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ORCIDAurélien Naldi
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2020 – today
- 2023
[j14]Aurélien Naldi
, Adrien Richard, Elisa Tonello:
Linear cuts in Boolean networks. Nat. Comput. 22(3): 431-451 (2023)- 2022
- [j13]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i2]Aurélien Naldi, Adrien Richard, Elisa Tonello:
Linear cuts in Boolean networks. CoRR abs/2203.01620 (2022) - [i1]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j12]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): 1848-1859 (2021) - [c7]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: 238-244 - 2020
- [j11]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): 4473-4482 (2020)
2010 – 2019
- 2017
- [j10]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): 2226-2228 (2017) - [j9]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) - 2016
- [j8]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: 3-14 (2016) - 2015
- [j7]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): 1154-1159 (2015) - [j6]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) - [c6]Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber:
Symbolic Dynamics of Biochemical Pathways as Finite States Machines. CMSB 2015: 104-120 - 2013
- [j5]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: 135 (2013) - 2012
- [c5]Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya:
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. CMSB 2012: 288-306 - 2011
- [j4]Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry:
Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. 10(2): 727-750 (2011) - [j3]Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. 412(21): 2207-2218 (2011) - 2010
- [j2]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) - [c4]Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry:
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA 2010: 524-529
2000 – 2009
- 2009
- [j1]Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, F. Lopez, Denis Thieffry, Claudine Chaouiya:
Logical modelling of regulatory networks with GINsim 2.3. Biosyst. 97(2): 134-139 (2009) - [c3]Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB 2009: 266-280 - 2007
- [c2]Aurélien Naldi, Denis Thieffry, Claudine Chaouiya:
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB 2007: 233-247 - 2006
- [c1]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: 124-131
Coauthor Index
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