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Plos One|September 11, 2020
Executable biochemical space for specification and analysis of biochemical systemsMatej Troják, David Šafránek, Lukrécia Mertová, et al.
Bioinformatics (Oxford, England)|May 24, 2026
Control-Guided Refinement of Partially Specified Boolean Networks: Applications to RTK SignallingEva Šmijáková, Luboš Brim, Samuel Pastva, et al.
Bio Systems|November 15, 2022
Temporary and permanent control of partially specified Boolean networksLuboš Brim, Samuel Pastva, David Šafránek, et al.
Bio Systems|February 3, 2023
Rule-based modelling of biological systems using regulated rewritingMatej Troják, David Šafránek, Samuel Pastva, et al.
Bioinformatics (Oxford, England)|April 2, 2023
Boolean network sketches: a unifying framework for logical model inferenceNikola Beneš, Luboš Brim, Ondřej Huvar, et al.
Microorganisms|November 14, 2019
Computational Modelling of Metabolic Burden and Substrate Toxicity in <i>Escherichia coli</i> Carrying a Synthetic Metabolic PathwayMartin Demko, Lukáš Chrást, Pavel Dvořák, et al.
BMC Bioinformatics|May 13, 2022
Exploring attractor bifurcations in Boolean networksNikola Beneš, Luboš Brim, Jakub Kadlecaj, et al.
Plos Computational Biology|September 15, 2022
Extracting individual characteristics from population data reveals a negative social effect during honeybee defenceTatjana Petrov, Matej Hajnal, Julia Klein, et al.
Bioinformatics Advances|February 11, 2026
Sketchbook: logical model inference from Boolean network sketchesOndřej Huvar, Nikola Beneš, Luboš Brim, et al.
Plos One|November 13, 2023
Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state dataJulia Klein, Huy Phung, Matej Hajnal, et al.
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