System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Structure and parameter estimation for cell systems biology models

Proceedings of the 10th annual conference on Genetic and evolutionary computation

Robust measurement selection for biochemical pathway experimental design

International Journal of Bioinformatics Research and Applications

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology

An Introduction to Metabolic Networks and Their Structural Analysis

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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

Parameter Tuning of a Stochastic Biological Simulator by Metaheuristics

AI*IA '09: Proceedings of the XIth International Conference of the Italian Association for Artificial Intelligence Reggio Emilia on Emergent Perspectives in Artificial Intelligence

Model checking genetic regulatory networks with parameter uncertainty

HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control

Characterizing the effect of coarse-scale PBN modeling on dynamics and intervention performance of genetic regulatory networks represented by stochastic master equation models

IEEE Transactions on Signal Processing

A Study on Gene Regulatory Network Reconstruction and Simulation

Proceedings of the 2011 conference on Neural Nets WIRN10: Proceedings of the 20th Italian Workshop on Neural Nets

BioSimWare: a software for the modeling, simulation and analysis of biological systems

CMC'10 Proceedings of the 11th international conference on Membrane computing

Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures

Theoretical Computer Science

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

A new evolutionary gene regulatory network reverse engineering tool

EvoBIO'11 Proceedings of the 9th European conference on Evolutionary computation, machine learning and data mining in bioinformatics

MABSys: modeling and analysis of biological systems

ANB'10 Proceedings of the 4th international conference on Algebraic and Numeric Biology

GeNet: a graph-based genetic programming framework for the reverse engineering of gene regulatory networks

EvoBIO'12 Proceedings of the 10th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

An excursion in reaction systems: From computer science to biology

Theoretical Computer Science

An integrated computational environment for elementary modes analysis of biochemical networks

International Journal of Data Mining and Bioinformatics

Towards an evolutionary procedure for reverse-engineering biological networks

ICARIS'12 Proceedings of the 11th international conference on Artificial Immune Systems

An outline of MP modeling framework

CMC'12 Proceedings of the 13th international conference on Membrane Computing

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets

Journal of Biomedical Informatics