Executable LOTOS: Using PARLOG to Implement an FDT. - David R. Gilbert (PSTV, 1987)

Specification and Implementation of Concurrent Systems using PARLOG. - David R. Gilbert (Specification and Verification of Concurrent Systems, 1988)

A LOTOS to PARLOG Translator. - David R. Gilbert (FORTE, 1988)

Specifying Concurrent Systems Using Logic. - David R. Gilbert (FORTE, 1989)

Specifying and reasoning about concurrent systems in logic. - David Roger Gilbert (1990)

Deriving Logic Programs from Observations. - David R. Gilbert; Christopher J. Hogger (ICLP Workshop on Construction of Logic Programs, 1991)

Logic for Representing and Implementing Knowledge about System Behaviour. - David R. Gilbert; Christopher J. Hogger (Advanced Topics in Artificial Intelligence, 1992)

Transforming Specifications of Observable Behaviour into Programs. - David R. Gilbert; Christopher J. Hogger; Jirí Zlatuska (LOPSTR, 1994)

Synchronisation in Scc. - Lubos Brim; David R. Gilbert; Jean-Marie Jacquet; Mojmír Kretínský (ILPS, 1995)

A Process Algebra for Synchronous Concurrent Constraint Programming. - Lubos Brim; Jean-Marie Jacquet; David R. Gilbert; Mojmír Kretínský (ALP, 1996)

Transformations Between HCLP and PCSP. - Michael Jampel; Jean-Marie Jacquet; David R. Gilbert; Sebastian Hunt (CP, 1996)

A General Framework for Integrating HCLP and PCSP (Poster Abstract). - Michael Jampel; Jean-Marie Jacquet; David R. Gilbert (JICSLP, 1996)

Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems? - David R. Gilbert (ACM Comput. Surv., 1996)

FlyBase: a Drosophila database. The FlyBase consortium. - 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; et al. (Nucleic Acids Res., 1997)

Approaches to the Automatic Discovery of Patterns in Biosequences. - Alvis Brazma; Inge Jonassen; Ingvar Eidhammer; David R. Gilbert (J. Comput. Biol., 1998)

Pattern discovery methods for protein topology diagrams. - David R. Gilbert; Juris Viksna (German Conference on Bioinformatics, 1999)

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. - Jacques van Helden; David R. Gilbert; Lorenz Wernisch; Renato Mancuso 002; Matthew D. Eldridge; Kirill Degtyarenko; Shoshana J. Wodak (German Conference on Bioinformatics, 1999)

A Model for Interaction of Agents and Environments. - Alexander A. Letichevsky; David R. Gilbert (WADT, 1999)

Motif-based searching in TOPS protein topology databases. - David R. Gilbert; David R. Westhead; Nozomi Nagano; Janet M. Thornton (Bioinform., 1999)

The development of interactive algorithms for the Mathematical Environment. - Alexander A. Letichevsky; Julia V. Kapitonova; Vladislav A. Volkov; A. Chugayenko; Victor Khomenko; David R. Gilbert (Calculemus, 1999)

FURY: Fuzzy Unification and Resolution Based on Edit Distance. - David R. Gilbert; Michael Schroeder 001 (BIBE, 2000)

Concurrent Constraint Programming with Process Mobility. - David R. Gilbert; Catuscia Palamidessi (Computational Logic, 2000)

Tutoriel I: Bioinformatique et contraintes. - David R. Gilbert (JFPLC, 2000)

Une technique déclarative pour filtrer des motifs topologiques de protéines. - David R. Gilbert; David R. Westhead; Janet M. Thornton; Karine Yvon (JFPLC, 2000)

Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. - Jacques van Helden; David R. Gilbert; Lorenz Wernisch; Michael Schroeder 001; Shoshana J. Wodak (JOBIM, 2000)

Multi-agent Systems as Concurrent Constraint Processes. - Lubos Brim; David R. Gilbert; Jean-Marie Jacquet; Mojmír Kretínský (SOFSEM, 2001)

Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. - Juris Viksna; David R. Gilbert (WABI, 2001)

Bioinformatics and Constraints. - Rolf Backofen; David R. Gilbert (Constraints An Int. J., 2001)

A Constraint Based Structure Description Language for Biosequences. - Ingvar Eidhammer; Inge Jonassen; Svenn Helge Grindhaug; David R. Gilbert; Madu Ratnayake (Constraints An Int. J., 2001)

