@incollection{HeinerGilbertDonaldson, author = {Heiner, Monika and Gilbert, David and Donaldson, Robin}, title = {Petri Nets for Systems and Synthetic Biology}, language = {en} } @incollection{Heiner, author = {Heiner, Monika}, title = {Understanding Network Behaviour by Structured Representations of Transition Invariants - A Petri Net Perspective on Systems and Synthetic Biology}, language = {en} } @incollection{HeinerKoch, author = {Heiner, Monika and Koch, Ina}, title = {Petri Nets}, language = {en} } @misc{HeinerYangLiu, author = {Heiner, Monika and Yang, Ming and Liu, Fei}, title = {Modeling and analyzing biological systems using colored hierarchical Petri nets illustrated by C. elegans vulval development}, series = {Journal of Biological Systems}, volume = {22}, journal = {Journal of Biological Systems}, number = {3}, issn = {1793-6470}, doi = {10.1142/S0218339014500181}, pages = {463 -- 493}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks}, series = {Fundamenta Informaticae}, volume = {129}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {0169-2968}, pages = {49 -- 67}, language = {en} } @misc{BlaetkeDittrichRohretal., author = {Bl{\"a}tke, Mary-Ann and Dittrich, Anna and Rohr, Christian and Heiner, Monika and Schaper, Fred and Marwan, Wolfgang}, title = {JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology}, series = {Molecular BioSystems}, volume = {9}, journal = {Molecular BioSystems}, number = {6}, issn = {1742-2051}, doi = {10.1039/C3MB25593J}, pages = {1290 -- 1307}, language = {en} } @incollection{HeinerLehrackGilbertetal., author = {Heiner, Monika and Lehrack, Sebastian and Gilbert, David and Marwan, Wolfgang}, title = {Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments}, series = {Transactions on Computational Systems Biology XI}, booktitle = {Transactions on Computational Systems Biology XI}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-04185-3}, pages = {138 -- 163}, language = {en} } @misc{GrafahrendBelauSchreiberHeineretal., author = {Grafahrend-Belau, Eva and Schreiber, Falk and Heiner, Monika and Sackmann, Andrea and Junker, Bj{\"o}rn H. and Grunwald, Stefanie and Speer, Astrid and Winder, Katja and Koch, Ina}, title = {Modularization of biochemical networks based on classification of Petri net T-invariants}, series = {BMC Bioinformatics}, volume = {Vol. 9}, journal = {BMC Bioinformatics}, issn = {1471-2105}, doi = {10.1186/1471-2105-9-90}, language = {en} } @misc{BreitlingGilbertHeineretal., author = {Breitling, Rainer and Gilbert, David and Heiner, Monika and Orton, Richard}, title = {A structured approach for the engineering of biochemical network models, illustrated for signalling pathways}, series = {Briefings in Bioinformatics}, volume = {9}, journal = {Briefings in Bioinformatics}, number = {5}, issn = {1477-4054}, doi = {10.1093/bib/bbn026}, pages = {404 -- 421}, language = {en} } @misc{SackmannHeinerKoch, author = {Sackmann, Andrea and Heiner, Monika and Koch, Ina}, title = {Application of Petri net based analysis techniques to signal transduction pathways}, series = {BMC Bioinformatics}, volume = {Vol. 7}, journal = {BMC Bioinformatics}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-482}, language = {en} } @misc{PopovaZeugmannHeinerKoch, author = {Popova-Zeugmann, Louchka and Heiner, Monika and Koch, Ina}, title = {Time Petri Nets for Modelling and Analysis of Biochemical Networks}, series = {Fundamenta Informaticae}, volume = {67}, journal = {Fundamenta Informaticae}, number = {1-3}, issn = {1875-8681}, pages = {149 -- 162}, language = {en} } @misc{KochJunkerHeiner, author = {Koch, Ina and Junker, Bj{\"o}rn H. and Heiner, Monika}, title = {Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber}, series = {Bioinformatics}, volume = {21}, journal = {Bioinformatics}, number = {7}, issn = {1460-2059}, pages = {1219 -- 1226}, language = {en} } @misc{KochSchuelerHeiner, author = {Koch, Ina and Sch{\"u}ler, Markus and Heiner, Monika}, title = {STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks}, series = {In silico biology}, volume = {Vol. 5}, journal = {In silico biology}, issn = {1434-3207}, language = {en} } @misc{HeinerKochWill, author = {Heiner, Monika and Koch, Ina and Will, J{\"u}rgen}, title = {Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis}, series = {BioSystems}, volume = {75}, journal = {BioSystems}, number = {1-3}, doi = {10.1016/j.biosystems.2004.03.003}, pages = {15 -- 28}, language = {en} } @misc{VossHeinerKoch, author = {Voss, Klaus and Heiner, Monika and Koch, Ina}, title = {Steady State Analysis of Metabolic Pathways Using Petri Nets}, series = {In silico biology}, volume = {Vol. 3}, journal = {In silico biology}, issn = {1434-3207}, language = {en} } @misc{HeinerGilbert, author = {Heiner, Monika and Gilbert, David}, title = {BioModel Engineering for Multiscale Systems Biology}, series = {Progress in Biophysics and Molecular Biology}, volume = {111}, journal = {Progress in Biophysics and Molecular Biology}, number = {2-3}, issn = {1873-1732}, doi = {10.1016/j.pbiomolbio.2012.10.001}, pages = {119 -- 128}, language = {en} } @misc{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Modeling membrane systems using colored stochastic Petri nets}, series = {Natural Computing}, volume = {12}, journal = {Natural Computing}, number = {4}, issn = {1572-9796}, doi = {10.1007/s11047-013-9367-8}, pages = {617 -- 629}, language = {en} } @incollection{HerajySchwarickHeiner, author = {Herajy, Mostafa and Schwarick, Martin and Heiner, Monika}, title = {Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle}, series = {Transactions on petri nets and other models of concurrency VIII}, booktitle = {Transactions on petri nets and other models of concurrency VIII}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-40464-1}, doi = {10.1007/978-3-642-40465-8_7}, pages = {123 -- 141}, language = {en} } @misc{LiuHeiner, author = {Liu, Fei and Heiner, Monika}, title = {Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets}, series = {IET Systems Biology}, volume = {7}, journal = {IET Systems Biology}, number = {4}, issn = {1751-8849}, pages = {106 -- 113}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Hybrid Representation and Simulation of Stiff Biochemical Networks}, series = {Nonlinear Analysis: Hybrid Systems}, volume = {6}, journal = {Nonlinear Analysis: Hybrid Systems}, number = {4}, issn = {1751-570X}, pages = {942 -- 959}, language = {en} } @incollection{HeinerBreitlingDonaldsonetal., author = {Heiner, Monika and Breitling, Rainer and Donaldson, Robin and Gilbert, David}, title = {Biomodel Engineering - From Structure to Behavior}, series = {Transactions on Computational Systems Biology XII : Special Issue on Modeling Methodologies}, booktitle = {Transactions on Computational Systems Biology XII : Special Issue on Modeling Methodologies}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-11711-4}, doi = {10.1007/978-3-642-11712-1}, pages = {1 -- 12}, language = {en} } @misc{HeinerSriram, author = {Heiner, Monika and Sriram, K.}, title = {Structural Analysis to Determine the Core of Hypoxia Response Network}, series = {PLoS ONE}, volume = {5}, journal = {PLoS ONE}, number = {1}, issn = {1932-6203}, doi = {10.1371/journal.pone.0008600}, language = {en} } @misc{RohrMarwanHeiner, author = {Rohr, Christian and Marwan, Wolfgang and Heiner, Monika}, title = {Snoopy - a unifying Petri net framework to investigate biomolecular networks}, series = {Bioinformatics}, volume = {26}, journal = {Bioinformatics}, number = {7}, issn = {1460-2059}, pages = {974 -- 975}, language = {en} } @misc{HeinerSoliman, author = {Heiner, Monika and Soliman, Sylvain}, title = {A Unique Transformation from Ordinary Differential Equations to Reaction Networks}, series = {PLoS one}, volume = {5}, journal = {PLoS one}, number = {12}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014284}, language = {en} } @misc{HeinerVentreWikarski, author = {Heiner, Monika and Ventre, Giorgio and Wikarski, Dietmar}, title = {A Petri Net Based Methodology to Integrate Qaulitative and Quantitative Analysis}, series = {Information and Software Technology}, volume = {36}, journal = {Information and Software Technology}, number = {7}, issn = {0950-5849}, doi = {10.1016/0950-5849(94)90066-3}, pages = {435 -- 441}, language = {en} } @inproceedings{BarbotHaddadHeineretal., author = {Barbot, Benoit and Haddad, Serge and Heiner, Monika and Picaronny, Claudine}, title = {Rare Event Handling in Signalling Cascades}, series = {Proceedings, SIMUL 2014, Sixth International Conference on Advances in System Simulation}, booktitle = {Proceedings, SIMUL 2014, Sixth International Conference on Advances in System Simulation}, publisher = {IARIA}, isbn = {978-1-61208-371-1}, pages = {126 -- 131}, language = {en} } @inproceedings{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {A Steering Server for Collaborative Simulation of Quantitative Petri Nets}, series = {Application and Theory of Petri Nets and Concurrency, 35th International Conference, PETRI NETS 2014, Tunis, Tunisia, June 23-27, 2014, Proceedings}, booktitle = {Application and Theory of Petri Nets and Concurrency, 35th International Conference, PETRI NETS 2014, Tunis, Tunisia, June 23-27, 2014, Proceedings}, editor = {Ciardo, Gianfranco and Kindler, Ekkart}, publisher = {Springer}, address = {Cham [u.a.]}, isbn = {978-3-319-07733-8}, pages = {374 -- 384}, language = {en} }