Monika Heiner

ORCID

Publication Activity (10 Years)

Years Active: 1992-2022
Publications (10 Years): 31

Top Venues

Dresden University of Technology, Germany (PHD)

Education History

Dresden University of Technology, Germany

PHD

Publications

Fei Liu, Monika Heiner, David R. Gilbert
Hybrid modelling of biological systems: current progress and future prospects. Briefings Bioinform. 23 (3) (2022)
George Assaf, Monika Heiner, Fei Liu
Coloured fuzzy Petri nets for modelling and analysing membrane systems. Biosyst. 212 (2022)
Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert
Hybrid modelling of biological systems using fuzzy continuous Petri nets. Briefings Bioinform. 22 (1) (2021)
Shannon Connolly, David R. Gilbert, Monika Heiner
From Epidemic to Pandemic Modelling. CoRR (2021)
Fei Liu, George Assaf, Ming Chen, Monika Heiner
A Petri nets-based framework for whole-cell modeling. Biosyst. 210 (2021)
George Assaf, Monika Heiner, Fei Liu
Colouring fuzziness for systems biology. Theor. Comput. Sci. 875 (2021)
Fei Liu, Monika Heiner, David R. Gilbert
Fuzzy Petri nets for modelling of uncertain biological systems. Briefings Bioinform. 21 (1) (2020)
Martin Schwarick, Christian Rohr, Fei Liu, George Assaf, Jacek Chodak, Monika Heiner
Efficient Unfolding of Coloured Petri Nets Using Interval Decision Diagrams. Petri Nets (2020)
Fei Liu, Monika Heiner, David R. Gilbert
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. Briefings Bioinform. 20 (3) (2019)
David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinform. (4) (2019)
Jacek Chodak, Monika Heiner
Spike - Reproducible Simulation Experiments with Configuration File Branching. CMSB (2019)
David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
Towards dynamic genome-scale models. Briefings Bioinform. 20 (4) (2019)
George Assaf, Monika Heiner, Fei Liu
Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy. CMSB (2019)
Paolo Baldan, Martina Bocci, Daniele Brigolin, Nicoletta Cocco, Monika Heiner, Marta Simeoni
Petri Nets for Modelling and Analysing Trophic Networks. Fundam. Informaticae 160 (1-2) (2018)
Mostafa Herajy, Monika Heiner
An Improved simulation of Hybrid biological Models with Many stochastic Events and quasi-Disjoint Subnets. WSC (2018)
Anna Gambin, Monika Heiner
Preface. Fundam. Informaticae 160 (1-2) (2018)
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks. Comput. Biol. Chem. 76 (2018)
Timothy Self, David R. Gilbert, Monika Heiner
Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. CMSB (2018)
David R. Gilbert, Monika Heiner, Christian Rohr
Petri-net-based 2D design of DNA walker circuits. Nat. Comput. 17 (1) (2018)
Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song
Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets. BMC Syst. Biol. 12 (4) (2018)
Mostafa Herajy, Monika Heiner
Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation. Fundam. Informaticae 160 (1-2) (2018)
Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinform. (7) (2018)
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models. BMC Syst. Biol. 11 (1) (2017)
Monika Heiner, Christian Rohr, Martin Schwarick, Alexey A. Tovchigrechko
MARCIE's Secrets of Efficient Model Checking. Trans. Petri Nets Other Model. Concurr. 11 (2016)
Laura M. F. Bertens, Jetty Kleijn, Sander C. Hille, Monika Heiner, Maciej Koutny, Fons J. Verbeek
Modeling biological gradient formation: combining partial differential equations and Petri nets. Nat. Comput. 15 (4) (2016)
Fei Liu, Monika Heiner, Ming Yang
Representing network reconstruction solutions with colored Petri nets. Neurocomputing 174 (2016)
Judith Somekh, Mor Peleg, Alal Eran, Itay Koren, Ariel Feiglin, Alik Demishtein, Ruth Shiloh, Monika Heiner, Sek Won Kong, Zvulun Elazar, Isaac S. Kohane
A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. J. Biomed. Informatics 63 (2016)
Mostafa Herajy, Monika Heiner
Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets. HSB (2016)
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders, Simon Shaw
Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. ACM Trans. Model. Comput. Simul. 25 (2) (2015)
Monika Heiner, Martin Schwarick, Jan-Thierry Wegener
Charlie - An Extensible Petri Net Analysis Tool. Petri Nets (2015)
David R. Gilbert, Monika Heiner
Advances in Computational Methods in Systems Biology. Theor. Comput. Sci. 599 (2015)
David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher
Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports 4 (11) (2014)
Mostafa Herajy, Monika Heiner
A Steering Server for Collaborative Simulation of Quantitative Petri Nets. Petri Nets (2014)
Mostafa Herajy, Monika Heiner
Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. Fundam. Informaticae 129 (1-2) (2014)
Fei Liu, Mary Ann Blätke, Monika Heiner, Ming Yang
Modelling and simulating reaction-diffusion systems using coloured Petri nets. Comput. Biol. Medicine 53 (2014)
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
Modelling and Analysis of Phase Variation in Bacterial Colony Growth. CMSB (2013)
David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. Petri Nets (2013)
Monika Heiner, Christian Rohr, Martin Schwarick
MARCIE - Model Checking and Reachability Analysis Done Efficiently. Petri Nets (2013)
Fei Liu, Monika Heiner
Modeling membrane systems using colored stochastic Petri nets. Nat. Comput. 12 (4) (2013)
Mostafa Herajy, Martin Schwarick, Monika Heiner
Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle. Trans. Petri Nets Other Model. Concurr. 8 (2013)
Qian Gao, David R. Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (2) (2013)
