Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
Maximally Parallel Probabilistic Semantics for Multiset Rewriting
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P)
Colouring space - a coloured framework for spatial modelling in systems biology
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
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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Motivation: Understanding the processes involved in multi-cellular pattern formation is a central problem of developmental biology, hopefully leading to many new insights, e.g. in the treatment of various diseases. Defining suitable computational techniques for development modelling, able to perform in silico simulation experiments, is an open and challenging problem. Results: Previously, we proposed a coarse-grained, quantitative approach based on the basic Petri net formalism, to mimic the behaviour of the biological processes during multicellular differentiation. Here, we apply our modelling approach to the well-studied process of Caenorhabditis elegans vulval development. We show that our model correctly reproduces a large set of in vivo experiments with statistical accuracy. It also generates gene expression time series in accordance with recent biological evidence. Finally, we modelled the role of microRNA mir-61 during vulval development and predict its contribution in stabilizing cell pattern formation. Contact: feenstra@few.vu.nl Supplementary information: Supplementary data are available at Bioinformatics online.