@misc{GaoGilbertHeineretal., author = {Gao, Quian and Gilbert, David and Heiner, Monika and Liu, Fei and Maccagnola, Daniele and Tree, David}, title = {Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing}, series = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {10}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, number = {2}, issn = {1545-5963}, doi = {10.1109/TCBB.2012.101}, pages = {337 -- 351}, language = {en} } @misc{GilbertBreitlingHeineretal., author = {Gilbert, David and Breitling, Rainer and Heiner, Monika and Donaldson, Robin}, title = {An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways}, language = {en} } @inproceedings{HeinerBreitlingGilbertetal., author = {Heiner, Monika and Breitling, Rainer and Gilbert, David and Priami, C.}, title = {Formal Methods in Molecular Biology}, language = {en} } @inproceedings{LehrackGilbertHeiner, author = {Lehrack, Sebastian and Gilbert, David and Heiner, Monika}, title = {A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets}, language = {en} } @incollection{HeinerDonaldsonGilbert, author = {Heiner, Monika and Donaldson, Robin and Gilbert, David}, title = {Petri Nets for Systems Biology}, series = {Symbolic systems biology}, booktitle = {Symbolic systems biology}, editor = {Iyengar, M. Sriram}, publisher = {Jones and Bartlett Learning}, address = {Sudbury, Mass. [u.a.]}, isbn = {978-0-7637-5370-2}, language = {en} } @incollection{HeinerGilbertBreitlingetal., author = {Heiner, Monika and Gilbert, David and Breitling, Rainer and Orton, Richard}, title = {Computation modelling of kinase signalling cascades}, language = {en} } @incollection{HeinerGilbert, author = {Heiner, Monika and Gilbert, David}, title = {How Might Petri Nets Enhance Your Systems Biology Toolkit}, language = {en} } @incollection{HeinerGilbertDonaldson, author = {Heiner, Monika and Gilbert, David and Donaldson, Robin}, title = {Petri Nets for Systems and Synthetic Biology}, 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{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{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} } @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{ParvuGilbertHeineretal., author = {P{\^a}rvu, Ovidiu and Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel and Shaw, Simon}, title = {Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes}, series = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, volume = {25}, journal = {ACM Transactions on Modeling and Computer Simulation (TOMACS)}, number = {2}, issn = {1558-1195}, doi = {10.1145/2742546}, pages = {13}, language = {en} } @misc{GilbertHeiner, author = {Gilbert, David and Heiner, Monika}, title = {Preface Advances in Computational Methods in Systems Biology}, series = {Theoretical Computer Science}, volume = {599}, journal = {Theoretical Computer Science}, issn = {0304-3975}, doi = {doi:10.1016/j.tcs.2015.08.013}, pages = {2 -- 3}, language = {en} } @inproceedings{ParvuGilbertHeineretal., author = {Parvu, Ovidiu and Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel}, title = {Modelling and Analysis of Phase Variation in Bacterial Colony Growth}, series = {Computational Methods in Systems Biology, 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013}, booktitle = {Computational Methods in Systems Biology, 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013}, editor = {Gupta, Ashutosh and Henzinger, Thomas A.}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-40707-9}, doi = {10.1007/978-3-642-40708-6_7}, pages = {78 -- 91}, language = {en} } @inproceedings{GilbertHeinerLiuetal., author = {Gilbert, David and Heiner, Monika and Liu, Fei and Saunders, Nigel}, title = {Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology}, series = {Application and Theory of Petri Nets and Concurrency, 34th International Conference, PETRI NETS 2013, Milan, Italy, June 24-28, 2013}, booktitle = {Application and Theory of Petri Nets and Concurrency, 34th International Conference, PETRI NETS 2013, Milan, Italy, June 24-28, 2013}, publisher = {Springer}, address = {Berlin [u.a.]}, pages = {230 -- 249}, language = {en} } @misc{LiuHeinerGilbert, author = {Liu, Fei and Heiner, Monika and Gilbert, David}, title = {Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems}, series = {Briefings in Bioinformatics}, volume = {20}, journal = {Briefings in Bioinformatics}, number = {3}, issn = {1477-4054}, doi = {10.1093/bib/bbx150}, pages = {877 -- 886}, language = {en} } @misc{GilbertHeinerJayaweeraetal., author = {Gilbert, David and Heiner, Monika and Jayaweera, Yasoda and Rohr, Christian}, title = {Towards dynamic genome scale models}, series = {Briefings in Bioinformatics}, volume = {20}, journal = {Briefings in Bioinformatics}, number = {4}, issn = {1477-4054}, doi = {10.1093/bib/bbx096}, pages = {1167 -- 1180}, language = {en} } @misc{GilbertHeinerGhanbar, author = {Gilbert, David and Heiner, Monika and Ghanbar, Leila}, title = {Personalised models for human - gut microbiota interaction}, series = {PeerJ preprints}, volume = {5}, journal = {PeerJ preprints}, number = {e3267v1}, issn = {2167-9843}, doi = {10.7287/peerj.preprints.3267v1}, pages = {4}, language = {en} } @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} }