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I maintain here a complete list of international, peer-reviewed publications (journals and conferences proceedings). This list should also be available on my Google scholar, Mendeley, and ResearcherID profiles.

See also: the list of presentations at conferences or seminars.

Since 2016

BioLQM: a java toolkit for the manipulation and conversion of Logical Qualitative Models of biological networks
A. Naldi (2018)
Frontiers in Physiology 9:1605 [doi:10.3389/fphys.2018.01605] Open Access
Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)
N. Levy, A. Naldi, C. Hernandez, G. Stoll, D. Thieffry, A. Zinovyev, L. Calzone, L. Paulevé (2018)
Frontiers in Physiology 9:787 [doi:10.3389/fphys.2018.00787] Open Access
Logical modelling and analysis of cellular regulatory networks with GINsim 3.0
A. Naldi, C. Hernandez, W. Abou-Jaoudé, P.T. Monteiro, C. Chaouiya, D. Thieffry (2018)
Frontiers in Physiology 9:646 [doi:10.3389/fphys.2018.00646] Open Access
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
A. Naldi, C. Hernandez, N. Levy, G. Stoll, P.T. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé (2018)
Frontiers in Physiology 9:680 [doi:10.3389/fphys.2018.00680] Open Access
GOATOOLS: A Python library for Gene Ontology analyses
D. Klopfenstein, L. Zhang, B. Pedersen, F. Ramirez, A. Warwick Vesztrocy, A. Naldi, C. Mungall, J. Yunes, O. Botvinnik, M. Weigel, W. Dampier, C. Dessimoz, P. Flick, H. Tang (2018)
Scientific Reports 8:10872 [doi:10.1038/s41598-018-28948-z] Open Access
Reconstruction and Signal Propagation Analysis of the Syk Signaling Network in Breast Cancer Cells
A. Naldi, R.M. Larive, U. Czerwinska, S. Urbach, P. Montcourrier, C. Roy, J. Solassol, G. Freiss, P.J. Coopman, O. Radulescu (2017)
PLoS Computational Biology 13(3):e1005432 [doi:10.1371/journal.pcbi.1005432] Open Access
MaBoSS 2.0: an environment for stochastic Boolean modeling
G. Stoll, B. Caron, E. Viara, A. Dugourd, A. Naldi, G. Kroemer, A. Zinovyev, E. Barillot, L. Calzone (2017)
Bioinformatics 33(14):2226-8 [doi:10.1093/bioinformatics/btx123] [pubmed:28881959]
The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks
E. Azpeitia, S. Muñoz, D. González-Tokman, M.E. Martínez-Sánchez, N. Weinstein, A. Naldi, E.R. Álvarez-Buylla, D.A. Rosenblueth, L. Mendoza (2017)
Scientific Reports 7:42023 [doi:10.1038/srep42023] Open Access
Geometric analysis of pathways dynamics: application to versatility of TGF-beta receptors
S.S. Samal, A. Naldi, D. Grigoriev, A. Weber, N. Théret, O. Radulescu (2016)
Biosystems 149:3-14 [doi:10.1016/j.biosystems.2016.07.004] Open Access


Symbolic Dynamics of Biochemical Pathways as Finite States Machines
O. Radulescu, S.S. Samal, A. Naldi, D. Grigoriev, A. Weber (2015)
Computational Methods in Systems Biology. Lecture Notes in Computer Science 9308:104-120 [doi:10.1007/978-3-319-23401-4_10]
Cooperative development of logical modelling standards and tools with CoLoMoTo
A. Naldi, P.T. Monteiro, C. Müssel, t. Consortium for Logical Models and Tools, H.A. Kestler, D. Thieffry, I. Xenarios, J. Saez-Rodriguez, T. Helikar, C. Chaouiya (2015)
Bioinformatics 31(7):1154-1159 [doi:10.1093/bioinformatics/btv013] [pubmed:25619997] Open Access
Model checking to assess T-helper cell plasticity
W. Abou-Jaoudé, P.T. Monteiro, A. Naldi, M. Grandclaudon, V. Soumelis, C. Chaouiya, D. Thieffry (2015)
Front Bioeng Biotechnol 2:86 [doi:10.3389/Fbioe.2014.00086] [pubmed:25674559] Open Access
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, N. Guex, B. Desvergne (2014)
PLoS Genetics 10(3):e1004155 [doi:10.1371/journal.pgen.1004155] [pubmed:24603613] Open Access
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
C. Chaouiya, D. Bérenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar (2013)
BMC Systems Biology 7(1):135 [doi:10.1186/1752-0509-7-135] [pubmed:24321545] Open Access
Dynamical modeling and analysis of large cellular regulatory networks.
D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, E. Remy, D. Thieffry, L. Tichit (2013)
Chaos 23(2):025114 [doi:10.1063/1.4809783] [pubmed:23822512] Open Access
On circuit functionality in boolean networks.
J. Comet, M. Noual, A. Richard, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E.H. Snoussi, D. Thieffry (2013)
Bulletin of Mathematical Biology 75(6):906—19 [doi:10.1007/s11538-013-9829-2] [pubmed:23504387]
Logical modelling of gene regulatory networks with GINsim.
C. Chaouiya, A. Naldi, D. Thieffry (2012)
Bacterial Molecular Networks. Methods in Molecular Biology 804:463—79 [doi:10.1007/978-1-61779-361-5_23] [pubmed:22144167]
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control
A. Naldi, P. Monteiro, C. Chaouiya (2012)
Computational Methods in Systems Biology. Lecture Notes in Computer Science :288—306 [doi:10.1007/978-3-642-33636-2_17]
Petri net representation of multi-valued logical regulatory graphs
C. Chaouiya, A. Naldi, E. Remy, D. Thieffry (2011)
Natural Computing 10(2):727—750 [doi:10.1007/s11047-010-9178-0]
Dynamically consistent reduction of logical regulatory graphs
A. Naldi, E. Remy, D. Thieffry, C. Chaouiya (2011)
Theoretical Computer Science 412(21):2207—2218 [doi:10.1016/j.tcs.2010.10.021]


Diversity and plasticity of Th cell types predicted from regulatory network modelling.
A. Naldi, J. Carneiro, C. Chaouiya, D. Thieffry (2010)
PLoS Computational Biology 6(9):e1000912 [doi:10.1371/journal.pcbi.1000912] [pubmed:20824124] Open Access
Reduction of logical models of regulatory networks yields insight into dynamical properties
C. Chaouiya, A. Naldi (2010)
IEEE International Conference on Control Applications :524—529 [doi:10.1109/CCA.2010.5611238]
Logical modelling of regulatory networks with GINsim 2.3.
A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, C. Chaouiya (2009)
Bio Systems 97(2):134—9 [doi:10.1016/j.biosystems.2009.04.008] [pubmed:19426782]
Modular logical modelling of the budding yeast cell cycle.
A. Fauré, A. Naldi, F. Lopez, C. Chaouiya, A. Ciliberto, D. Thieffry (2009)
Molecular BioSystems 5(12):1787—96 [doi:10.1039/B910101m] [pubmed:19763337]
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties
A. Naldi, E. Remy, D. Thieffry, C. Chaouiya (2009)
Computational Methods in Systems Biology. Lecture Notes in Computer Science 5688:266—280 [doi:10.1007/978-3-642-03845-7_18]
Decision diagrams for the representation and analysis of logical models of genetic networks
A. Naldi, D. Thieffry, C. Chaouiya (2007)
Computational Methods in Systems Biology. Lecture Notes in Computer Science 4695:233—247 [doi:10.1007/978-3-540-75140-3_16]
GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.
A.G. Gonzalez, A. Naldi, L. Sánchez, D. Thieffry, C. Chaouiya (2006)
Bio Systems 84(2):91—100 [doi:10.1016/j.biosystems.2005.10.003] [pubmed:16434137]
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.
A. Fauré, A. Naldi, C. Chaouiya, D. Thieffry (2006)
Bioinformatics 22(14):e124—31 [doi:10.1093/bioinformatics/btl210] [pubmed:16873462] Open Access