Computational Methods in Systems Biology

A Formal Approach for Tuning Stochastic Oscillators.- Phenotype Control of Partially Specified Boolean Networks.- A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI.- Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants.- Cell-Level Pathway Scoring Comparison with a Bconstrained Variational Autoencoder.- On Estimating Derivatives of Input Signals in Biochemistry.- Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting.- Approximate Constrained Lumping of Polynomial Differential Equations.- Core SBML and its Formal Semantics.- Average Sensitivity of Canalizing Multivalued Functions.- Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks.- SAF: SAT-Based Attractor Finder in Asynchronous Automata Networks.- Condition for Periodic Attractor in 4-Dimensional Repressilators.- Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction.- 3D Hybrid Cellular Automata for Cardiac Electrophysiology: a Concept Study.- Fridge Compiler: Optimal Circuits from Molecular Inventories.- Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution.