Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. - Adrien Fauré; Aurélien Naldi; Claudine Chaouiya; Denis Thieffry (ISMB (Supplement of Bioinformatics), 2006)

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. - Aurélien Naldi; Denis Thieffry; Claudine Chaouiya (CMSB, 2007)

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (CMSB, 2009)

Logical modelling of regulatory networks with GINsim 2.3. - Aurélien Naldi; Duncan Bérenguier; Adrien Fauré; F. Lopez; Denis Thieffry; Claudine Chaouiya (Biosyst., 2009)

Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (CCA, 2010)

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. - Aurélien Naldi; Jorge Carneiro; Claudine Chaouiya; Denis Thieffry (PLoS Comput. Biol., 2010)

Petri net representation of multi-valued logical regulatory graphs. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (Nat. Comput., 2011)

Dynamically consistent reduction of logical regulatory graphs. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (Theor. Comput. Sci., 2011)

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. - Aurélien Naldi; Pedro T. Monteiro 001; Claudine Chaouiya (CMSB, 2012)

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)

Symbolic Dynamics of Biochemical Pathways as Finite States Machines. - Ovidiu Radulescu; Satya Swarup Samal; Aurélien Naldi; Dima Grigoriev; Andreas Weber 004 (CMSB, 2015)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. - Claudine Chaouiya; Sarah M. Keating; Duncan Bérenguier; Aurélien Naldi; Denis Thieffry; Martijn P. van Iersel; Nicolas Le Novère; Tomás Helikar (J. Integr. Bioinform., 2015)

Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors. - Satya Swarup Samal; Aurélien Naldi; Dima Grigoriev; Andreas Weber 004; Nathalie Théret; Ovidiu Radulescu (Biosyst., 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)

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. - Aurélien Naldi; Romain M. Larive; Urszula Czerwinska; Serge Urbach; Philippe Montcourrier; Christian Roy; Jérôme Solassol; Gilles Freiss; Peter J. Coopman; Ovidiu Radulescu (PLoS Comput. Biol., 2017)

Automated inference of Boolean models from molecular interaction maps using CaSQ. - Sara Sadat Aghamiri; Vidisha Singh; Aurélien Naldi; Tomás Helikar; Sylvain Soliman; Anna Niarakis; Jinbo Xu (Bioinform., 2020)

LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. - Marion Buffard; Aurélien Desoeuvres; Aurélien Naldi; Clément Requilé; Andrei Yu. Zinovyev; Ovidiu Radulescu (CMSB, 2021)

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)

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)

Linear cuts in Boolean networks. - Aurélien Naldi; Adrien Richard; Elisa Tonello (Nat. Comput., 2023)