Gilbert, D., Heiner, M., Ghanbar, L. and Chodak, J. (2019) 'Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking'. BMC Bioinformatics, 20 (Suppl 4). pp. 1 - 23. ISSN: 1471-2105 Open Access Link

Self, T., Gilbert, D. and Heiner, M. (2018) 'Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models'.Computational Methods in Systems Biology: CMSB 2018. Brno, Czech Republic. 12 - 14 September. Springer International Publishing. pp. 39 - 58. ISSN: 0302-9743 Open Access Link

Colombo, R., Damiani, C., Gilbert, D., Heiner, M., Mauri, G. and Pescini, D. (2018) 'Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes'. BMC Bioinformatics, 19 (251). pp. 251. ISSN: 1471-2105 Open Access Link

Gilbert, D., Heiner, M. and Rohr, C. (2018) 'Petri-net-based 2D Design of DNA Walker Circuits'. Natural Computing, 17 (1). pp. 161 - 182. ISSN: 1567-7818 Open Access Link

Lui, F., Heiner, M. and Gilbert, D. (2017) 'Coloured Petri nets for multi-level, multiscale, and multi-dimensional modelling of biological systems'. Briefings in Bioinformatics, 20 (3). pp. 877 - 886. ISSN: 1467-5463 Open Access Link

Gilbert, D., Heiner, M., Jayaweera, Y. and Rohr, C. (2017) 'Towards dynamic genome scale models'. Briefings in Bioinformatics, 20 (4). pp. 1167 - 1180. ISSN: 1467-5463 Open Access Link

Pârvu, O. and Gilbert, D. (2016) 'A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking'. PLOS ONE, 11 (5). pp. e0154847 - e0154847. ISSN: 1932-6203 Open Access Link

Pârvu, O., Gilbert, D., Heiner, M., Liu, F., Saunders, N. and Shaw, S. (2015) 'Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes'. ACM Transactions on Modeling and Computer Simulation, 25 (2). pp. 1 - 25. ISSN: 1049-3301 Open Access Link

Parvu, O. and Gilbert, D. (2014) 'Automatic validation of computational models using pseudo-3D spatio-temporal model checking'. BMC Systems Biology, 8 (124). pp. 124. ISSN: 1752-0509 Open Access Link

Rausanu, S., Grosan, C., Wu, Z., Parvu, O., Stoica, R. and Gilbert, D. (2014) 'Computational models for inferring biochemical networks'. Neural Computing and Applications, 26 (2). pp. 299 - 311. ISSN: 0941-0643 Open Access Link

Wu, Z., Grosan, C. and Gilbert, D. (2014) 'Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling', in Terrazas, G., Otero, F. and Masegosa, A. (eds.) Nature Inspired Cooperative Strategies for Optimization (NICSO 2013). Cham : Springer International Publishing. , 512. pp. 245 - 260. ISBN 13: 978-3-319-01692-4.

Gilbert, D. and Parvu, O. (2014) 'Implementation of linear minimum area enclosing traingle algorithm'. Computational and Applied Mathematics, Forthcoming. ISSN: 2238-3603 Open Access Link

Gao, Q., Gilbert, D., Heiner, M., Liu, F., MacCagnola, D. and Tree, D. (2013) 'Multiscale modeling and analysis of planar cell polarity in the drosophila wing'. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (2). pp. 337 - 351. ISSN: 1545-5963

Heiner, M. and Gilbert, D. (2013) 'BioModel engineering for multiscale Systems Biology'. Progress in Biophysics and Molecular Biology, 111 (2-3). pp. 119 - 128. ISSN: 0079-6107 Open Access Link

Gu, X., Reid, D., Higham, DJ. and Gilbert, D. (2013) 'Mathematical Modelling of Polyamine Metabolism in Bloodstream-Form Trypanosoma brucei: An Application to Drug Target Identification'. PLoS One, 8 (1). pp. e53734 - e53734.Open Access Link

Kerkhoven, EJ., Achcar, F., Alibu, VP., Burchmore, RJ., Gilbert, IH., Trybi lo, M., Driessen, NN., Gilbert, D., Breitling, R., Bakker, BM. and others. et al. (2013) 'Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei'. PLoS computational biology, 9 (12). pp. e1003371 - e1003371. ISSN: 1553-734X

Rausanu, S., Grosan, C., Wu, Z., Parvu, O. and Gilbert, D. (2013) 'Evolving biochemical systems'.2013 IEEE Congress on Evolutionary Computation (CEC). IEEE. IEEE. pp. 1602 - 1609.

Pârvu, O., Gilbert, D., Heiner, M., Liu, F. and Saunders, N. (2013) 'Modelling and Analysis of Phase Variation in Bacterial Colony Growth', in Gupta, A. and Henzinger, TA. (eds.) Computational Methods in Systems Biology. Springer Berlin Heidelberg. , 8130 LNBI. pp. 78 - 91. ISBN 13: 9783642407079.

