Aurélien Naldi

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 10

Top Topics

Value Added Services

Dynamic Networks

Qualitative Models

Top Venues

Publications

Aurélien Naldi, Adrien Richard, Elisa Tonello
Linear cuts in Boolean networks. Nat. Comput. 22 (3) (2023)
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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50 (W1) (2022)
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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR (2022)
Aurélien Naldi, Adrien Richard, Elisa Tonello
Linear cuts in Boolean networks. CoRR (2022)
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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
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. Briefings Bioinform. 22 (2) (2021)
Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Yu. Zinovyev, Ovidiu Radulescu
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. CMSB (2021)
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinform. 36 (16) (2020)
Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu
Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLoS Comput. Biol. 13 (3) (2017)
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinform. 33 (14) (2017)
Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber, Nathalie Théret, Ovidiu Radulescu
Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors. Biosyst. 149 (2016)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. 12 (2) (2015)
Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber
Symbolic Dynamics of Biochemical Pathways as Finite States Machines. CMSB (2015)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. CMSB (2012)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. 412 (21) (2011)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. 10 (2) (2011)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA (2010)
Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput. Biol. 6 (9) (2010)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB (2009)
Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, F. Lopez, Denis Thieffry, Claudine Chaouiya
Logical modelling of regulatory networks with GINsim 2.3. Biosyst. 97 (2) (2009)
Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB (2007)
Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. ISMB (Supplement of Bioinformatics) (2006)