Monika Heiner

106 papers B 11C 1Misc 2Journal 48Unranked 31
YearRankTypeTitle / Venue / Authors
2025 J jnl
A workflow for the hybrid modelling and simulation of multi-timescale biological systems.
Biosyst.
Mostafa Herajy, Fei Liu, Monika Heiner
2025 J jnl
Addressing data uncertainty of Caulobacter crescentus cell cycles using hybrid Petri nets with fuzzy kinetics.
Comput. Biol. Medicine
George Assaf, Fei Liu, Monika Heiner, Mostafa Herajy
2025 J jnl
Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets.
Briefings Bioinform.
George Assaf, Fei Liu, Monika Heiner
2024 J jnl
Design patterns for the construction of computational biological models.
Briefings Bioinform.
Mostafa Herajy, Fei Liu, Monika Heiner
2022 J jnl
Coloured fuzzy Petri nets for modelling and analysing membrane systems.
Biosyst.
George Assaf, Monika Heiner, Fei Liu
2022 J jnl
Hybrid modelling of biological systems: current progress and future prospects.
Briefings Bioinform.
Fei Liu, Monika Heiner, David R. Gilbert
2021 J jnl
A Petri nets-based framework for whole-cell modeling.
Biosyst.
Fei Liu, George Assaf, Ming Chen, Monika Heiner
2021 J jnl
Colouring fuzziness for systems biology.
Theor. Comput. Sci.
George Assaf, Monika Heiner, Fei Liu
2021 J jnl
From Epidemic to Pandemic Modelling.
CoRR
Shannon Connolly, David R. Gilbert, Monika Heiner
2021 J jnl
Hybrid modelling of biological systems using fuzzy continuous Petri nets.
Briefings Bioinform.
Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert
2020 B conf
Efficient Unfolding of Coloured Petri Nets Using Interval Decision Diagrams.
Petri Nets
Martin Schwarick, Christian Rohr, Fei Liu, George Assaf, Jacek Chodak, Monika Heiner
2020 J jnl
Fuzzy Petri nets for modelling of uncertain biological systems.
Briefings Bioinform.
Fei Liu, Monika Heiner, David R. Gilbert
2019 — ch.
A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets.
Automated Reasoning for Systems Biology and Medicine
Amr Ismail, Mostafa Herajy, Monika Heiner
2019 — conf
Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy.
CMSB
George Assaf, Monika Heiner, Fei Liu
2019 J jnl
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems.
Briefings Bioinform.
Fei Liu, Monika Heiner, David R. Gilbert
2019 — ch.
Petri Nets for BioModel Engineering: A Personal Perspective.
Carl Adam Petri: Ideas, Personality, Impact
Monika Heiner
2019 J jnl
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking.
BMC Bioinform.
David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
2019 — conf
Spike - Reproducible Simulation Experiments with Configuration File Branching.
CMSB
Jacek Chodak, Monika Heiner
2019 J jnl
Towards dynamic genome-scale models.
Briefings Bioinform.
David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
2018 J jnl
Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation.
Fundam. Informaticae
Mostafa Herajy, Monika Heiner
2018 Misc conf
An Improved simulation of Hybrid biological Models with Many stochastic Events and quasi-Disjoint Subnets.
WSC
Mostafa Herajy, Monika Heiner
2018 J jnl
Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks.
Comput. Biol. Chem.
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
2018 — conf
Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models.
CMSB
Timothy Self, David R. Gilbert, Monika Heiner
2018 J jnl
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes.
BMC Bioinform.
Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
2018 J jnl
Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets.
BMC Syst. Biol.
Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song
2018 J jnl
Petri Nets for Modelling and Analysing Trophic Networks.
Fundam. Informaticae
Paolo Baldan, Martina Bocci, Daniele Brigolin, Nicoletta Cocco, Monika Heiner, Marta Simeoni
2018 J jnl
Petri-net-based 2D design of DNA walker circuits.
Nat. Comput.