Introduction to the Special Issue on Bioinformatics. - David R. Gilbert; Rolf Backofen; Roland H. C. Yap (Constraints An Int. J., 2001)

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. - Michael Schroeder 001; David R. Gilbert; Jacques van Helden; Penny Noy (Inf. Sci., 2001)

Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes. - Lubos Brim; Mojmír Kretínský; Jean-Marie Jacquet; David R. Gilbert (Comput. Artif. Intell., 2002)

A Computer System to Perform Structure Comparison using Representations of Protein Structure. - David R. Gilbert; David R. Westhead; Juris Viksna; Janet M. Thornton (Comput. Chem., 2002)

Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming. - Jean-Marie Jacquet; Lubos Brim; David R. Gilbert; Mojmír Kretínský (FOCLASA, 2002)

An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. - Aik Choon Tan; David R. Gilbert (APBC, 2003)

Integrative machine learning approach for multi-class SCOP protein fold classification. - Aik Choon Tan; David R. Gilbert; Yves Deville (German Conference on Bioinformatics, 2003)

Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples. - Juris Viksna; David R. Gilbert; Gilleain M. Torrance (German Conference on Bioinformatics, 2003)

An overview of data models for the analysis of biochemical pathways. - Yves Deville; David R. Gilbert; Jacques van Helden; Shoshana J. Wodak (Briefings Bioinform., 2003)

An Assessment of Feature Relevance in Predicting Protein Function from Sequence. - Ali Al-Shahib; Chao He; Aik Choon Tan; Mark A. Girolami; David R. Gilbert (IDEAL, 2004)

ISMB/ECCB 2004. - Janet M. Thornton; David R. Gilbert; Catherine Brooksbank (ISMB/ECCB (Supplement of Bioinformatics), 2004)

ISMB/ECCB 2004 Organization. - Janet M. Thornton; David R. Gilbert; Catherine Brooksbank (ISMB/ECCB (Supplement of Bioinformatics), 2004)

TOPS: an enhanced database of protein structural topology. - Ioannis Michalopoulos; Gilleain M. Torrance; David R. Gilbert; David R. Westhead (Nucleic Acids Res., 2004)

Protein structure topological comparison, discovery and matching service. - Gilleain M. Torrance; David R. Gilbert; Ioannis Michalopoulos; David R. Westhead (Bioinform., 2005)

GeneRank: Using search engine technology for the analysis of microarray experiments. - Julie L. Morrison; Rainer Breitling; Desmond J. Higham; David R. Gilbert (BMC Bioinform., 2005)

Franksum: new feature selection method for protein function prediction. - Ali Al-Shahib; Rainer Breitling; David R. Gilbert (Int. J. Neural Syst., 2005)

Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations. - Sung-Hee Park; Keun Ho Ryu; David R. Gilbert (Int. J. Neural Syst., 2005)

From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. - David R. Gilbert; Monika Heiner (ICATPN, 2006)

Computational methodologies for modelling, analysis and simulation of signalling networks. - David R. Gilbert; Hendrik Fuß; Xu Gu; Richard J. Orton; Steve Robinson; Vladislav Vyshemirsky; Mary Jo Kurth; C. Stephen Downes; Werner Dubitzky (Briefings Bioinform., 2006)

A lock-and-key model for protein-protein interactions. - Julie L. Morrison; Rainer Breitling; Desmond J. Higham; David R. Gilbert (Bioinform., 2006)

Analysis of Signalling Pathways Using Continuous Time Markov Chains. - Muffy Calder; Vladislav Vyshemirsky; David R. Gilbert; Richard J. Orton (Trans. Comp. Sys. Biology, 2006)

Bioinformatics and Constraints. - Rolf Backofen; David R. Gilbert (Handbook of Constraint Programming, 2006)

Fast Structural Similarity Search Based on Topology String Matching. - Sung-Hee Park; David R. Gilbert; Keun Ho Ryu (APBC, 2007)

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. - David R. Gilbert; Monika Heiner; Sebastian Lehrack (CMSB, 2007)

Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. - Ali Al-Shahib; David R. Gilbert; Rainer Breitling (IDEAL, 2007)

Assessment of the probabilities for evolutionary structural changes in protein folds. - Juris Viksna; David R. Gilbert (Bioinform., 2007)

Automatic generation of 3D motifs for classification of protein binding sites. - Jean-Christophe Nebel; Pawel Herzyk; David R. Gilbert (BMC Bioinform., 2007)

