David R. Gilbert

119 papers A 1B 7C 9Misc 2Journal 58Unranked 38

Year	Rank	Type	Title / Venue / Authors
2025	C	`conf`	Insensitive Games: Game Semantics for Modal Insensitivity. WoLLIC Can Baskent, David R. Gilbert, Giorgio Venturi
2025	J	`jnl`	Logics of spatial isolation. J. Log. Comput. Can Baskent, David R. Gilbert, Giorgio Venturi
2024	C	`conf`	A Logic of Isolation. WoLLIC Can Baskent, David R. Gilbert, Giorgio Venturi
2022	J	`jnl`	Hybrid modelling of biological systems: current progress and future prospects. Briefings Bioinform. Fei Liu, Monika Heiner, David R. Gilbert
2022	J	`jnl`	Logics of Ignorance and Being Wrong. Log. J. IGPL David R. Gilbert, Ekaterina Kubyshkina, Mattia Petrolo, Giorgio Venturi
2021	J	`jnl`	From Epidemic to Pandemic Modelling. CoRR Shannon Connolly, David R. Gilbert, Monika Heiner
2021	J	`jnl`	Hybrid modelling of biological systems using fuzzy continuous Petri nets. Briefings Bioinform. Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert
2021	J	`jnl`	Reflexive-Insensitive Logics, the Boxdot Translation, and the Modal Logic of Generic Absoluteness. Notre Dame J. Formal Log. David R. Gilbert, Giorgio Venturi
2020	J	`jnl`	A note on logics of essence and accident. Log. J. IGPL David R. Gilbert, Giorgio Venturi
2020	J	`jnl`	Fuzzy Petri nets for modelling of uncertain biological systems. Briefings Bioinform. Fei Liu, Monika Heiner, David R. Gilbert
2019	J	`jnl`	Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. Briefings Bioinform. Fei Liu, Monika Heiner, David R. Gilbert
2019	J	`jnl`	Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinform. David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
2019	J	`jnl`	Towards dynamic genome-scale models. Briefings Bioinform. David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
2018	—	`conf`	Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. CMSB Timothy Self, David R. Gilbert, Monika Heiner
2018	J	`jnl`	Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinform. Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
2018	J	`jnl`	Petri-net-based 2D design of DNA walker circuits. Nat. Comput. David R. Gilbert, Monika Heiner, Christian Rohr
2017	J	`jnl`	Neighborhood Semantics for Logics of Unknown Truths and False Beliefs. Australas. J. Log. David R. Gilbert, Giorgio Venturi
2016	J	`jnl`	Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure. Balt. J. Mod. Comput. Juris Viksna, David R. Gilbert
2016	J	`jnl`	Reflexive-Insensitive Modal Logics. Rev. Symb. Log. David R. Gilbert, Giorgio Venturi
2015	J	`jnl`	Advances in Computational Methods in Systems Biology. Theor. Comput. Sci. David R. Gilbert, Monika Heiner
2015	J	`jnl`	Computational models for inferring biochemical networks. Neural Comput. Appl. Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, Ramona Stoica, David R. Gilbert
2015	J	`jnl`	Modular Sequent Calculi for Classical Modal Logics. Stud Logica David R. Gilbert, Paolo Maffezioli
2015	J	`jnl`	Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. ACM Trans. Model. Comput. Simul. Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders, Simon Shaw
2014	—	`ed.`	2014 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2014, Belfast, United Kingdom, November 2-5, 2014 BIBM Huiru Jane Zheng, Werner Dubitzky, Xiaohua Hu, Jin-Kao Hao, Daniel P. Berrar, Kwang-Hyun Cho, Yadong Wang, David R. Gilbert
2014	J	`jnl`	Automatic validation of computational models using pseudo-3D spatio-temporal model checking. BMC Syst. Biol. Ovidiu Parvu, David R. Gilbert
2014	Misc	`conf`	Investigating the speedup of systems biology simulation using the sztaki desktop grid. WSC Simon J. E. Taylor, Mohammadmersad Ghorbani, Navonil Mustafee, Tamás Kiss, Péter Borsody, Annette M. Payne, David R. Gilbert
2014	J	`jnl`	Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher
2014	J	`jnl`	Speeding up systems biology simulations of biochemical pathways using condor. Concurr. Comput. Pract. Exp. Xuan Liu, Simon J. E. Taylor, Navonil Mustafee, Jun Wang, Qian Gao, David R. Gilbert
2013	B	`conf`	Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. Petri Nets David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
2013	—	`conf`	Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling. NICSO Zujian Wu, Crina Grosan, David R. Gilbert
2013	B	`conf`	Evolving biochemical systems. IEEE Congress on Evolutionary Computation Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, David R. Gilbert
2013	J	`jnl`	Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in PLoS Comput. Biol. Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybilo, Nicole N. Driessen, David R. Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett
2013	—	`conf`	Modelling and Analysis of Phase Variation in Bacterial Colony Growth. CMSB Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
2013	J	`jnl`	Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing. IEEE ACM Trans. Comput. Biol. Bioinform. Qian Gao, David R. Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree
2012	—	`conf`	A Hybrid Approach to Piecewise Modelling of Biochemical Systems. PPSN (1) Zujian Wu, Shengxiang Yang, David R. Gilbert
2012	Misc	`conf`	A machine learning approach for generating temporal logic classifications of complex model behaviours. WSC Daniele Maccagnola, Enza Messina, Qian Gao, David R. Gilbert
2012	J	`jnl`	Completeness Results for some two-Dimensional Logics of actuality. Rev. Symb. Log. David R. Gilbert, Edwin D. Mares
2012	—	`ed.`	Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings CMSB David R. Gilbert, Monika Heiner
2012	—	`conf`	Towards an Ontology of Biomodelling. CMSB Larisa N. Soldatova, Qian Gao, David R. Gilbert
2011	—	`conf`	A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. CMSB Qian Gao, Fei Liu, David R. Gilbert, Monika Heiner, David Tree
2011	B	`conf`	Bootstrapping Parameter Estimation in Dynamic Systems. Discovery Science Huma Lodhi, David R. Gilbert
2011	B	`conf`	How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets Monika Heiner, David R. Gilbert
2010	J	`jnl`	An optimized TOPS+ comparison method for enhanced TOPS models. BMC Bioinform. Mallika Veeramalai, David R. Gilbert, Gabriel Valiente
2010	J	`jnl`	Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
2010	—	`conf`	Formal Models of Virtual Enterprise Architecture: Motivations and Approaches. PACIS Amit Goel, Heinz Schmidt, David R. Gilbert
2010	—	`conf`	Target driven biochemical network reconstruction based on petri nets and simulated annealing. CMSB Zujian Wu, Qian Gao, David R. Gilbert
2010	—	`ed.`	Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies Trans. Computational Systems Biology Corrado Priami, Rainer Breitling, David R. Gilbert, Monika Heiner, Adelinde M. Uhrmacher
2009	J	`jnl`	Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Syst. Biol. Richard J. Orton, Michiel E. Adriaens, Amelie Gormand, Oliver E. Sturm, Walter Kolch, David R. Gilbert
2009	J	`jnl`	Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. Trans. Comp. Sys. Biology Monika Heiner, Sebastian Lehrack, David R. Gilbert, Wolfgang Marwan
2009	J	`jnl`	Prediction of protein-protein interaction types using association rule based classification. BMC Bioinform. Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim
2009	—	`conf`	Towards formalizing Virtual Enterprise Architecture. EDOCW Amit Goel, Heinz Schmidt, David R. Gilbert
2008	—	`conf`	A Case Study in Model-driven Synthetic Biology. BICC David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo
2008	—	`conf`	A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. CMSB Robin Donaldson, David R. Gilbert
2008	J	`jnl`	A novel method for comparing topological models of protein structures enhanced with ligand information. Bioinform. Mallika Veeramalai, David R. Gilbert
2008	J	`jnl`	A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings Bioinform. Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton
2008	—	`conf`	An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
2008	—	`conf`	BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment. HealthGrid Xuan Liu, Jipu Jiang, Oluwafemi O. Ajayi, Xu Gu, David R. Gilbert, Richard O. Sinnott
2008	—	`conf`	Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. DILS José A. Reyes, David R. Gilbert
2008	J	`jnl`	Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. Sebastian Oehm, David R. Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann
