Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. - Gautier Stoll; Jacques Rougemont; Felix Naef (Bioinform., 2006)

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. - Sylvain Blachon; Gautier Stoll; Carito Guziolowski; Andrei Yu. Zinovyev; Emmanuel Barillot; Anne Siegel; Ovidiu Radulescu (AIAI (Workshops), 2009)

Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. - Gautier Stoll; Mirko Bischofberger; Jacques Rougemont; Felix Naef (Biosyst., 2010)

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. - Tatiana Baumuratova; Didier Surdez; Bernard Delyon; Gautier Stoll; Olivier Delattre; Ovidiu Radulescu; Anne Siegel (BMC Syst. Biol., 2010)

Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. - Carito Guziolowski; Sylvain Blachon; Tatiana Baumuratova; Gautier Stoll; Ovidiu Radulescu; Anne Siegel (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. - Gautier Stoll; Eric Viara; Emmanuel Barillot; Laurence Calzone (BMC Syst. Biol., 2012)

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. - Eric Bonnet; Laurence Calzone; Daniel Rovera; Gautier Stoll; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

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)

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. - Gaëlle Letort; Arnau Montagud; Gautier Stoll; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Andrei Yu. Zinovyev; Laurence Calzone (Bioinform., 2019)

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)