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ORCIDMonika Heiner
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- affiliation: Brandenburg University of Technology, Cottbus, Germany
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2020 – today
- 2025
[j44]Mostafa Herajy
, Fei Liu, Monika Heiner:
A workflow for the hybrid modelling and simulation of multi-timescale biological systems. Biosyst. 247: 105365 (2025)- 2024
- [j43]Mostafa Herajy, Fei Liu, Monika Heiner:
Design patterns for the construction of computational biological models. Briefings Bioinform. 25(4) (2024) - 2022
- [j42]Fei Liu, Monika Heiner, David R. Gilbert:
Hybrid modelling of biological systems: current progress and future prospects. Briefings Bioinform. 23(3) (2022) - [j41]George Assaf, Monika Heiner, Fei Liu:
Coloured fuzzy Petri nets for modelling and analysing membrane systems. Biosyst. 212: 104592 (2022) - 2021
- [j40]Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert:
Hybrid modelling of biological systems using fuzzy continuous Petri nets. Briefings Bioinform. 22(1): 438-450 (2021) - [j39]Fei Liu, George Assaf, Ming Chen, Monika Heiner:
A Petri nets-based framework for whole-cell modeling. Biosyst. 210: 104533 (2021) - [j38]George Assaf, Monika Heiner, Fei Liu:
Colouring fuzziness for systems biology. Theor. Comput. Sci. 875: 52-64 (2021) - [i5]Shannon Connolly, David R. Gilbert, Monika Heiner:
From Epidemic to Pandemic Modelling. CoRR abs/2107.00835 (2021) - 2020
- [j37]Fei Liu, Monika Heiner, David R. Gilbert:
Fuzzy Petri nets for modelling of uncertain biological systems. Briefings Bioinform. 21(1): 198-210 (2020) - [c41]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: 324-344
2010 – 2019
- 2019
- [j36]Fei Liu, Monika Heiner, David R. Gilbert:
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. Briefings Bioinform. 20(3): 877-886 (2019) - [j35]David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr:
Towards dynamic genome-scale models. Briefings Bioinform. 20(4): 1167-1180 (2019) - [j34]David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak:
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinform. 20-S(4): 173:1-173:23 (2019) - [c40]George Assaf, Monika Heiner, Fei Liu:
Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy. CMSB 2019: 302-307 - [c39]Jacek Chodak, Monika Heiner:
Spike - Reproducible Simulation Experiments with Configuration File Branching. CMSB 2019: 315-321 - [p4]Monika Heiner:
Petri Nets for BioModel Engineering: A Personal Perspective. Carl Adam Petri: Ideas, Personality, Impact 2019: 205-216 - [p3]Amr Ismail, Mostafa Herajy, Monika Heiner:
A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets. Automated Reasoning for Systems Biology and Medicine 2019: 349-367 - 2018
- [j33]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. 19-S(7): 45-59 (2018) - [j32]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): 63-74 (2018) - [j31]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: 87-100 (2018) - [j30]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): 27-52 (2018) - [j29]Mostafa Herajy, Monika Heiner:
Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation. Fundam. Informaticae 160(1-2): 53-80 (2018) - [j28]Anna Gambin, Monika Heiner:
Preface. Fundam. Informaticae 160(1-2): v-vii (2018) - [j27]David R. Gilbert, Monika Heiner, Christian Rohr:
Petri-net-based 2D design of DNA walker circuits. Nat. Comput. 17(1): 161-182 (2018) - [c38]Timothy Self, David R. Gilbert, Monika Heiner:
Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. CMSB 2018: 39-58 - [c37]Mostafa Herajy, Monika Heiner:
An Improved simulation of Hybrid biological Models with Many stochastic Events and quasi-Disjoint Subnets. WSC 2018: 1346-1357 - 2017
- [j26]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): 71:1-71:16 (2017) - 2016
- [j25]Fei Liu, Monika Heiner, Ming Yang:
Representing network reconstruction solutions with colored Petri nets. Neurocomputing 174: 483-493 (2016) - [j24]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: 366-378 (2016) - [j23]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): 665-675 (2016) - [j22]Monika Heiner, Christian Rohr, Martin Schwarick, Alexey A. Tovchigrechko:
MARCIE's Secrets of Efficient Model Checking. Trans. Petri Nets Other Model. Concurr. 11: 286-296 (2016) - [c36]Mostafa Herajy, Monika Heiner:
Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets. HSB 2016: 20-38 - 2015
- [j21]David R. Gilbert, Monika Heiner:
Advances in Computational Methods in Systems Biology. Theor. Comput. Sci. 599: 2-3 (2015) - [j20]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): 13:1-13:25 (2015) - [c35]Monika Heiner, Martin Schwarick, Jan-Thierry Wegener:
Charlie - An Extensible Petri Net Analysis Tool. Petri Nets 2015: 200-211 - [e9]Monika Heiner, Annegret Katrin Wagler:
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. CEUR Workshop Proceedings 1373, CEUR-WS.org 2015 [contents] - 2014