2008	J	`jnl`	MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinform. Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert
2008	—	`conf`	Petri Nets for Systems and Synthetic Biology. SFM Monika Heiner, David R. Gilbert, Robin Donaldson
2007	—	`conf`	A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB David R. Gilbert, Monika Heiner, Sebastian Lehrack
2007	J	`jnl`	Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinform. Juris Viksna, David R. Gilbert
2007	J	`jnl`	Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinform. Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert
2007	C	`conf`	Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL Ali Al-Shahib, David R. Gilbert, Rainer Breitling
2007	B	`conf`	Fast Structural Similarity Search Based on Topology String Matching. APBC Sung-Hee Park, David R. Gilbert, Keun Ho Ryu
2007	J	`jnl`	Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs. BMC Syst. Biol. Xu Gu, David R. Gilbert, Desmond J. Higham, Miles Houslay
2007	J	`jnl`	Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data. J. Integr. Bioinform. José A. Reyes, David R. Gilbert
2006	J	`jnl`	A lock-and-key model for protein-protein interactions. Bioinform. Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
2006	J	`jnl`	Analysis of Signalling Pathways Using Continuous Time Markov Chains. Trans. Comp. Sys. Biology Muffy Calder, Vladislav Vyshemirsky, David R. Gilbert, Richard J. Orton
2006	—	`ch.`	Bioinformatics and Constraints. Handbook of Constraint Programming Rolf Backofen, David R. Gilbert
2006	J	`jnl`	Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings Bioinform. David R. Gilbert, Hendrik Fuß, Xu Gu, Richard J. Orton, Steve Robinson, Vladislav Vyshemirsky, Mary Jo Kurth, C. Stephen Downes, Werner Dubitzky
2006	—	`conf`	From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN David R. Gilbert, Monika Heiner
2005	J	`jnl`	Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations. Int. J. Neural Syst. Sung-Hee Park, Keun Ho Ryu, David R. Gilbert
2005	J	`jnl`	Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. Ali Al-Shahib, Rainer Breitling, David R. Gilbert
2005	J	`jnl`	GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinform. Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
2005	J	`jnl`	Protein structure topological comparison, discovery and matching service. Bioinform. Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead
2004	C	`conf`	An Assessment of Feature Relevance in Predicting Protein Function from Sequence. IDEAL Ali Al-Shahib, Chao He, Aik Choon Tan, Mark A. Girolami, David R. Gilbert
2004	—	`conf`	ISMB/ECCB 2004 Organization. ISMB/ECCB (Supplement of Bioinformatics) Janet M. Thornton, David R. Gilbert, Catherine Brooksbank
2004	—	`conf`	ISMB/ECCB 2004. ISMB/ECCB (Supplement of Bioinformatics) Janet M. Thornton, David R. Gilbert, Catherine Brooksbank
2004	J	`jnl`	TOPS: an enhanced database of protein structural topology. Nucleic Acids Res. Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead
2003	B	`conf`	An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. APBC Aik Choon Tan, David R. Gilbert
2003	—	`conf`	An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
2003	J	`jnl`	An overview of data models for the analysis of biochemical pathways. Briefings Bioinform. Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
2003	—	`conf`	Integrative machine learning approach for multi-class SCOP protein fold classification. German Conference on Bioinformatics Aik Choon Tan, David R. Gilbert, Yves Deville
2003	—	`conf`	Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples. German Conference on Bioinformatics Juris Viksna, David R. Gilbert, Gilleain M. Torrance
2002	J	`jnl`	A Computer System to Perform Structure Comparison using Representations of Protein Structure. Comput. Chem. David R. Gilbert, David R. Westhead, Juris Viksna, Janet M. Thornton
2002	—	`conf`	Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming. FOCLASA Jean-Marie Jacquet, Lubos Brim, David R. Gilbert, Mojmír Kretínský
2002	J	`jnl`	Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes. Comput. Artif. Intell. Lubos Brim, Mojmír Kretínský, Jean-Marie Jacquet, David R. Gilbert
