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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
6912006
GOATOOLS: A Python library for Gene Ontology analyses
DV Klopfenstein, L Zhang, BS Pedersen, F Ramírez, AW Vesztrocy, ...
Scientific Reports 8 (1), 10872, 2018
5012018
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
2042006
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
2032009
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
1872010
Logical Modelling of Gene Regulatory Networks with GINsim.
C Chaouiya, A Naldi, D Thieffry
Methods in molecular biology (Clifton, NJ) 804, 463, 2012
1722012
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
1582013
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
1422007
Dynamically consistent reduction of logical regulatory graphs
A Naldi, E Remy, D Thieffry, C Chaouiya
Theoretical Computer Science 412 (21), 2207-2218, 2011
1392011
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular Systems Biology 16 (8), 2020
1162020
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
902015
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
862017
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
772015
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
752013
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
732009
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
682018
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
Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer
L Cantini, P Zakeri, C Hernandez, A Naldi, D Thieffry, E Remy, A Baudot
Nature Communications 12 (1), 1-12, 2021
602021
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
582018
Petri net representation of multi-valued logical regulatory graphs
C Chaouiya, A Naldi, E Remy, D Thieffry
Natural Computing 10 (2), 727-750, 2011
532011
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Articles 1–20