RNDr. Nikola Beneš, Ph.D.

2026

• AEON 2025: Robust Control of Partially-Specified Boolean Networks

  VESELÝ Vojtěch ŠMIJÁKOVÁ Eva PASTVA Samuel BENEŠ Nikola ŠAFRÁNEK David

  Article in Proceedings

  International Conference on Computational Methods in Systems Biology, CMSB 2025, year: 2026

• Sketchbook: logical model inference from Boolean network sketches

  HUVAR Ondřej BENEŠ Nikola BRIM Luboš PASTVA Samuel ŠAFRÁNEK David

  Article in Periodical

  BIOINFORMATICS ADVANCES, year: 2026, volume: 6, edition: 1, DOI

2025

• Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures

  BENEŠ Nikola BRIM Luboš HUVAR Ondřej PASTVA Samuel ŠAFRÁNEK David

  Article in Proceedings

  International Symposium on Automated Technology for Verification and Analysis, ATVA 2024, year: 2025

2024

• BNClassifier: Classifying Boolean Models by Dynamic Properties

  BENEŠ Nikola BRIM Luboš HUVAR Ondřej PASTVA Samuel ŠAFRÁNEK David

  Article in Proceedings

  Computational Methods in Systems Biology, year: 2024

2023

• Boolean network sketches: a unifying framework for logical model inference

  BENEŠ Nikola BRIM Luboš HUVAR Ondřej PASTVA Samuel ŠAFRÁNEK David

  Article in Periodical

  Bioinformatics, year: 2023, volume: 39, edition: 4, DOI

• Phenotype Control of Partially Specified Boolean Networks

  BENEŠ Nikola BRIM Luboš PASTVA Samuel ŠAFRÁNEK David ŠMIJÁKOVÁ Eva

  Article in Proceedings

  Computational Methods in Systems Biology, year: 2023

2022

• AEON.py: Python library for attractor analysis in asynchronous Boolean networks

  BENEŠ Nikola BRIM Luboš HUVAR Ondřej PASTVA Samuel ŠAFRÁNEK David ŠMIJÁKOVÁ Eva

  Article in Periodical

  BIOINFORMATICS, year: 2022, volume: 38, edition: 21, DOI

• BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs

  BENEŠ Nikola BRIM Luboš PASTVA Samuel ŠAFRÁNEK David

  Article in Periodical

  Logical Methods in Computer Science, year: 2022, volume: 18, edition: 1, DOI

• Exploring attractor bifurcations in Boolean networks

  BENEŠ Nikola BRIM Luboš KADLECAJ Jakub PASTVA Samuel ŠAFRÁNEK David

  Article in Periodical

  BMC Bioinformatics, year: 2022, volume: 23, edition: 173, DOI

2021

• Aeon 2021: Bifurcation Decision Trees in Boolean Networks

  BENEŠ Nikola BRIM Luboš PASTVA Samuel ŠAFRÁNEK David

  Article in Proceedings

  International Conference on Computational Methods in Systems Biology (CMSB 2021), year: 2021