Aurélien Naldi
Aurélien Naldi
INRIA, France
Verified email at inria.fr - Homepage
Title
Cited by
Cited by
Year
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
A Fauré, A Naldi, C Chaouiya, D Thieffry
Bioinformatics 22 (14), e124-e131, 2006
6102006
Logical modelling of regulatory networks with GINsim 2.3
A Naldi, D Berenguier, A Fauré, F Lopez, D Thieffry, C Chaouiya
Biosystems 97 (2), 134-139, 2009
1792009
GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks
AG Gonzalez, A Naldi, L Sanchez, D Thieffry, C Chaouiya
Biosystems 84 (2), 91-100, 2006
1752006
Diversity and plasticity of Th cell types predicted from regulatory network modelling
A Naldi, J Carneiro, C Chaouiya, D Thieffry
PLoS computational biology 6 (9), e1000912, 2010
1612010
GOATOOLS: A Python library for Gene Ontology analyses
DV Klopfenstein, L Zhang, BS Pedersen, F Ramírez, AW Vesztrocy, ...
Scientific Reports 8 (1), 10872, 2018
1582018
Decision diagrams for the representation and analysis of logical models of genetic networks
A Naldi, D Thieffry, C Chaouiya
Proceedings of the 2007 international conference on Computational methods in …, 2007
1292007
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ...
BMC systems biology 7 (1), 135, 2013
1232013
Logical Modelling of Gene Regulatory Networks with GINsim.
C Chaouiya, A Naldi, D Thieffry
Methods in molecular biology (Clifton, NJ) 804, 463, 2012
1212012
Dynamically consistent reduction of logical regulatory graphs
A Naldi, E Remy, D Thieffry, C Chaouiya
Theoretical Computer Science 412 (21), 2207-2218, 2011
1182011
Model checking to assess T-helper cell plasticity
W Abou-Jaoudé, PT Monteiro, A Naldi, M Grandclaudon, V Soumelis, ...
Frontiers in bioengineering and biotechnology 2, 86, 2015
702015
Dynamical modeling and analysis of large cellular regulatory networks
D Bérenguier, C Chaouiya, PT Monteiro, A Naldi, E Remy, D Thieffry, ...
Chaos: An Interdisciplinary Journal of Nonlinear Science 23 (2), 025114, 2013
662013
A reduction of logical regulatory graphs preserving essential dynamical properties
A Naldi, E Remy, D Thieffry, C Chaouiya
Computational Methods in Systems Biology, 266-280, 2009
662009
Modular logical modelling of the budding yeast cell cycle
A Fauré, A Naldi, F Lopez, C Chaouiya, A Ciliberto, D Thieffry
Mol. BioSyst. 5 (12), 1787-1796, 2009
642009
Cooperative development of logical modelling standards and tools with CoLoMoTo
A Naldi, PT Monteiro, C Müssel, HA Kestler, D Thieffry, I Xenarios, ...
Bioinformatics 31 (7), 1154-1159, 2015
522015
Petri net representation of multi-valued logical regulatory graphs
C Chaouiya, A Naldi, E Remy, D Thieffry
Natural Computing 10 (2), 727-750, 2011
502011
MaBoSS 2.0: an environment for stochastic Boolean modeling
G Stoll, B Caron, E Viara, A Dugourd, A Zinovyev, A Naldi, G Kroemer, ...
Bioinformatics, 2017
472017
Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals
F Gilardi, E Migliavacca, A Naldi, M Baruchet, D Canella, G Le Martelot, ...
PLoS Genet 10 (3), e1004155, 2014
402014
On circuit functionality in Boolean networks
JP Comet, M Noual, A Richard, J Aracena, L Calzone, J Demongeot, ...
Bulletin of mathematical biology 75 (6), 906-919, 2013
372013
Logical modelling and analysis of cellular regulatory networks with GINsim 3.0
A Naldi, C Hernandez, W Abou-Jaoudé, PT Monteiro, C Chaouiya, ...
Frontiers in Physiology 9, 646, 2018
342018
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
A Naldi, C Hernandez, N Levy, G Stoll, PT Monteiro, C Chaouiya, ...
Frontiers in Physiology 9, 680, 2018
282018
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Articles 1–20