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs. - Xu Gu; David R. Gilbert; Desmond J. Higham; Miles Houslay (BMC Syst. Biol., 2007)

Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data. - José A. Reyes; David R. Gilbert (J. Integr. Bioinform., 2007)

A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. - Robin Donaldson; David R. Gilbert (CMSB, 2008)

Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. - José A. Reyes; David R. Gilbert (DILS, 2008)

BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment. - Xuan Liu; Jipu Jiang; Oluwafemi O. Ajayi; Xu Gu; David R. Gilbert; Richard O. Sinnott (HealthGrid, 2008)

A Case Study in Model-driven Synthetic Biology. - David R. Gilbert; Monika Heiner; Susan Rosser; Rachael Fulton; Xu Gu; Maciej Trybilo (BICC, 2008)

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. - David R. Gilbert; Rainer Breitling; Monika Heiner; Robin Donaldson (Workshop on Membrane Computing, 2008)

Petri Nets for Systems and Synthetic Biology. - Monika Heiner; David R. Gilbert; Robin Donaldson (SFM, 2008)

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. - Rainer Breitling; David R. Gilbert; Monika Heiner; Richard J. Orton (Briefings Bioinform., 2008)

MetaNetter: inference and visualization of high-resolution metabolomic networks. - Fabien Jourdan; Rainer Breitling; Michael P. Barrett; David R. Gilbert (Bioinform., 2008)

A novel method for comparing topological models of protein structures enhanced with ligand information. - Mallika Veeramalai; David R. Gilbert (Bioinform., 2008)

Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. - Sebastian Oehm; David R. Gilbert; Andreas Tauch; Jens Stoye; Alexander Goesmann (Nucleic Acids Res., 2008)

09091 Abstracts Collection - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

09091 Executive Summary - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

BioModel Engineering: Its role in Systems Biology and Synthetic Biology. - David Roger Gilbert; Rainer Breitling; Monika Heiner (Formal Methods in Molecular Biology, 2009)

Towards formalizing Virtual Enterprise Architecture. - Amit Goel; Heinz Schmidt; David R. Gilbert (EDOCW, 2009)

Prediction of protein-protein interaction types using association rule based classification. - Sung-Hee Park; José A. Reyes; David R. Gilbert; Ji Woong Kim; Sangsoo Kim (BMC Bioinform., 2009)

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. - Richard J. Orton; Michiel E. Adriaens; Amelie Gormand; Oliver E. Sturm; Walter Kolch; David R. Gilbert (BMC Syst. Biol., 2009)

Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. - Monika Heiner; Sebastian Lehrack; David R. Gilbert; Wolfgang Marwan (Trans. Comp. Sys. Biology, 2009)

Target driven biochemical network reconstruction based on petri nets and simulated annealing. - Zujian Wu; Qian Gao 001; David R. Gilbert (CMSB, 2010)

Formal Models of Virtual Enterprise Architecture: Motivations and Approaches. - Amit Goel; Heinz Schmidt; David R. Gilbert (PACIS, 2010)

An optimized TOPS+ comparison method for enhanced TOPS models. - Mallika Veeramalai; David R. Gilbert; Gabriel Valiente (BMC Bioinform., 2010)

Biomodel Engineering - From Structure to Behavior. - Rainer Breitling; Robin Donaldson; David R. Gilbert; Monika Heiner (Trans. Comp. Sys. Biology, 2010)

How Might Petri Nets Enhance Your Systems Biology Toolkit. - Monika Heiner; David R. Gilbert (Petri Nets, 2011)

A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. - Qian Gao 001; Fei Liu 006; David R. Gilbert; Monika Heiner; David Tree (CMSB, 2011)

Bootstrapping Parameter Estimation in Dynamic Systems. - Huma Lodhi; David R. Gilbert (Discovery Science, 2011)

Towards an Ontology of Biomodelling. - Larisa N. Soldatova; Qian Gao 001; David R. Gilbert (CMSB, 2012)

A Hybrid Approach to Piecewise Modelling of Biochemical Systems. - Zujian Wu; Shengxiang Yang; David R. Gilbert (PPSN (1), 2012)

A machine learning approach for generating temporal logic classifications of complex model behaviours. - Daniele Maccagnola; Enza Messina; Qian Gao 001; David R. Gilbert (WSC, 2012)