Gilbert, D., Heiner, M., Liu, F. and Saunders, N. (2013) 'Colouring space-a coloured framework for spatial modelling in systems biology', inApplication and Theory of Petri Nets and Concurrency. Springer Berlin Heidelberg. , 7927 LNCS. pp. 230 - 249. ISBN 13: 9783642386961.

Soldatova, L., Gao, Q. and Gilbert, D. (2012) 'Towards an ontology of biomodelling'. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7605 LNBI. pp. 390 - 393. ISSN: 0302-9743

Maccagnola, D., Messina, E., Gao, Q. and Gilbert, D. (2012) 'A machine learning approach for generating temporal logic classifications of complex model behaviours'.2012 Winter Simulation Conference - (WSC 2012). Winter Simulation Conference. IEEE. pp. 294 - 294. ISSN: 0891-7736

Wu, Z., Yang, S. and Gilbert, D. (2012) 'A hybrid approach to piecewise modelling of biochemical systems', inParallel Problem Solving from Nature-PPSN XII. Springer Berlin Heidelberg. , 7491 LNCS. pp. 519 - 528. ISBN 13: 9783642329364.

Lodhi, H. and Gilbert, D. (2011) 'Bootstrapping parameter estimation in dynamic systems', in Elomaa, T., Hollmen, J. and Mannila, H. (eds.) Discovery Science: Proceedings of the 14th International Conference, DS 2011, Espoo, Finland, October 5-7, 2011. Springer. , 6926. pp. 194 - 208. ISBN 10: 3642244769. ISBN 13: 978-3642244766.

Gao, Q., Liu, F., Gilbert, D., Heiner, M. and Tree, D. (2011) 'A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured petri nets'.9th International Conference on Computational Methods in Systems Biology (CMSB 2011). Paris, France. 21 - 23 September. ACM. pp. 209 - 218.

Vijayakrishnan, S., Callow, P., Nutley, MA., McGow, DP., Gilbert, D., Kropholler, P., Cooper, A., Byron, O. and Lindsay, JG. et al. (2011) 'Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly'. Biochemical Journal, 437 (3). pp. 565 - 574. ISSN: 0264-6021 Open Access Link

Gao, Q., Liu, F., Tree, D. and Gilbert, D. (2011) 'Multi-cell modelling using coloured petri nets applied to planar cell polarity'.2nd International Workshop on Biological Processes & Petri Nets (BioPPN 2011). Newcastle, UK. 20 CEUR Workshop Proceedings (http://ceur-ws.org). pp. 135 - 150. ISSN: 1613-0073

Gilbert, D. and Heiner, M. (2011) 'How might petri nets enhance your systems biology toolkit'.Applications and Theory of Petri Nets 32nd International Conference (PETRI NETS 2011). Newcastle, UK. 20 - 24 June. Springer. pp. 17 - 37. ISSN: 0302-9743

Wu, Z., Gao, Q. and Gilbert, D. (2010) 'Target driven biochemical network reconstruction based on petri nets and simulated annealing'.8th Conference on Computational Methods in Systems Biology (CMSB 2010). Trento, Italy. 29 - 1 October. ACM. pp. 33 - 42.

Gilbert, D., Jaramillo, A., Krasnogor, N. and de Lorenzo, V. (2010) 'Editorial: Synthetic biology gains momentum in Europe'. Systems and Synthetic Biology, 4 (3). pp. 145 - 147. ISSN: 1872-5325

Kolch, W., Birtwistle, M., Kholodenko, B., Grindlay, J., Sturm, O., Orton, R., Gilbert, D. and von Kriegsheim, A. et al. (2010) 'From benchside to byteside: what we can learn from computational modelling'.21st Meeting of the European-Association-for-Cancer-Research. Oslo, NORWAY. 26 - 29 June. PERGAMON-ELSEVIER SCIENCE LTD. pp. 3 - 3. ISSN: 1359-6349

Veeramalai, M., Gilbert, D. and Valiente, G. (2010) 'An optimized TOPS plus comparison method for enhanced TOPS models'. BMC Bioinformatics, 11 (1). pp. 138. ISSN: 1471-2105 Open Access Link

Gilbert, D., Heiner, M., Breitling, R. and Orton, R. (2010) 'Computational modelling of kinase signalling cascades'. Methods in Molecular Biology, 661. pp. 369 - 384. ISSN: 1064-3745

Priami, C., Breitling, R., Gilbert, D., Heiner, M. and Uhrmacher, AM. (2010) 'Transactions on computational systems biology XII'. Berlin/Heidelberg: Springer. ISSN 10: 3642117112 ISSN 13: 9783642117114

Breitling, R., Donaldson, RA., Gilbert, DR. and Heiner, M. (2010) 'Biomodel engineering – from structure to behavior', in Priami, C., Donaldson, RA., Gilbert, DR. and Heiner, M. (eds.) Transactions on Computational Systems Biology XII. Berlin/Heidelberg : Springer. , 5945/2010. pp. 1 - 12. ISBN 10: 3642117112. ISBN 13: 978-3-642-11711-4.