- [j19]Fei Liu, Mary Ann Blätke, Monika Heiner, Ming Yang:
Modelling and simulating reaction-diffusion systems using coloured Petri nets. Comput. Biol. Medicine 53: 297-308 (2014) - [j18]Mostafa Herajy, Monika Heiner:
Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. Fundam. Informaticae 129(1-2): 49-67 (2014) - [c34]Mostafa Herajy, Monika Heiner:
A Steering Server for Collaborative Simulation of Quantitative Petri Nets. Petri Nets 2014: 374-384 - [p2]Fei Liu, Monika Heiner:
Petri Nets for Modeling and Analyzing Biochemical Reaction Networks. Approaches in Integrative Bioinformatics 2014: 245-272 - [p1]Mary Ann Blätke, Christian Rohr, Monika Heiner, Wolfgang Marwan:
A Petri-Net-Based Framework for Biomodel Engineering. Large-Scale Networks in Engineering and Life Sciences 2014: 317-366 - [e8]Monika Heiner:
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. CEUR Workshop Proceedings 1159, CEUR-WS.org 2014 [contents] - [i4]David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher:
Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports 4(11): 138-226 (2014) - 2013
- [j17]Fei Liu, Monika Heiner:
Modeling membrane systems using colored stochastic Petri nets. Nat. Comput. 12(4): 617-629 (2013) - [j16]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): 337-351 (2013) - [j15]Mostafa Herajy, Martin Schwarick, Monika Heiner:
Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle. Trans. Petri Nets Other Model. Concurr. 8: 123-141 (2013) - [c33]David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders:
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. Petri Nets 2013: 230-249 - [c32]Monika Heiner, Christian Rohr, Martin Schwarick:
MARCIE - Model Checking and Reachability Analysis Done Efficiently. Petri Nets 2013: 389-399 - [c31]Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders:
Modelling and Analysis of Phase Variation in Bacterial Colony Growth. CMSB 2013: 78-91 - [e7]Gianfranco Balbo, Monika Heiner:
Proceedings of the International Workshop on Biological Processes & Petri Nets, Milano, Italy, June 24, 2013. CEUR Workshop Proceedings 988, CEUR-WS.org 2013 [contents] - 2012
- [c30]Monika Heiner, Mostafa Herajy, Fei Liu, Christian Rohr, Martin Schwarick:
Snoopy - A Unifying Petri Net Tool. Petri Nets 2012: 398-407 - [c29]Mary Ann Blätke, Monika Heiner, Wolfgang Marwan:
Predicting Phenotype from Genotype through Automatically Composed Petri Nets. CMSB 2012: 87-106 - [c28]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: 362-365 - [c27]Mostafa Herajy, Monika Heiner:
Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks. CS&P 2012: 147-159 - [c26]Fei Liu, Monika Heiner, Ming Yang:
An efficient method for unfolding colored Petri nets. WSC 2012: 295:1-295:12 - [e6]David R. Gilbert, Monika Heiner:
Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Lecture Notes in Computer Science 7605, Springer 2012, ISBN 978-3-642-33635-5 [contents] - 2011
- [j14]Monika Heiner:
Preface: Petri nets for Systems and Synthetic Biology. Nat. Comput. 10(2): 633-638 (2011) - [j13]Monika Heiner:
Preface: Petri nets for Systems and Synthetic Biology. Nat. Comput. 10(3): 987-992 (2011) - [j12]Monika Heiner, Adelinde M. Uhrmacher:
Foundations of formal reconstruction of biochemical networks. Theor. Comput. Sci. 412(26): 2798-2799 (2011) - [c25]Monika Heiner, David R. Gilbert:
How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets 2011: 17-37 - [c24]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: 209-218 - [c23]Martin Schwarick, Monika Heiner, Christian Rohr:
MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly. QEST 2011: 91-100 - 2010
- [j11]Christian Rohr, Wolfgang Marwan, Monika Heiner:
Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinform. 26(7): 974-975 (2010) - [j10]Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner:
Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology 12: 1-12 (2010) - [c22]Claudine Chaouiya, Monika Heiner:
Introduction. ACSD/Petri Nets Workshops 2010: 5-6 - [c21]Monika Heiner, Cristian Mahulea, Manuel Silva Suárez:
On the Importance of the Deadlock Trap Property for Monotonic Liveness. ACSD/Petri Nets Workshops 2010: 23-38 - [c20]Fei Liu, Monika Heiner:
Colored Petri nets to Model and Simulate Biological Systems. ACSD/Petri Nets Workshops 2010: 71-85 - [c19]Fei Liu, Monika Heiner:
Computation of Enabled Transition Instances for Colored Petri Nets. AWPN 2010: 51-65 - [c18]Mostafa Herajy, Monika Heiner:
Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions. AWPN 2010: 66-79 - [c17]Monika Heiner, Christian Rohr, Martin Schwarick, Stefan Streif:
A comparative study of stochastic analysis techniques. CMSB 2010: 96-106 - [e5]Martin Schwarick, Monika Heiner:
Proceedings of the 17th German Workshop on Algorithms and Tools for Petri Nets, Cottbus, Germany, October 07-08, 2010. CEUR Workshop Proceedings 643, CEUR-WS.org 2010 [contents] - [e4]Corrado Priami, Rainer Breitling, David R. Gilbert, Monika Heiner, Adelinde M. Uhrmacher:
Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies. Lecture Notes in Computer Science 5945, Springer 2010, ISBN 978-3-642-11711-4 [contents]
2000 – 2009
- 2009
- [j9]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: 138-163 (2009) - [c16]Monika Heiner, Martin Schwarick, Alexej Tovchigrechko:
DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets. Petri Nets 2009: 323-332 - [c15]Monika Heiner:
Understanding Network Behavior by Structured Representations of Transition Invariants. Algorithmic Bioprocesses 2009: 367-389 - [c14]Martin Schwarick, Monika Heiner:
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams. CMSB 2009: 296-312 - [e3]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
Formal Methods in Molecular Biology, 22.02. - 27.02.2009. Dagstuhl Seminar Proceedings 09091, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Germany 2009 [contents] - [i3]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
09091 Abstracts Collection - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology 2009 - [i2]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
09091 Executive Summary - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology 2009 - [i1]David Roger Gilbert, Rainer Breitling, Monika Heiner:
BioModel Engineering: Its role in Systems Biology and Synthetic Biology. Formal Methods in Molecular Biology 2009 - 2008
- [j8]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): 404-421 (2008) - [j7]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) - [c13]David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo:
A Case Study in Model-driven Synthetic Biology. BICC 2008: 163-175 - [c12]David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson:
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing 2008: 13-28 - [c11]Monika Heiner, David R. Gilbert, Robin Donaldson:
Petri Nets for Systems and Synthetic Biology. SFM 2008: 215-264 - [c10]Monika Heiner, Ronny Richter, Martin Schwarick:
Snoopy: a tool to design and animate/simulate graph-based formalisms. SimuTools 2008: 15 - [e2]Monika Heiner, Adelinde M. Uhrmacher:
Computational Methods in Systems Biology, 6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings. Lecture Notes in Computer Science 5307, Springer 2008, ISBN 978-3-540-88561-0 [contents] - 2007
- [c9]David R. Gilbert, Monika Heiner, Sebastian Lehrack:
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB 2007: 200-216 - 2006
- [j6]Andrea Sackmann, Monika Heiner, Ina Koch:
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform. 7: 482 (2006) - [c8]David R. Gilbert, Monika Heiner:
From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN 2006: 181-200 - 2005
- [j5]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): 1219-1226 (2005) - [j4]Louchka Popova-Zeugmann, Monika Heiner, Ina Koch:
Time Petri Nets for Modelling and Analysis of Biochemical Networks. Fundam. Informaticae 67(1-3): 149-162 (2005) - 2004
- [j3]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): 129-137 (2004) - [c7]Monika Heiner, Ina Koch:
Petri Net Based Model Validation in Systems Biology. ICATPN 2004: 216-237 - 2003
- [j2]Klaus Voss, Monika Heiner, Ina Koch:
Steady state analysis of metabolic pathways using Petri nets. Silico Biol. 3(3): 367-387 (2003) - [c6]Monika Heiner, Ina Koch, Jürgen Will:
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB 2003: 173 - [e1]Hartmut König, Monika Heiner, Adam Wolisz:
Formal Techniques for Networked and Distributed Systems - FORTE 2003, 23rd IFIP WG 6.1 International Conference, Berlin, Germany, September 29 - October 2, 2003, Proceedings. Lecture Notes in Computer Science 2767, Springer 2003, ISBN 3-540-20175-0 [contents] - 2002
- [c5]Thomas Rottke, Denis Hatebur, Maritta Heisel, Monika Heiner:
A Problem-Oriented Approach to Common Criteria Certification. SAFECOMP 2002: 334-346
1990 – 1999
- 1999
- [c4]Ina Koch, Stefan Schuster, Monika Heiner:
Simulation and analysis of metabolic networks by time-dependent Petri nets. German Conference on Bioinformatics 1999: 208-209 - [c3]Monika Heiner, Maritta Heisel:
Modeling Safety-Critical Systems with Z and Petri Nets. SAFECOMP 1999: 361-374 - 1998
- [c2]Monika Heiner, Thomas Menzel:
Instruction list verification using a Petri net semantics. SMC 1998: 716-721 - 1994
- [j1]Monika Heiner, Giorgio Ventre, Dietmar Wikarski:
A Petri net based methodology to integrate qualitative and quantitative analysis. Inf. Softw. Technol. 36(7): 435-441 (1994) - 1992
- [c1]Monika Heiner:
A Petri Net View of Process Communication. FBT 1992: 126-141
1980 – 1989
- 1980
- [b1]Monika Heiner:
Ein Beitrag zur Deadlockanalyse auf der Grundlage einer sprachlich geführten Programmiermethodik. Dresden University of Technology, Germany, 1980
Coauthor Index
David R. Gilbert
aka: David Roger Gilbert
aka: David Roger Gilbert
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