurélien Naldi; Guido Kroemer; Emmanuel Barillot; Laurence Calzone (Bioinform., 2017)

Converting networks to predictive logic models from perturbation signalling data with CellNOpt. - Enio Gjerga; Panuwat Trairatphisan; Attila Gábor; Hermann Koch; Céline Chevalier; Franceco Ceccarelli; Aurélien Dugourd; Alexander Mitsos; Julio Saez-Rodriguez; Jonathan D. Wren (Bioinform., 2020)

FUNKI: interactive functional footprint-based analysis of omics data. - Rosa D. Hernansaiz-Ballesteros; Christian H. Holland; Aurélien Dugourd; Julio Saez-Rodriguez (Bioinform., 2022)

Bridging the gap between signalling and metabolism through functional and mechanistic analysis of multi-omic data - Aurélien Dugourd (2022)

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions. - Elias Farr; Daniel Dimitrov; Christina Schmidt; Dénes Türei; Sebastian Lobentanzer; Aurélien Dugourd; Julio Saez-Rodriguez (Briefings Bioinform., 2024)