How to cite GINsim:
A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, C. Chaouiya (2009)
Logical modelling of regulatory networks with GINsim 2.3
Biosystems, 97(2):134-9
http://dx.doi.org/10.1016/j.biosystems.2009.04.008
Publications citing GINsim:
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Methods implemented within GINsim:
GINsim tutorial
C. Chaouiya, A. Naldi, D. Thieffry (2012)
Logical Modelling of Gene Regulatory Networks with GINsim
Methods in Molecular Biology, 1, Volume 804, Bacterial Molecular Networks, Part 3, Pages 463-479
http://dx.doi.org/10.1007/978-1-61779-361-5_23
Priority classes
A. Fauré, A. Naldi, C.Chaouiya, D.Thieffry (2006)
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Bioinformatics, ISMB'06 Special Issue, 22(14):124-131
http://dx.doi.org/10.1093/bioinformatics/btl210
Identification of all stable states
A. Naldi, D. Thieffry, C. Chaouiya (2007)
Decision diagrams for the representation and analysis of logical models of genetic networks
CMSB’07. LNCS/LNBI 4695:233-247
http://dx.doi.org/10.1007/978-3-540-75140-3
Functionality context of regulatory circuits
A. Naldi, D. Thieffry, C. Chaouiya (2007)
Decision diagrams for the representation and analysis of logical models of genetic networks
CMSB’07. LNCS/LNBI 4695:233-247
http://dx.doi.org/10.1007/978-3-540-75140-3
Model reduction
A. Naldi, E. Remy, D. Thieffry, C. Chaouiya (2009)
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties
CMSB’09, LNCS/LNBI: 5688:266-80
http://dx.doi.org/10.1007/978-3-642-03845-7_18
A. Naldi, P.T. Monteiro, C. Chaouiya (2012)
Efficient handling of large signalling-regulatory networks by focusing on their core control
CMSB’12, LNCS, 2012:288-306
http://dx.doi.org/10.1007/978-3-642-33636-2_17
Export to NuSMV and model-checking applied to logical regulatory graphs
P.T. Monteiro, C. Chaouiya (2012)
Efficient verification for logical models of regulatory networks
In PACBB'12. Advances in Intelligent and Soft Computing, Vol. 154:259-267
http://dx.doi.org/10.1007/978-3-642-28839-5_30
Composition and abstraction of logical regulatory modules
N.D. Mendes, F. Lang, Y-S. Le Cornec, R. Mateescu, G. Batt, C. Chaouiya (2013)
Composition and abstraction of logical regulatory modules: application to multicellular systems
Bioinformatics, 29(6): 749-757
http://dx.doi.org/10.1093/bioinformatics/btt033