Mary Ann Blätke, Monika Heiner, Wolfgang Marwan
Predicting Phenotype from Genotype through Automatically Composed Petri Nets. CMSB (2012)
Fei Liu, Monika Heiner, Ming Yang
An efficient method for unfolding colored Petri nets. WSC (2012)
Mostafa Herajy, Monika Heiner
Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks. CS&P (2012)
Mary Ann Blätke, Anna Dittrich, Monika Heiner, Fred Schaper, Wolfgang Marwan
JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept. CMSB (2012)
Monika Heiner, Mostafa Herajy, Fei Liu, Christian Rohr, Martin Schwarick
Snoopy - A Unifying Petri Net Tool. Petri Nets (2012)
Monika Heiner, David R. Gilbert
How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets (2011)
Monika Heiner, Adelinde M. Uhrmacher
Foundations of formal reconstruction of biochemical networks. Theor. Comput. Sci. 412 (26) (2011)
Qian Gao, Fei Liu, David R. Gilbert, Monika Heiner, David Tree
A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. CMSB (2011)
Monika Heiner
Preface: Petri nets for Systems and Synthetic Biology. Nat. Comput. 10 (2) (2011)
Martin Schwarick, Monika Heiner, Christian Rohr
MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly. QEST (2011)
Monika Heiner
Preface: Petri nets for Systems and Synthetic Biology. Nat. Comput. 10 (3) (2011)
Christian Rohr, Wolfgang Marwan, Monika Heiner
Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinform. 26 (7) (2010)
Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology 12 (2010)
Monika Heiner, Cristian Mahulea, Manuel Silva Suárez
On the Importance of the Deadlock Trap Property for Monotonic Liveness. ACSD/Petri Nets Workshops (2010)
Claudine Chaouiya, Monika Heiner
Introduction. ACSD/Petri Nets Workshops (2010)
Fei Liu, Monika Heiner
Colored Petri nets to Model and Simulate Biological Systems. ACSD/Petri Nets Workshops (2010)
Fei Liu, Monika Heiner
Computation of Enabled Transition Instances for Colored Petri Nets. AWPN (2010)
Mostafa Herajy, Monika Heiner
Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions. AWPN (2010)
Monika Heiner, Christian Rohr, Martin Schwarick, Stefan Streif
A comparative study of stochastic analysis techniques. CMSB (2010)
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
09091 Executive Summary - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology (2009)
Martin Schwarick, Monika Heiner
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams. CMSB (2009)
David Roger Gilbert, Rainer Breitling, Monika Heiner
BioModel Engineering: Its role in Systems Biology and Synthetic Biology. Formal Methods in Molecular Biology (2009)
Monika Heiner, Sebastian Lehrack, David R. Gilbert, Wolfgang Marwan
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. Trans. Comp. Sys. Biology 11 (2009)
Monika Heiner
Understanding Network Behavior by Structured Representations of Transition Invariants. Algorithmic Bioprocesses (2009)
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
09091 Abstracts Collection - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology (2009)
Monika Heiner, Martin Schwarick, Alexej Tovchigrechko
DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets. Petri Nets (2009)
David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo
A Case Study in Model-driven Synthetic Biology. BICC (2008)
Monika Heiner, Ronny Richter, Martin Schwarick
Snoopy: a tool to design and animate/simulate graph-based formalisms. SimuTools (2008)
Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinform. 9 (2008)
David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing (2008)
Monika Heiner, David R. Gilbert, Robin Donaldson
Petri Nets for Systems and Synthetic Biology. SFM (2008)
Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings Bioinform. 9 (5) (2008)
David R. Gilbert, Monika Heiner, Sebastian Lehrack
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB (2007)
Andrea Sackmann, Monika Heiner, Ina Koch
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform. 7 (2006)
David R. Gilbert, Monika Heiner
From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN (2006)
Ina Koch, Björn H. Junker, Monika Heiner
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinform. 21 (7) (2005)
Louchka Popova-Zeugmann, Monika Heiner, Ina Koch
Time Petri Nets for Modelling and Analysis of Biochemical Networks. Fundam. Informaticae 67 (1-3) (2005)
Ina Koch, Markus Schüler, Monika Heiner
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks. Silico Biol. 5 (2) (2004)
Monika Heiner, Ina Koch
Petri Net Based Model Validation in Systems Biology. ICATPN (2004)
Klaus Voss, Monika Heiner, Ina Koch
Steady state analysis of metabolic pathways using Petri nets. Silico Biol. 3 (3) (2003)
Monika Heiner, Ina Koch, Jürgen Will
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB (2003)
Thomas Rottke, Denis Hatebur, Maritta Heisel, Monika Heiner
A Problem-Oriented Approach to Common Criteria Certification. SAFECOMP (2002)
Ina Koch, Stefan Schuster, Monika Heiner
Simulation and analysis of metabolic networks by time-dependent Petri nets. German Conference on Bioinformatics (1999)
Monika Heiner, Maritta Heisel
Modeling Safety-Critical Systems with Z and Petri Nets. SAFECOMP (1999)
Monika Heiner, Thomas Menzel
Instruction list verification using a Petri net semantics. SMC (1998)
Monika Heiner, Giorgio Ventre, Dietmar Wikarski
A Petri net based methodology to integrate qualitative and quantitative analysis. Inf. Softw. Technol. 36 (7) (1994)
Monika Heiner
A Petri Net View of Process Communication. FBT (1992)

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Publication Activity (10 Years)

Top Topics

Top Venues

Monika Heiner