Sturm, OE., Orton, R., Grindlay, J., Birtwistle, M., Vyshemirsky, V., Gilbert, D., Calder, M., Pitt, A., Kholodenko, B. and Kolch, W. et al. (2010) 'The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier.'. Science Signaling, 3 (153). pp. ra90. ISSN: 1945-0877

Gu, X., Trybilo, M., Ramsey, S., Jensen, M., Fulton, R., Rosser, S. and Gilbert, D. et al. (2010) 'Engineering a novel self-powering electrochemical biosensor'. Systems and Synthetic Biology, 4 (3). pp. 203 - 214. ISSN: 1872-5325 Open Access Link

Wang, J., Liu, X., Mustafee, N., Gao, Q., Taylor, SJE. and Gilbert, D. (2009) 'Grid-enabled SIMAP utility: motivation, integration technology and performance results'.UK e-Science All Hands Meeting (AHM 2009). Oxford, UK. 7 - 9 December.Open Access Link

Orton, RJ., Adriaens, ME., Gormand, A., Sturm, OE., Kolch, W. and Gilbert, DR. (2009) 'Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway'. BMC Systems Biology, 3 (1). pp. 100. ISSN: 1752-0509 Open Access Link

Heiner, M., Lehrack, S., Gilbert, D. and Marwan, W. (2009) 'Extended stochastic petri nets for model-based design of wetlab experiments', in Priami, C., Back, R-J. and Petre, I. (eds.) Transactions on Computational Systems Biology XI. Berlin/Heidelberg : Springer. , 5750/2009. pp. 138 - 163. ISBN 10: 364204185X. ISBN 13: 978-3-642-04185-3.

Park, SH., Reyes, JA., Gilbert, DR., Kim, JW. and Kim, S. (2009) 'Prediction of protein-protein interaction types using association rule based classification'. BMC Bioinformatics, 10 (1). pp. 36. ISSN: 1471-2105 Open Access Link

Torrance, GM., Leader, DP., Gilbert, DR. and Milner-White, EJ. (2009) 'A novel main chain motif in proteins bridged by cationic groups: the niche'. Journal of Molecular Biology, 385 (4). pp. 1076 - 1086. ISSN: 0022-2836

Gilbert, D., Breitling, R., Heiner, M. and Donaldson, R. (2009) 'An introduction to BioModel Engineering, illustrated for signal transduction pathways', in Corne, DW., Frisco, P., Paun, G., Rozenberg, G. and Salomaa, A. (eds.) Membrane Computing. Springer Berlin Heidelberg. , 5391/2009. pp. 13 - 28. ISBN 13: 9783540958840. Open Access Link

von Kriegsheim, A., Baiocchi, D., Birtwistle, M., Sumpton, D., Bienvenut, W., Morrice, N., Yamada, K., Lamond, A., Kalna, G., Orton, R., Gilbert, D. and Kolch, W. et al. (2009) 'Cell fate decisions are specified by the dynamic ERK interactome'. Nature Cell Biology, 11 (12). pp. 1458 - 1464. ISSN: 1476-4679

Breitling, R., Gilbert, D., Heiner, M. and Orton, R. (2008) 'A structured approach for the engineering of biochemical network models, illustrated for signalling pathways'. Briefings in Bioinformatics, 9 (5). pp. 404 - 421. ISSN: 1467-5463 Open Access Link

Heiner, M., Gilbert, D. and Donaldson, R. (2008) 'Petri nets for systems and synthetic biology', in Bernardo, M., Degano, P. and Zavattaro, G. (eds.) Formal Methods for Computational Systems Biology. Berlin/Heidelberg : Springer. , 5016/2008. pp. 215 - 264. ISBN 10: 3540688927. ISBN 13: 978-3-540-68892-1. Open Access Link

Donaldson, R. and Gilbert, D. (2008) 'A model checking approach to the parameter estimation of biochemical pathways', in Heiner, M. and Uhrmacher, AM. (eds.) Computational Methods in Systems Biology. Springer Berlin Heidelberg. , 5307/2008. pp. 269 - 287. ISBN 10: 3540885617. ISBN 13: 9783540885610. Open Access Link

Gilbert, D., Heiner, M., Rosser, S., Fulton, R., Gu, X. and Trybilo, M. (2008) 'A case study in model-driven synthetic biology', in Hinchey, M., Pagnoni, A., Rammig, FJ. and Schmeck, H. (eds.) Biologically-Inspired Collaborative Computing. Springer US. , 268/2008. pp. 163 - 175. ISBN 13: 9780387096544. Open Access Link

Veeramalai, M. and Gilbert, D. (2008) 'A novel method for comparing topological models of protein structures enhanced with ligand information'. Bioinformatics, 24 (23). pp. 2698 - 2705. ISSN: 1367-4803 Open Access Link

Donaldson, R. and Gilbert, D. (2008) 'A Monte Carlo Model checker for probabilistic LTL with numerical constraints'. Place of publication: Department of Computer Science at University of Glasgow.Open Access Link

Orton, RJ., Sturm, OE., Gormand, A., Kolch, W. and Gilbert, DR. (2008) 'Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway'. IET Systems Biology, 2 (4). pp. 173 - 183. ISSN: 1751-8849