Aurélien Naldi

23 papers C 1Journal 16Unranked 6
YearRankTypeTitle / Venue / Authors
2023 J jnl
Linear cuts in Boolean networks.
Nat. Comput.
Aurélien Naldi, Adrien Richard, Elisa Tonello
2022 J jnl
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR
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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022 J jnl
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res.
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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. 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
2022 J jnl
Linear cuts in Boolean networks.
CoRR
Aurélien Naldi, Adrien Richard, Elisa Tonello
2021 — conf
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales.
CMSB
Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Yu. Zinovyev, Ovidiu Radulescu
2021 J jnl
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.
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
2020 J jnl
Automated inference of Boolean models from molecular interaction maps using CaSQ.
Bioinform.
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
2017 J jnl
MaBoSS 2.0: an environment for stochastic Boolean modeling.
Bioinform.
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
2017 J jnl
Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells.
PLoS Comput. Biol.
Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu
2016 J jnl
Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors.
Biosyst.
Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber, Nathalie Théret, Ovidiu Radulescu
2015 J jnl
Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinform.
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
2015 — conf
Symbolic Dynamics of Biochemical Pathways as Finite States Machines.
CMSB
Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber
2015 J jnl
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
J. Integr. Bioinform.
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
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
2012 — conf
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control.
CMSB
Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya
2011 J jnl
Dynamically consistent reduction of logical regulatory graphs.
Theor. Comput. Sci.
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2011 J jnl
Petri net representation of multi-valued logical regulatory graphs.
Nat. Comput.
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2010 J jnl
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.
PLoS Comput. Biol.
Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
2010 C conf
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties.
CCA
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2009 — conf
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties.
CMSB
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2009 J jnl
Logical modelling of regulatory networks with GINsim 2.3.
Biosyst.
Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, Fabrice Lopez, Denis Thieffry, Claudine Chaouiya
2007 — conf
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks.
CMSB
Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
2006 — conf
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.
ISMB (Supplement of Bioinformatics)
Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry