David Safránek

Orcid: 0000-0002-0713-2431

According to our database1, David Safránek authored at least 75 papers between 2002 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2023
Boolean network sketches: a unifying framework for logical model inference.
Bioinform., April, 2023

Rule-based modelling of biological systems using regulated rewriting.
Biosyst., March, 2023

Temporary and permanent control of partially specified Boolean networks.
Biosyst., January, 2023

Phenotype Control of Partially Specified Boolean Networks.
Proceedings of the Computational Methods in Systems Biology, 2023

2022
AEON.py: Python library for attractor analysis in asynchronous Boolean networks.
Bioinform., October, 2022

Extracting individual characteristics from population data reveals a negative social effect during honeybee defence.
PLoS Comput. Biol., September, 2022

BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs.
Log. Methods Comput. Sci., 2022

Robust Control of Partially Specified Boolean Networks.
CoRR, 2022

Biochemical Space Language in Relation to Multiset Rewriting Systems.
CoRR, 2022

Exploring attractor bifurcations in Boolean networks.
BMC Bioinform., 2022

eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems.
Proceedings of the Computational Methods in Systems Biology, 2022

2021
Regulated Multiset Rewriting Systems.
CoRR, 2021

Symbolic Coloured SCC Decomposition.
Proceedings of the Tools and Algorithms for the Construction and Analysis of Systems, 2021

DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications.
Proceedings of the Performance Engineering and Stochastic Modeling, 2021

Aeon 2021: Bifurcation Decision Trees in Boolean Networks.
Proceedings of the Computational Methods in Systems Biology, 2021

Computing Bottom SCCs Symbolically Using Transition Guided Reduction.
Proceedings of the Computer Aided Verification - 33rd International Conference, 2021

2020
Parallel parameter synthesis algorithm for hybrid CTL.
Sci. Comput. Program., 2020

Digital Bifurcation Analysis of Internet Congestion Control Protocols.
Int. J. Bifurc. Chaos, 2020

The need for standardisation in life science research - an approach to excellence and trust.
F1000Research, 2020

Parallel One-Step Control of Parametrised Boolean Networks.
CoRR, 2020

Executable Biochemical Space for Specification and Analysis of Biochemical Systems.
CoRR, 2020

Executable Biochemical Space for Specification and Analysis of Biochemical Systems.
Proceedings of SASB 2018, the Ninth International Workshop on Static Analysis and Systems Biology, Freiburg, Germany, 2020

Parameter Synthesis and Robustness Analysis of Rule-Based Models.
Proceedings of the NASA Formal Methods - 12th International Symposium, 2020

eBCSgen: A Software Tool for Biochemical Space Language.
Proceedings of the Computational Methods in Systems Biology, 2020

Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications.
Proceedings of the Computational Methods in Systems Biology, 2020

AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks.
Proceedings of the Computer Aided Verification - 32nd International Conference, 2020

2019
Model Checking Approach to the Analysis of Biological Systems.
Proceedings of the Automated Reasoning for Systems Biology and Medicine, 2019

Parameter space abstraction and unfolding semantics of discrete regulatory networks.
Theor. Comput. Sci., 2019

Preface.
Theor. Comput. Sci., 2019

Digital Bifurcation Analysis of TCP Dynamics.
Proceedings of the Tools and Algorithms for the Construction and Analysis of Systems, 2019

Accelerating Parameter Synthesis Using Semi-algebraic Constraints.
Proceedings of the Integrated Formal Methods - 15th International Conference, 2019

Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks.
Proceedings of the Formal Methods and Software Engineering, 2019

Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT.
Proceedings of the 22nd ACM International Conference on Hybrid Systems: Computation and Control, 2019

Data-Informed Parameter Synthesis for Population Markov Chains.
Proceedings of the Hybrid Systems Biology - 6th International Workshop, 2019

Barbaric Robustness Monitoring Revisited for STL* in Parasim.
Proceedings of the Computational Methods in Systems Biology, 2019

2018
Preface.
Proceedings of SASB 2018, 2018

Unfolding of Parametric Boolean Networks.
Proceedings of SASB 2018, 2018

2017
Detecting Attractors in Biological Models with Uncertain Parameters.
Proceedings of the Computational Methods in Systems Biology, 2017

Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems.
Proceedings of the Computer Aided Verification - 29th International Conference, 2017

2016
Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways.
Proceedings of the Hybrid Systems Biology - 5th International Workshop, 2016

A Model Checking Approach to Discrete Bifurcation Analysis.
Proceedings of the FM 2016: Formal Methods, 2016

E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria.
Proceedings of the Computational Methods in Systems Biology, 2016

High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study.
Proceedings of the Computational Methods in Systems Biology, 2016

Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems.
Proceedings of the Automated Technology for Verification and Analysis, 2016

2015
Formal Biochemical Space with Semantics in Kappa and BNGL.
Proceedings of the 6th International Workshop on Static Analysis and Systems Biology, 2015

High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems.
Proceedings of the Hybrid Systems Biology - Fourth International Workshop, 2015

Parameter Synthesis by Parallel Coloured CTL Model Checking.
Proceedings of the Computational Methods in Systems Biology, 2015

2014
STL<sup>⁎</sup>: Extending signal temporal logic with signal-value freezing operator.
Inf. Comput., 2014

Biochemical Space: A Framework for Systemic Annotation of Biological Models.
Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology, 2014

Compact Representation of Photosynthesis Dynamics by Rule-based Models.
Proceedings of the 5th International Workshop on Static Analysis and Systems Biology, 2014

Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version).
CoRR, 2014

2013
A Comprehensive Web-based Platform For Domain-Specific Biological Models.
Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology, 2013

Robustness Analysis for Value-Freezing Signal Temporal Logic.
Proceedings of the Proceedings Second International Workshop on Hybrid Systems and Biology, 2013

On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking.
CoRR, 2013

Model Checking of Biological Systems.
Proceedings of the Formal Methods for Dynamical Systems, 2013

Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking.
Proceedings of the Computer Aided Verification - 25th International Conference, 2013

Qualitative modelling and analysis of Photosystem II.
Proceedings of the International Workshop on Biological Processes & Petri Nets, 2013

2012
On Approximative Reachability Analysis of Biochemical Dynamical Systems.
Trans. Comp. Sys. Biology, 2012

On Parameter Synthesis by Parallel Model Checking.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization.
Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology, 2012

On Expressing and Monitoring Oscillatory Dynamics
Proceedings of the Proceedings First International Workshop on Hybrid Systems and Biology, 2012

Parameter Identification and Model Ranking of Thomas Networks.
Proceedings of the Computational Methods in Systems Biology, 2012

2011
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)
Proceedings of the Proceedings Third International Workshop on Computational Models for Cell Processes, 2011

Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation
CoRR, 2011

E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes.
Biosyst., 2011

2010
High-performance analysis of biological systems dynamics with the DiVinE model checker.
Briefings Bioinform., 2010

2009
On algorithmic analysis of transcriptional regulation by LTL model checking.
Theor. Comput. Sci., 2009

BioDiVinE: A Framework for Parallel Analysis of Biological Models
Proceedings of the Proceedings Second International Workshop on Computational Models for Cell Processes, 2009

2007
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE.
Proceedings of the First Workshop "From Biology To Concurrency and back", 2007

2006
Architectural Interoperability Checking in Visual Coordination Networks.
Proceedings of the Combined Proceedings of the Second International Workshop on Coordination and Organization (CoOrg 2006) and the Second International Workshop on Methods and Tools for Coordinating Concurrent, 2006

Verifying VHDL Designs with Multiple Clocks in SMV.
Proceedings of the Formal Methods: Applications and Technology, 2006

2005
VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures.
Proceedings of the SOFSEM 2005: Theory and Practice of Computer Science, 2005

2004
Visual Specification of Systems with Heterogeneous Coordination Models.
Proceedings of the Third International Workshop on Foundations of Coordination Languages and Software Architectures, 2004

2003
Visual Specification of Concurrent Systems.
Proceedings of the 18th IEEE International Conference on Automated Software Engineering (ASE 2003), 2003

2002
SGCCS: A Graphical Language for Real-time Coordination.
Proceedings of the Foundations of Coordination Languages and Software Architectures, 2002


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