David R. Gilbert, Monika Heiner, Christian Rohr
2018 J jnl
Preface.
Fundam. Informaticae
Anna Gambin, Monika Heiner
2017 J jnl
Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.
BMC Syst. Biol.
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
2016 J jnl
A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease.
J. Biomed. Informatics
Judith Somekh, Mor Peleg, Alal Eran, Itay Koren, Ariel Feiglin, Alik Demishtein, Ruth Shiloh, Monika Heiner, Sek Won Kong, Zvulun Elazar, Isaac S. Kohane
2016 — conf
Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets.
HSB
Mostafa Herajy, Monika Heiner
2016 J jnl
MARCIE's Secrets of Efficient Model Checking.
Trans. Petri Nets Other Model. Concurr.
Monika Heiner, Christian Rohr, Martin Schwarick, Alexey A. Tovchigrechko
2016 J jnl
Modeling biological gradient formation: combining partial differential equations and Petri nets.
Nat. Comput.
Laura M. F. Bertens, Jetty Kleijn, Sander C. Hille, Monika Heiner, Maciej Koutny, Fons J. Verbeek
2016 J jnl
Representing network reconstruction solutions with colored Petri nets.
Neurocomputing
Fei Liu, Monika Heiner, Ming Yang
2015 J jnl
Advances in Computational Methods in Systems Biology.
Theor. Comput. Sci.
David R. Gilbert, Monika Heiner
2015 B conf
Charlie - An Extensible Petri Net Analysis Tool.
Petri Nets
Monika Heiner, Martin Schwarick, Jan-Thierry Wegener
2015 — ed.
Proceedings of the 6th International Workshop on Biological Processes & Petri Nets co-located with 36th International Conference on Application and Theory of Petri Nets and Concurreny (PETRI NETS 2015), Brussels, Belgium, June 22, 2015.
BioPPN@Petri Nets
Monika Heiner, Annegret K. Wagler
2015 J jnl
Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes.
ACM Trans. Model. Comput. Simul.
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders, Simon Shaw
2014 — ch.
A Petri-Net-Based Framework for Biomodel Engineering.
Large-Scale Networks in Engineering and Life Sciences
Mary Ann Blätke, Christian Rohr, Monika Heiner, Wolfgang Marwan
2014 B conf
A Steering Server for Collaborative Simulation of Quantitative Petri Nets.
Petri Nets
Mostafa Herajy, Monika Heiner
2014 J jnl
Modelling and simulating reaction-diffusion systems using coloured Petri nets.
Comput. Biol. Medicine
Fei Liu, Mary Ann Blätke, Monika Heiner, Ming Yang
2014 J jnl
Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481).
Dagstuhl Reports
David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher
2014 J jnl
Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks.
Fundam. Informaticae
Mostafa Herajy, Monika Heiner
2014 — ch.
Petri Nets for Modeling and Analyzing Biochemical Reaction Networks.
Approaches in Integrative Bioinformatics
Fei Liu, Monika Heiner
2014 — ed.
Proceedings of the 5th International Workshop on Biological Processes & Petri Nets co-located with 35th International Conference on Application and Theory of Petri Nets and Concurreny (PETRI NETS 2014), Tunis, Tunisia, June 23, 2014.
BioPPN@Petri Nets
Monika Heiner
2013 B conf
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology.
Petri Nets
David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
2013 J jnl
Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle.
Trans. Petri Nets Other Model. Concurr.
Mostafa Herajy, Martin Schwarick, Monika Heiner
2013 B conf
MARCIE - Model Checking and Reachability Analysis Done Efficiently.
Petri Nets
Monika Heiner, Christian Rohr, Martin Schwarick
2013 J jnl
Modeling membrane systems using colored stochastic Petri nets.
Nat. Comput.
Fei Liu, Monika Heiner
2013 — conf
Modelling and Analysis of Phase Variation in Bacterial Colony Growth.
CMSB
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
2013 J jnl
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing.
