Handbook of theoretical computer science (vol. B)
An introduction to assertional reasoning for concurrent systems
ACM Computing Surveys (CSUR)
A calculus of mobile processes, I
Information and Computation
Model checking
Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems
ICLP '02 Proceedings of the 18th International Conference on Logic Programming
On Solving Temporal Logic Queries
AMAST '02 Proceedings of the 9th International Conference on Algebraic Methodology and Software Technology
On Model Checking Durational Kripke Structures
FoSSaCS '02 Proceedings of the 5th International Conference on Foundations of Software Science and Computation Structures
CAV '00 Proceedings of the 12th International Conference on Computer Aided Verification
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Graphs for Core Molecular Biology
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Using Cutwidth to Improve Symbolic Simulation and Boolean Satisfiability
HLDVT '01 Proceedings of the Sixth IEEE International High-Level Design Validation and Test Workshop (HLDVT'01)
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Formal Molecular Biology Done in CCS-R
Electronic Notes in Theoretical Computer Science (ENTCS)
Temporal Logic Query Checking: A Tool for Model Exploration
IEEE Transactions on Software Engineering
ESOP'03 Proceedings of the 12th European conference on Programming
Symbolic modeling of signal transduction in pathway logic
Proceedings of the 38th conference on Winter simulation
Modelling, property verification and behavioural equivalence of lactose operon regulation
Computers in Biology and Medicine
A Calculus of Looping Sequences for Modelling Microbiological Systems
Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
Reasoning about non-immediate triggers in biological networks
Annals of Mathematics and Artificial Intelligence
Abstract interpretation and types for systems biology
Theoretical Computer Science
Parameter Synthesis for Piecewise Affine Systems from Temporal Logic Specifications
HSCC '08 Proceedings of the 11th international workshop on Hybrid Systems: Computation and Control
From Reaction Models to Influence Graphs and Back: A Theorem
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Computation Tree Regular Logic for Genetic Regulatory Networks
ATVA '08 Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis
Translating Stochastic CLS into Maude
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Transactions on Computational Systems Biology IX
Approximating Probabilistic Behaviors of Biological Systems Using Abstract Interpretation
Electronic Notes in Theoretical Computer Science (ENTCS)
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
Proceedings of the 2008 conference on ECAI 2008: 18th European Conference on Artificial Intelligence
Issues in reasoning about interaction networks in cells: necessity of event ordering knowledge
AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 2
IJCAI'05 Proceedings of the 19th international joint conference on Artificial intelligence
Algebraic systems biology: theses and hypotheses
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Finding state solutions to temporal logic queries
IFM'07 Proceedings of the 6th international conference on Integrated formal methods
On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
The calculus of looping sequences for modeling biological membranes
WMC'07 Proceedings of the 8th international conference on Membrane computing
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Formal cell biology in biocham
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Process algebras in systems biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
The calculus of looping sequences
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Model revision from temporal logic properties in computational systems biology
Probabilistic inductive logic programming
Abstract interpretation based verification of temporal properties for BioAmbients
Information and Computation
Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
A Model and Analysis of the AKAP Scaffold
Electronic Notes in Theoretical Computer Science (ENTCS)
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Theoretical Computer Science
Parameter inference for asynchronous logical networks using discrete time series
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Modelling coordination in biological systems
ISoLA'04 Proceedings of the First international conference on Leveraging Applications of Formal Methods
Temporal logic constraints in the biochemical abstract machine BIOCHAM
LOPSTR'05 Proceedings of the 15th international conference on Logic Based Program Synthesis and Transformation
Type inference in systems biology
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
From petri nets to differential equations – an integrative approach for biochemical network analysis
ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Simulating bacterial transcription and translation in a stochastic π calculus
Transactions on Computational Systems Biology VI
Multiple representations of biological processes
Transactions on Computational Systems Biology VI
Bisimulation congruences in the calculus of looping sequences
ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
Modeling and property verification of lactose operon regulation
BSB'05 Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
Graph-Based modeling of biological regulatory networks: introduction of singular states
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
From syntax to semantics in systems biology towards automated reasoning tools
Transactions on Computational Systems Biology IV
Adapting biochemical kripke structures for distributed model checking
Transactions on Computational Systems Biology VII
An analysis for proving temporal properties of biological systems
APLAS'06 Proceedings of the 4th Asian conference on Programming Languages and Systems
Simulation techniques for the calculus of wrapped compartments
Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences
Theoretical Computer Science
Time Series Dependent Analysis of Unparametrized Thomas Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Modular modelling of signalling pathways and their cross-talk
Theoretical Computer Science
A Calculus of Looping Sequences for Modelling Microbiological Systems
Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
A boolean model for enumerating minimal siphons and traps in petri nets
CP'12 Proceedings of the 18th international conference on Principles and Practice of Constraint Programming
An analysis for proving probabilistic termination of biological systems
Theoretical Computer Science
Trend-Based analysis of a population model of the AKAP scaffold protein
Transactions on Computational Systems Biology XIV
Model-Checking signal transduction networks through decreasing reachability sets
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
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We introduce a formalism to represent and analyze protein-protein and protein-DNA interaction networks. We illustrate the expressivity of this language, by proposing a formal counterpart of Kohn's compilation on the mammalian cell-cycle control. This effectively turns an otherwise static knowledge into a discrete transition system incorporating a qualitative description of the dynamics. We then propose to use the computation tree logic (CTL) as a query language for querying the possible behaviors of the system. We provide examples of biologically relevant queries expressed in CTL about the mammalian cell-cycle control and show the effectiveness of symbolic model checking tools to evaluate CTL queries in this context.