BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. - Laurence Calzone; François Fages; Sylvain Soliman (Bioinform., 2006)

Machine Learning Biochemical Networks from Temporal Logic Properties. - Laurence Calzone; Nathalie Chabrier-Rivier; François Fages; Sylvain Soliman (Trans. Comp. Sys. Biology, 2006)

Langages formels dans la machine abstraite biochimique BIOCHAM. - Laurence Calzone; Nathalie Chabrier-Rivier; François Fages; L. Fosse; Sylvain Soliman (Tech. Sci. Informatiques, 2007)

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. - Andrei Yu. Zinovyev; Eric Viara; Laurence Calzone; Emmanuel Barillot (Bioinform., 2008)

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. - Laurence Calzone; Laurent Tournier; Simon Fourquet; Denis Thieffry; Boris Zhivotovsky; Emmanuel Barillot; Andrei Yu. Zinovyev (PLoS Comput. Biol., 2010)

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)

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. - Inna Kuperstein; David P. A. Cohen; Stuart Pook; Eric Viara; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision. - Luca Grieco; Laurence Calzone; Isabelle Bernard-Pierrot; François Radvanyi; Brigitte Kahn-Perlès; Denis Thieffry (PLoS Comput. Biol., 2013)

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. - Urszula Czerwinska; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2015)

NaviCell Web Service for network-based data visualization. - Eric Bonnet; Eric Viara; Inna Kuperstein; Laurence Calzone; David P. A. Cohen; Emmanuel Barillot; Andrei Yu. Zinovyev (Nucleic Acids Res., 2015)

Integrative Multi-omics Module Network Inference with Lemon-Tree. - Eric Bonnet; Laurence Calzone; Tom Michoel (PLoS Comput. Biol., 2015)

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. - David P. A. Cohen; Loredana Martignetti; Sylvie Robine; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (PLoS Comput. Biol., 2015)

Qualitative dynamics semantics for SBGN process description. - Adrien Rougny; Christine Froidevaux; Laurence Calzone; Loïc Paulevé (BMC Syst. Biol., 2016)

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)

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. - Arnau Montagud; Pauline Traynard; Loredana Martignetti; Eric Bonnet; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (Briefings Bioinform., 2019)

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)

Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. - Stéphanie Chevalier; Vincent Noël; Laurence Calzone; Andrei Yu. Zinovyev; Loïc Paulevé (CMSB, 2020)

Exact solving and sensitivity analysis of stochastic continuous time Boolean models. - Mihály Koltai; Vincent Noel; Andrei Yu. Zinovyev; Laurence Calzone; Emmanuel Barillot (BMC Bioinform., 2020)

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)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Andreas Dräger; Tomás Helikar; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar (Bioinform., 2021)

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. - Jonas Béal; Lorenzo Pantolini; Vincent Noël; Emmanuel Barillot; Laurence Calzone (PLoS Comput. Biol., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. - Anna Niarakis; Juilee Thakar; Matteo Barberis; María Rodríguez Martínez; Tomás Helikar; Marc R. Birtwistle; Claudine Chaouiya; Laurence Calzone; Andreas Dräger (Bioinform., 2022)

Building multiscale models with PhysiBoSS, an agent-based modeling tool. - Marco Ruscone; Andrea Checcoli; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Laurence Calzone; Vincent Noël (Briefings Bioinform., 2024)

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. - Gustavo Magaña López; Laurence Calzone; Andrei Yu. Zinovyev; Loïc Paulevé (PLoS Comput. Biol., 2024)

Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies. - Ulrike Weirauch; Markus Kreuz; Colin Birkenbihl; Miriam Alb; Maria Quaranta; Laurence Calzone; Sophia Orozco-Ruiz; Stefanie Binder; Luise Fischer; Solène Clavreul; Morine Maguri; Maximilian Ferle; et al. (npj Digit. Medicine, 2025)