SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. - Julien Dorier; Isaac Crespo; Anne Niknejad; Robin Liechti; Martin Ebeling; Ioannis Xenarios (BMC Bioinform., 2016)

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. - Amel Bekkar; Anne Estreicher; Anne Niknejad; Cristina Casals-Casas; Alan J. Bridge; Ioannis Xenarios; Julien Dorier; Isaac Crespo (Database J. Biol. Databases Curation, 2018)

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids. - Julien Dorier; Dimos Goundaroulis; Fabrizio Benedetti; Andrzej Stasiak (Bioinform., 2018)

KnotProt 2.0: a database of proteins with knots and other entangled structures. - Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis; Julien Dorier; Piotr Sulkowski; Kenneth C. Millett; Eric J. Rawdon; Andrzej Stasiak; Joanna I. Sulkowska (Nucleic Acids Res., 2019)