Skip to Content

Publications

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:

.

 


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



page | about seo