IEEE ACM Trans. Comput. Biol. Bioinform.
Qian Gao, David R. Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree
2013 — ed.
Proceedings of the International Workshop on Biological Processes & Petri Nets, Milano, Italy, June 24, 2013
BioPPN@Petri Nets
Gianfranco Balbo, Monika Heiner
2012 Misc conf
An efficient method for unfolding colored Petri nets.
WSC
Fei Liu, Monika Heiner, Ming Yang
2012 — ed.
Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings
CMSB
David R. Gilbert, Monika Heiner
2012 — conf
JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept.
CMSB
Mary Ann Blätke, Anna Dittrich, Monika Heiner, Fred Schaper, Wolfgang Marwan
2012 — conf
Predicting Phenotype from Genotype through Automatically Composed Petri Nets.
CMSB
Mary Ann Blätke, Monika Heiner, Wolfgang Marwan
2012 B conf
Snoopy - A Unifying Petri Net Tool.
Petri Nets
Monika Heiner, Mostafa Herajy, Fei Liu, Christian Rohr, Martin Schwarick
2012 — conf
Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks.
CS&P
Mostafa Herajy, Monika Heiner
2011 — conf
A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets.
CMSB
Qian Gao, Fei Liu, David R. Gilbert, Monika Heiner, David Tree
2011 J jnl
Foundations of formal reconstruction of biochemical networks.
Theor. Comput. Sci.
Monika Heiner, Adelinde M. Uhrmacher
2011 B conf
How Might Petri Nets Enhance Your Systems Biology Toolkit.
Petri Nets
Monika Heiner, David R. Gilbert
2011 — conf
MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly.
QEST
Martin Schwarick, Monika Heiner, Christian Rohr
2011 J jnl
Preface: Petri nets for Systems and Synthetic Biology.
Nat. Comput.
Monika Heiner
2011 J jnl
Preface: Petri nets for Systems and Synthetic Biology.
Nat. Comput.
Monika Heiner
2010 — conf
A comparative study of stochastic analysis techniques.
CMSB
Monika Heiner, Christian Rohr, Martin Schwarick, Stefan Streif
2010 J jnl
Biomodel Engineering - From Structure to Behavior.
Trans. Comp. Sys. Biology
Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
2010 — conf
Colored Petri nets to Model and Simulate Biological Systems.
ACSD/Petri Nets Workshops
Fei Liu, Monika Heiner
2010 — conf
Computation of Enabled Transition Instances for Colored Petri Nets.
AWPN
Fei Liu, Monika Heiner
2010 — conf
Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions.
AWPN
Mostafa Herajy, Monika Heiner
2010 — conf
Introduction.
ACSD/Petri Nets Workshops
Claudine Chaouiya, Monika Heiner
2010 — conf
On the Importance of the Deadlock Trap Property for Monotonic Liveness.
ACSD/Petri Nets Workshops
Monika Heiner, Cristian Mahulea, Manuel Silva Suárez
2010 — ed.
Proceedings of the 17th German Workshop on Algorithms and Tools for Petri Nets, Cottbus, Germany, October 07-08, 2010
AWPN
Martin Schwarick, Monika Heiner
2010 J jnl
Snoopy - a unifying Petri net framework to investigate biomolecular networks.
Bioinform.
Christian Rohr, Wolfgang Marwan, Monika Heiner
2010 — ed.
Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies
Trans. Computational Systems Biology
Corrado Priami, Rainer Breitling, David R. Gilbert, Monika Heiner, Adelinde M. Uhrmacher
2009 — conf
09091 Abstracts Collection - Formal Methods in Molecular Biology.
Formal Methods in Molecular Biology
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009 — conf
09091 Executive Summary - Formal Methods in Molecular Biology.
Formal Methods in Molecular Biology
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009 — conf
BioModel Engineering: Its role in Systems Biology and Synthetic Biology.
Formal Methods in Molecular Biology
David Roger Gilbert, Rainer Breitling, Monika Heiner
2009 — conf
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams.
