@misc{GilbertHeinerRohr, author = {Gilbert, David and Heiner, Monika and Rohr, Christian}, title = {Petri-net-based 2D Design of DNA Walker Circuits}, series = {Natural Computing}, volume = {17}, journal = {Natural Computing}, number = {1}, issn = {1572-9796}, doi = {10.1007/s11047-018-9671-4}, pages = {161 -- 182}, language = {en} } @misc{XuCurtisPowersetal., author = {Xu, Hongwei and Curtis, Tanya Y. and Powers, Stephen J. and Raffan, Sarah and Gao, Runhong and Huang, Jianhua and Heiner, Monika and Gilbert, David and Halford, Nigel G.}, title = {Genomic, biochemical and modelling analyses of asparagine synthetases from wheat}, series = {Frontiers in Plant Science}, volume = {8}, journal = {Frontiers in Plant Science}, issn = {1664-462X}, doi = {10.3389/fpls.2017.02237}, pages = {12}, language = {en} } @misc{GambinHeiner, author = {Gambin, Anna and Heiner, Monika}, title = {Advances in Biological processes and Petri nets (BioPPN)}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {0169-2968}, doi = {10.3233/FI-2018-1671}, pages = {V -- VII}, language = {en} } @misc{LiuChenHeineretal., author = {Liu, Fei and Chen, Siyuan and Heiner, Monika and Song, Hengjie}, title = {Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets}, series = {BMC Systems Biology}, volume = {12}, journal = {BMC Systems Biology}, number = {Supplement 4}, issn = {1752-0509}, doi = {10.1186/s12918-018-0568-8}, pages = {64 -- 74}, language = {en} } @misc{BaldanBocciBrigolinetal., author = {Baldan, Paolo and Bocci, Martina and Brigolin, Daniele and Cocco, Nicoletta and Heiner, Monika and Simeoni, Marta}, title = {Petri Nets for modelling and analysing Trophic Networks}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {0169-2968}, doi = {10.3233/FI-2018-1673}, pages = {27 -- 52}, language = {en} } @misc{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation}, series = {Fundamenta Informaticae}, volume = {160}, journal = {Fundamenta Informaticae}, number = {1-2}, issn = {1875-8681}, doi = {10.3233/FI-2018-1674}, pages = {53 -- 80}, language = {en} } @misc{ColomboDamianiGilbertetal., author = {Colombo, Riccardo and Damiani, Chiara and Gilbert, David and Heiner, Monika and Mauri, Giancarlo and Pescini, Dario}, title = {Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes}, series = {BMC bioinformatics}, volume = {19}, journal = {BMC bioinformatics}, number = {Suppl. 7}, issn = {1471-2105}, doi = {10.1186/s12859-018-2181-7}, pages = {46 -- 59}, language = {en} } @misc{HerajyLiuRohretal., author = {Herajy, Mostafa and Liu, Fei and Rohr, Christian and Heiner, Monika}, title = {Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks}, series = {Computational Biology and Chemistry}, volume = {76}, journal = {Computational Biology and Chemistry}, issn = {1476-9271}, doi = {10.1016/j.compbiolchem.2018.05.023}, pages = {87 -- 100}, language = {en} } @inproceedings{ChodakHeiner, author = {Chodak, Jacek and Heiner, Monika}, title = {Spike - a command line tool for continuous, stochastic \& hybrid simulation of (coloured) Petri nets}, series = {Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018}, booktitle = {Algorithms and Tools for Petri Nets -Proceedings of the Workshop AWPN 2018}, editor = {Lorenz, Robert and Metzger, Johannes}, publisher = {Universit{\"a}t, Institut f{\"u}r Informatik}, address = {Augsburg}, pages = {1 -- 6}, language = {en} } @misc{LiuHeinerGilbert, author = {Liu, Fei and Heiner, Monika and Gilbert, David}, title = {Fuzzy Petri nets for modelling of uncertain biological systems}, series = {Briefings in Bioinformatics}, volume = {2018}, journal = {Briefings in Bioinformatics}, issn = {1477-4054}, doi = {10.1093/bib/bby118}, pages = {13}, language = {en} } @inproceedings{IsmailHerajyHeineretal., author = {Ismail, Amr and Herajy, Mostafa and Heiner, Monika and Atlam, Elsayed}, title = {An Efficient Approach for the Hybrid Simulation of Intracellular Calcium Dynamics}, series = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, booktitle = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-5111-7}, doi = {10.1109/ICCES.2018.8639261}, pages = {665 -- 670}, language = {en} } @inproceedings{BadawyHerajyAwadetal., author = {Badawy, Asmaa and Herajy, Mostafa and Awad, Wael and Heiner, Monika}, title = {Distributed Simulation of Bio-interpreted (Coloured) Stochastic Petri Nets}, series = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, booktitle = {13th International Conference on Computer Engineering and Systems (ICCES), 18-19 Dec. 2018, Cairo, Egypt}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-5111-7}, doi = {10.1109/ICCES.2018.8639484}, pages = {268 -- 272}, language = {en} } @inproceedings{HerajyHeiner, author = {Herajy, Mostafa and Heiner, Monika}, title = {An Improved Simulation of Hybrid Biological Models with Many Stochastic Events and Quasi-Disjoint Subnets}, series = {Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden}, booktitle = {Proceedings of the 2018 Winter Simulation Conference, (WSC 2018) Gothenburg, Sweden}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-5386-6572-5}, doi = {10.1109/WSC.2018.8632514}, pages = {1346 -- 1357}, language = {en} } @inproceedings{SelfGilbertHeiner, author = {Self, Timothy and Gilbert, David and Heiner, Monika}, title = {Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models}, series = {Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings}, booktitle = {Computational Methods in Systems Biology, 16th International Conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings}, editor = {Češka, Milan and Šafr{\´a}nek, David}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-99428-4}, doi = {10.1007/978-3-319-99429-1_3}, pages = {39 -- 58}, language = {en} }