24 citations · 25 across the 8 of their papers we have counts for
10 papers
Continuous Petri Nets for Fast Yield Computation: Polynomial-Time and MILP Approaches
Addie Jordon, Juri Kolčák, Daniel Merkle
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemic…
Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks
Stefan Haar, Juri Kolčák
The analysis of biological networks has benefited from the richness of Boolean networks (BNs) and the associated theory. These results have been further fortified in recent years b…
Automated Inference of Graph Transformation Rules
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg +6
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic system…
Representing catalytic mechanisms with rule composition
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph tra…
Efficient Modular Graph Transformation Rule Application
Jakob L. Andersen, Rolf Fagerberg, Juri Kolčák +3
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in…
Graph Transformation for Enzymatic Mechanisms
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and e…
Concurrency in Boolean networks
Thomas Chatain, Stefan Haar, Juraj Kolčák +2
Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect t…
Relational Differential Dynamic Logic
Juraj Kolčák, Ichiro Hasuo, Jérémy Dubut +3
In the field of quality assurance of hybrid systems (that combine continuous physical dynamics and discrete digital control), Platzer's differential dynamic logic (dL) is widely re…
Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics
Stefan Haar, Juraj Kolčák, Loïc Paulevé
Parametric models abstract part of the specification of dynamical models by integral parameters. They are for example used in computational systems biology, notably with parametric…
Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks
Juraj Kolčák, David Šafránek, Stefan Haar +1
The modelling of discrete regulatory networks combines a graph specifying the pairwise influences between the variables of the system, and a parametrisation from which can be deriv…