CMSB
Martin Schwarick, Monika Heiner
2009 B conf
DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets.
Petri Nets
Monika Heiner, Martin Schwarick, Alexej Tovchigrechko
2009 J jnl
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments.
Trans. Comp. Sys. Biology
Monika Heiner, Sebastian Lehrack, David R. Gilbert, Wolfgang Marwan
2009 — ed.
Formal Methods in Molecular Biology, 22.02. - 27.02.2009
Formal Methods in Molecular Biology
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009 — conf
Understanding Network Behavior by Structured Representations of Transition Invariants.
Algorithmic Bioprocesses
Monika Heiner
2008 — conf
A Case Study in Model-driven Synthetic Biology.
BICC
David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo
2008 J jnl
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.
Briefings Bioinform.
Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton
2008 — conf
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways.
Workshop on Membrane Computing
David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
2008 — ed.
Computational Methods in Systems Biology, 6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings
CMSB
Monika Heiner, Adelinde M. Uhrmacher
2008 J jnl
Modularization of biochemical networks based on classification of Petri net t-invariants.
BMC Bioinform.
Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
2008 — conf
Petri Nets for Systems and Synthetic Biology.
SFM
Monika Heiner, David R. Gilbert, Robin Donaldson
2008 — conf
Snoopy: a tool to design and animate/simulate graph-based formalisms.
SimuTools
Monika Heiner, Ronny Richter, Martin Schwarick
2007 — conf
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets.
CMSB
David R. Gilbert, Monika Heiner, Sebastian Lehrack
2006 J jnl
Application of Petri net based analysis techniques to signal transduction pathways.
BMC Bioinform.
Andrea Sackmann, Monika Heiner, Ina Koch
2006 — conf
From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis.
ICATPN
David R. Gilbert, Monika Heiner
2005 J jnl
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
Bioinform.
Ina Koch, Björn H. Junker, Monika Heiner
2005 J jnl
Time Petri Nets for Modelling and Analysis of Biochemical Networks.
Fundam. Informaticae
Louchka Popova-Zeugmann, Monika Heiner, Ina Koch
2004 — conf
Petri Net Based Model Validation in Systems Biology.
ICATPN
Monika Heiner, Ina Koch
2004 J jnl
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks.
Silico Biol.
Ina Koch, Markus Schüler, Monika Heiner
2003 C ed.
Formal Techniques for Networked and Distributed Systems - FORTE 2003, 23rd IFIP WG 6.1 International Conference, Berlin, Germany, September 29 - October 2, 2003, Proceedings
FORTE
Hartmut König, Monika Heiner, Adam Wolisz
2003 — conf
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis.
CMSB
Monika Heiner, Ina Koch, Jürgen Will
2003 J jnl
Steady state analysis of metabolic pathways using Petri nets.
Silico Biol.
Klaus Voss, Monika Heiner, Ina Koch
2002 B conf
A Problem-Oriented Approach to Common Criteria Certification.
SAFECOMP
Thomas Rottke, Denis Hatebur, Maritta Heisel, Monika Heiner
1999 B conf
Modeling Safety-Critical Systems with Z and Petri Nets.
SAFECOMP
Monika Heiner, Maritta Heisel
1999 — conf
Simulation and analysis of metabolic networks by time-dependent Petri nets.
German Conference on Bioinformatics
Ina Koch, Stefan Schuster, Monika Heiner
1998 B conf
Instruction list verification using a Petri net semantics.
SMC
Monika Heiner, Thomas Menzel
1994 J jnl
A Petri net based methodology to integrate qualitative and quantitative analysis.
Inf. Softw. Technol.
Monika Heiner, Giorgio Ventre, Dietmar Wikarski
1992 — conf
A Petri Net View of Process Communication.
FBT
Monika Heiner
1980 — —
Ein Beitrag zur Deadlockanalyse auf der Grundlage einer sprachlich geführten Programmiermethodik.
Monika Heiner