Petri net modelling of biological regulatory networks
Journal of Discrete Algorithms
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Polynomial-time controllability analysis of boolean networks
ACC'09 Proceedings of the 2009 conference on American Control Conference
IEEE Transactions on Signal Processing
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Computers in Biology and Medicine
Automated large-scale control of gene regulatory networks
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
Biological information as set-based complexity
IEEE Transactions on Information Theory - Special issue on information theory in molecular biology and neuroscience
Polynomial-time algorithm for controllability test of a class of Boolean biological networks
EURASIP Journal on Bioinformatics and Systems Biology
Dynamically consistent reduction of logical regulatory graphs
Theoretical Computer Science
Parameter estimation for Boolean models of biological networks
Theoretical Computer Science
A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
Brief paper: Controllability of Boolean control networks via the Perron-Frobenius theory
Automatica (Journal of IFAC)
Survey: Computational challenges in systems biology
Computer Science Review
Multi-scale modeling of gene regulation of morphogenesis
CiE'12 Proceedings of the 8th Turing Centenary conference on Computability in Europe: how the world computes
Limit cycles and update digraphs in Boolean networks
Discrete Applied Mathematics
Parameter identification and model ranking of thomas networks
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Efficient handling of large signalling-regulatory networks by focusing on their core control
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Interconnection of asynchronous Boolean networks, asymptotic and transient dynamics
Automatica (Journal of IFAC)
Observability of Boolean networks: A graph-theoretic approach
Automatica (Journal of IFAC)
Symbolic dynamics of Boolean control networks
Automatica (Journal of IFAC)
Learning from interpretation transition
Machine Learning
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Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks. Results: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge. Availability: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim ( ). Higher resolution state transitions graphs are also found on this web site (Model Repository page). Contact: thieffry@ibdm.univ-mrs.fr