2001	J	`jnl`	A Constraint Based Structure Description Language for Biosequences. Constraints An Int. J. Ingvar Eidhammer, Inge Jonassen, Svenn Helge Grindhaug, David R. Gilbert, Madu Ratnayake
2001	J	`jnl`	Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy
2001	J	`jnl`	Bioinformatics and Constraints. Constraints An Int. J. Rolf Backofen, David R. Gilbert
2001	J	`jnl`	Introduction to the Special Issue on Bioinformatics. Constraints An Int. J. David R. Gilbert, Rolf Backofen, Roland H. C. Yap
2001	B	`conf`	Multi-agent Systems as Concurrent Constraint Processes. SOFSEM Lubos Brim, David R. Gilbert, Jean-Marie Jacquet, Mojmír Kretínský
2001	C	`conf`	Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. WABI Juris Viksna, David R. Gilbert
2000	—	`conf`	Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. JOBIM Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak
2000	—	`conf`	Concurrent Constraint Programming with Process Mobility. Computational Logic David R. Gilbert, Catuscia Palamidessi
2000	C	`conf`	FURY: Fuzzy Unification and Resolution Based on Edit Distance. BIBE David R. Gilbert, Michael Schroeder
2000	—	`conf`	Tutoriel I: Bioinformatique et contraintes. JFPLC David R. Gilbert
2000	—	`conf`	Une technique déclarative pour filtrer des motifs topologiques de protéines. JFPLC David R. Gilbert, David R. Westhead, Janet M. Thornton, Karine Yvon
1999	—	`conf`	A Model for Interaction of Agents and Environments. WADT Alexander A. Letichevsky, David R. Gilbert
1999	—	`conf`	Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak
1999	J	`jnl`	Motif-based searching in TOPS protein topology databases. Bioinform. David R. Gilbert, David R. Westhead, Nozomi Nagano, Janet M. Thornton
1999	—	`conf`	Pattern discovery methods for protein topology diagrams. German Conference on Bioinformatics David R. Gilbert, Juris Viksna
1999	—	`conf`	The development of interactive algorithms for the Mathematical Environment. Calculemus Alexander A. Letichevsky, Julia V. Kapitonova, Vladislav A. Volkov, A. Chugayenko, Victor Khomenko, David R. Gilbert
1998	J	`jnl`	Approaches to the Automatic Discovery of Patterns in Biosequences. J. Comput. Biol. Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David R. Gilbert
1997	J	`jnl`	FlyBase: a Drosophila database. The FlyBase consortium. Nucleic Acids Res. William M. Gelbart, Madeline A. Crosby, Beverley Matthews, W. P. Rindone, J. Chillemi, S. Russo Twombly, David B. Emmert, Michael Ashburner, Rachel A. Drysdale, E. Whitfield, Gillian H. Millburn, A. de Grey, Thomas C. Kaufman, K. Matthews, David R. Gilbert, Victor B. Strelets, C. Tolstoshev
1996	—	`conf`	A General Framework for Integrating HCLP and PCSP (Poster Abstract). JICSLP Michael Jampel, Jean-Marie Jacquet, David R. Gilbert
1996	—	`conf`	A Process Algebra for Synchronous Concurrent Constraint Programming. ALP Lubos Brim, Jean-Marie Jacquet, David R. Gilbert, Mojmír Kretínský
1996	J	`jnl`	Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems? ACM Comput. Surv. David R. Gilbert
1996	A	`conf`	Transformations Between HCLP and PCSP. CP Michael Jampel, Jean-Marie Jacquet, David R. Gilbert, Sebastian Hunt
1995	—	`conf`	Synchronisation in Scc. ILPS Lubos Brim, David R. Gilbert, Jean-Marie Jacquet, Mojmír Kretínský
1994	C	`conf`	Transforming Specifications of Observable Behaviour into Programs. LOPSTR David R. Gilbert, Christopher J. Hogger, Jirí Zlatuska
1992	—	`conf`	Logic for Representing and Implementing Knowledge about System Behaviour. Advanced Topics in Artificial Intelligence David R. Gilbert, Christopher J. Hogger
1991	—	`conf`	Deriving Logic Programs from Observations. ICLP Workshop on Construction of Logic Programs David R. Gilbert, Christopher J. Hogger
1989	C	`conf`	Specifying Concurrent Systems Using Logic. FORTE David R. Gilbert
1988	C	`conf`	A LOTOS to PARLOG Translator. FORTE David R. Gilbert
1988	—	`conf`	Specification and Implementation of Concurrent Systems using PARLOG. Specification and Verification of Concurrent Systems David R. Gilbert
1987	—	`conf`	Executable LOTOS: Using PARLOG to Implement an FDT. PSTV David R. Gilbert