Ein Beitrag zur Deadlockanalyse auf der Grundlage einer sprachlich geführten Programmiermethodik. - Monika Heiner (1980)

A Petri Net View of Process Communication. - Monika Heiner (FBT, 1992)

A Petri net based methodology to integrate qualitative and quantitative analysis. - Monika Heiner; Giorgio Ventre; Dietmar Wikarski (Inf. Softw. Technol., 1994)

Instruction list verification using a Petri net semantics. - Monika Heiner; Thomas Menzel (SMC, 1998)

Simulation and analysis of metabolic networks by time-dependent Petri nets. - Ina Koch; Stefan Schuster; Monika Heiner (German Conference on Bioinformatics, 1999)

Modeling Safety-Critical Systems with Z and Petri Nets. - Monika Heiner; Maritta Heisel (SAFECOMP, 1999)

A Problem-Oriented Approach to Common Criteria Certification. - Thomas Rottke; Denis Hatebur; Maritta Heisel; Monika Heiner (SAFECOMP, 2002)

Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. - Monika Heiner; Ina Koch; Jürgen Will (CMSB, 2003)

Steady state analysis of metabolic pathways using Petri nets. - Klaus Voss; Monika Heiner; Ina Koch (Silico Biol., 2003)

Petri Net Based Model Validation in Systems Biology. - Monika Heiner; Ina Koch (ICATPN, 2004)

STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks. - Ina Koch; Markus Schüler; Monika Heiner (Silico Biol., 2004)

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. - Ina Koch; Björn H. Junker; Monika Heiner (Bioinform., 2005)

Time Petri Nets for Modelling and Analysis of Biochemical Networks. - Louchka Popova-Zeugmann; Monika Heiner; Ina Koch (Fundam. Informaticae, 2005)

From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. - David R. Gilbert; Monika Heiner (ICATPN, 2006)

Application of Petri net based analysis techniques to signal transduction pathways. - Andrea Sackmann; Monika Heiner; Ina Koch (BMC Bioinform., 2006)

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. - David R. Gilbert; Monika Heiner; Sebastian Lehrack (CMSB, 2007)

A Case Study in Model-driven Synthetic Biology. - David R. Gilbert; Monika Heiner; Susan Rosser; Rachael Fulton; Xu Gu; Maciej Trybilo (BICC, 2008)

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. - David R. Gilbert; Rainer Breitling; Monika Heiner; Robin Donaldson (Workshop on Membrane Computing, 2008)

Petri Nets for Systems and Synthetic Biology. - Monika Heiner; David R. Gilbert; Robin Donaldson (SFM, 2008)

Snoopy: a tool to design and animate/simulate graph-based formalisms. - Monika Heiner; Ronny Richter; Martin Schwarick (SimuTools, 2008)

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. - Rainer Breitling; David R. Gilbert; Monika Heiner; Richard J. Orton (Briefings Bioinform., 2008)

Modularization of biochemical networks based on classification of Petri net t-invariants. - Eva Grafahrend-Belau; Falk Schreiber; Monika Heiner; Andrea Sackmann; Björn H. Junker; Stefanie Grunwald; Astrid Speer; Katja Winder; Ina Koch (BMC Bioinform., 2008)

DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets. - Monika Heiner; Martin Schwarick; Alexej Tovchigrechko (Petri Nets, 2009)

Understanding Network Behavior by Structured Representations of Transition Invariants. - Monika Heiner (Algorithmic Bioprocesses, 2009)

CSL Model Checking of Biochemical Networks with Interval Decision Diagrams. - Martin Schwarick; Monika Heiner (CMSB, 2009)

09091 Abstracts Collection - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

09091 Executive Summary - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

BioModel Engineering: Its role in Systems Biology and Synthetic Biology. - David Roger Gilbert; Rainer Breitling; Monika Heiner (Formal Methods in Molecular Biology, 2009)

Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. - Monika Heiner; Sebastian Lehrack; David R. Gilbert; Wolfgang Marwan (Trans. Comp. Sys. Biology, 2009)

Introduction. - Claudine Chaouiya; Monika Heiner (ACSD/Petri Nets Workshops, 2010)

On the Importance of the Deadlock Trap Property for Monotonic Liveness. - Monika Heiner; Cristian Mahulea; Manuel Silva Suárez (ACSD/Petri Nets Workshops, 2010)

Colored Petri nets to Model and Simulate Biological Systems. - Fei Liu 006; Monika Heiner (ACSD/Petri Nets Workshops, 2010)

Computation of Enabled Transition Instances for Colored Petri Nets. - Fei Liu 006; Monika Heiner (AWPN, 2010)

Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions. - Mostafa Herajy; Monika Heiner (AWPN, 2010)

A comparative study of stochastic analysis techniques. - Monika Heiner; Christian Rohr; Martin Schwarick; Stefan Streif (CMSB, 2010)

Snoopy - a unifying Petri net framework to investigate biomolecular networks. - Christian Rohr; Wolfgang Marwan; Monika Heiner (Bioinform., 2010)

Biomodel Engineering - From Structure to Behavior. - Rainer Breitling; Robin Donaldson; David R. Gilbert; Monika Heiner (Trans. Comp. Sys. Biology, 2010)

How Might Petri Nets Enhance Your Systems Biology Toolkit. - Monika Heiner; David R. Gilbert (Petri Nets, 2011)

A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. - Qian Gao 001; Fei Liu 006; David R. Gilbert; Monika Heiner; David Tree (CMSB, 2011)

MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly. - Martin Schwarick; Monika Heiner; Christian Rohr (QEST, 2011)

Preface: Petri nets for Systems and Synthetic Biology. - Monika Heiner (Nat. Comput., 2011)

Foundations of formal reconstruction of biochemical networks. - Monika Heiner; Adelinde M. Uhrmacher (Theor. Comput. Sci., 2011)

Snoopy - A Unifying Petri Net Tool. - Monika Heiner; Mostafa Herajy; Fei Liu 006; Christian Rohr; Martin Schwarick (Petri Nets, 2012)

JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept. - Mary Ann Blätke; Anna Dittrich; Monika Heiner; Fred Schaper; Wolfgang Marwan (CMSB, 2012)

Predicting Phenotype from Genotype through Automatically Composed Petri Nets. - Mary Ann Blätke; Monika Heiner; Wolfgang Marwan (CMSB, 2012)

Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks. - Mostafa Herajy; Monika Heiner (CS&P, 2012)

An efficient method for unfolding colored Petri nets. - Fei Liu 006; Monika Heiner; Ming Yang 015 (WSC, 2012)

Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. - David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders (Petri Nets, 2013)

Modelling and Analysis of Phase Variation in Bacterial Colony Growth. - Ovidiu Parvu; David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders (CMSB, 2013)

Modeling membrane systems using colored stochastic Petri nets. - Fei Liu 006; Monika Heiner (Nat. Comput., 2013)

Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing. - Qian Gao 001; David R. Gilbert; Monika Heiner; Fei Liu 006; Daniele Maccagnola; David Tree (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle. - Mostafa Herajy; Martin Schwarick; Monika Heiner (Trans. Petri Nets Other Model. Concurr., 2013)

Petri Nets for Modeling and Analyzing Biochemical Reaction Networks. - Fei Liu 006; Monika Heiner (Approaches in Integrative Bioinformatics, 2014)

A Petri-Net-Based Framework for Biomodel Engineering. - Mary Ann Blätke; Christian Rohr; Monika Heiner; Wolfgang Marwan (Large-Scale Networks in Engineering and Life Sciences, 2014)

A Steering Server for Collaborative Simulation of Quantitative Petri Nets. - Mostafa Herajy; Monika Heiner (Petri Nets, 2014)

Modelling and simulating reaction-diffusion systems using coloured Petri nets. - Fei Liu 006; Mary Ann Blätke; Monika Heiner; Ming Yang 015 (Comput. Biol. Medicine, 2014)

Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). - David R. Gilbert; Monika Heiner; Koichi Takahashi; Adelinde M. Uhrmacher (Dagstuhl Reports, 2014)

Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. - Mostafa Herajy; Monika Heiner (Fundam. Informaticae, 2014)

Charlie - An Extensible Petri Net Analysis Tool. - Monika Heiner; Martin Schwarick; Jan-Thierry Wegener (Petri Nets, 2015)

Advances in Computational Methods in Systems Biology. - David R. Gilbert; Monika Heiner (Theor. Comput. Sci., 2015)

Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. - Ovidiu Parvu; David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders; Simon Shaw (ACM Trans. Model. Comput. Simul., 2015)

Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets. - Mostafa Herajy; Monika Heiner (HSB, 2016)

Representing network reconstruction solutions with colored Petri nets. - Fei Liu 006; Monika Heiner; Ming Yang 015 (Neurocomputing, 2016)

A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. - Judith Somekh; Mor Peleg; Alal Eran; Itay Koren; Ariel Feiglin; Alik Demishtein; Ruth Shiloh; Monika Heiner; Sek Won Kong; Zvulun Elazar; Isaac S. Kohane (J. Biomed. Informatics, 2016)

Modeling biological gradient formation: combining partial differential equations and Petri nets. - Laura M. F. Bertens; Jetty Kleijn; Sander C. Hille; Monika Heiner; Maciej Koutny; Fons J. Verbeek (Nat. Comput., 2016)

MARCIE's Secrets of Efficient Model Checking. - Monika Heiner; Christian Rohr; Martin Schwarick; Alexey A. Tovchigrechko (Trans. Petri Nets Other Model. Concurr., 2016)

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models. - Mostafa Herajy; Fei Liu 006; Christian Rohr; Monika Heiner (BMC Syst. Biol., 2017)

Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. - Timothy Self; David R. Gilbert; Monika Heiner (CMSB, 2018)

An Improved simulation of Hybrid biological Models with Many stochastic Events and quasi-Disjoint Subnets. - Mostafa Herajy; Monika Heiner (WSC, 2018)

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. - Riccardo Colombo; Chiara Damiani; David R. Gilbert; Monika Heiner; Giancarlo Mauri; Dario Pescini (BMC Bioinform., 2018)

Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets. - Fei Liu 006; Siyuan Chen; Monika Heiner; Hengjie Song (BMC Syst. Biol., 2018)

Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks. - Mostafa Herajy; Fei Liu 006; Christian Rohr; Monika Heiner (Comput. Biol. Chem., 2018)

Petri Nets for Modelling and Analysing Trophic Networks. - Paolo Baldan; Martina Bocci; Daniele Brigolin; Nicoletta Cocco; Monika Heiner; Marta Simeoni (Fundam. Informaticae, 2018)

Preface. - Anna Gambin; Monika Heiner (Fundam. Informaticae, 2018)

Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation. - Mostafa Herajy; Monika Heiner (Fundam. Informaticae, 2018)

Petri-net-based 2D design of DNA walker circuits. - David R. Gilbert; Monika Heiner; Christian Rohr (Nat. Comput., 2018)

Petri Nets for BioModel Engineering: A Personal Perspective. - Monika Heiner (Carl Adam Petri: Ideas, Personality, Impact, 2019)

Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy. - George Assaf; Monika Heiner; Fei Liu 006 (CMSB, 2019)

Spike - Reproducible Simulation Experiments with Configuration File Branching. - Jacek Chodak; Monika Heiner (CMSB, 2019)

Towards dynamic genome-scale models. - David R. Gilbert; Monika Heiner; Yasoda Jayaweera; Christian Rohr (Briefings Bioinform., 2019)

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2019)

Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. - David R. Gilbert; Monika Heiner; Leila Ghanbar; Jacek Chodak (BMC Bioinform., 2019)

A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets. - Amr Ismail; Mostafa Herajy; Monika Heiner (Automated Reasoning for Systems Biology and Medicine, 2019)

Efficient Unfolding of Coloured Petri Nets Using Interval Decision Diagrams. - Martin Schwarick; Christian Rohr; Fei Liu 006; George Assaf; Jacek Chodak; Monika Heiner (Petri Nets, 2020)

Fuzzy Petri nets for modelling of uncertain biological systems. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2020)

Hybrid modelling of biological systems using fuzzy continuous Petri nets. - Fei Liu 006; Wujie Sun; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2021)

A Petri nets-based framework for whole-cell modeling. - Fei Liu 006; George Assaf; Ming Chen 005; Monika Heiner (Biosyst., 2021)

From Epidemic to Pandemic Modelling. - Shannon Connolly; David R. Gilbert; Monika Heiner (CoRR, 2021)

Colouring fuzziness for systems biology. - George Assaf; Monika Heiner; Fei Liu 006 (Theor. Comput. Sci., 2021)

Hybrid modelling of biological systems: current progress and future prospects. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2022)

Coloured fuzzy Petri nets for modelling and analysing membrane systems. - George Assaf; Monika Heiner; Fei Liu 006 (Biosyst., 2022)

Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets. - George Assaf; Fei Liu 006; Monika Heiner (Briefings Bioinform., 2024)

Design patterns for the construction of computational biological models. - Mostafa Herajy; Fei Liu 006; Monika Heiner (Briefings Bioinform., 2024)

A workflow for the hybrid modelling and simulation of multi-timescale biological systems. - Mostafa Herajy; Fei Liu 006; Monika Heiner (Biosyst., 2025)

Addressing data uncertainty of Caulobacter crescentus cell cycles using hybrid Petri nets with fuzzy kinetics. - George Assaf; Fei Liu 006; Monika Heiner; Mostafa Herajy (Comput. Biol. Medicine, 2025)