Completeness Results for some two-Dimensional Logics of actuality. - David R. Gilbert; Edwin D. Mares (Rev. Symb. Log., 2012)

Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. - David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders (Petri Nets, 2013)

Evolving biochemical systems. - Silvia Rausanu; Crina Grosan; Zujian Wu; Ovidiu Parvu; David R. Gilbert (IEEE Congress on Evolutionary Computation, 2013)

Modelling and Analysis of Phase Variation in Bacterial Colony Growth. - Ovidiu Parvu; David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders (CMSB, 2013)

Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling. - Zujian Wu; Crina Grosan; David R. Gilbert (NICSO, 2013)

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. - 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 (PLoS Comput. Biol., 2013)

Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing. - Qian Gao 001; David R. Gilbert; Monika Heiner; Fei Liu 006; Daniele Maccagnola; David Tree (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Investigating the speedup of systems biology simulation using the sztaki desktop grid. - Simon J. E. Taylor; Mohammadmersad Ghorbani; Navonil Mustafee; Tamás Kiss; Péter Borsody; Annette M. Payne; David R. Gilbert (WSC, 2014)

Automatic validation of computational models using pseudo-3D spatio-temporal model checking. - Ovidiu Parvu; David R. Gilbert (BMC Syst. Biol., 2014)

Speeding up systems biology simulations of biochemical pathways using condor. - Xuan Liu; Simon J. E. Taylor; Navonil Mustafee; Jun Wang; Qian Gao 001; David R. Gilbert (Concurr. Comput. Pract. Exp., 2014)

Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). - David R. Gilbert; Monika Heiner; Koichi Takahashi; Adelinde M. Uhrmacher (Dagstuhl Reports, 2014)

Computational models for inferring biochemical networks. - Silvia Rausanu; Crina Grosan; Zujian Wu; Ovidiu Parvu; Ramona Stoica; David R. Gilbert (Neural Comput. Appl., 2015)

Modular Sequent Calculi for Classical Modal Logics. - David R. Gilbert; Paolo Maffezioli (Stud Logica, 2015)

Advances in Computational Methods in Systems Biology. - David R. Gilbert; Monika Heiner (Theor. Comput. Sci., 2015)

Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. - Ovidiu Parvu; David R. Gilbert; Monika Heiner; Fei Liu 006; Nigel J. Saunders; Simon Shaw (ACM Trans. Model. Comput. Simul., 2015)

Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure. - Juris Viksna; David R. Gilbert (Balt. J. Mod. Comput., 2016)

Reflexive-Insensitive Modal Logics. - David R. Gilbert; Giorgio Venturi (Rev. Symb. Log., 2016)

Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. - Timothy Self; David R. Gilbert; Monika Heiner (CMSB, 2018)

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. - Riccardo Colombo; Chiara Damiani; David R. Gilbert; Monika Heiner; Giancarlo Mauri; Dario Pescini (BMC Bioinform., 2018)

Petri-net-based 2D design of DNA walker circuits. - David R. Gilbert; Monika Heiner; Christian Rohr (Nat. Comput., 2018)

Towards dynamic genome-scale models. - David R. Gilbert; Monika Heiner; Yasoda Jayaweera; Christian Rohr (Briefings Bioinform., 2019)

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2019)

Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. - David R. Gilbert; Monika Heiner; Leila Ghanbar; Jacek Chodak (BMC Bioinform., 2019)

Fuzzy Petri nets for modelling of uncertain biological systems. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2020)

A note on logics of essence and accident. - David R. Gilbert; Giorgio Venturi (Log. J. IGPL, 2020)

Hybrid modelling of biological systems using fuzzy continuous Petri nets. - Fei Liu 006; Wujie Sun; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2021)

From Epidemic to Pandemic Modelling. - Shannon Connolly; David R. Gilbert; Monika Heiner (CoRR, 2021)

Reflexive-Insensitive Logics, the Boxdot Translation, and the Modal Logic of Generic Absoluteness. - David R. Gilbert; Giorgio Venturi (Notre Dame J. Formal Log., 2021)

Hybrid modelling of biological systems: current progress and future prospects. - Fei Liu 006; Monika Heiner; David R. Gilbert (Briefings Bioinform., 2022)

Logics of Ignorance and Being Wrong. - David R. Gilbert; Ekaterina Kubyshkina; Mattia Petrolo; Giorgio Venturi (Log. J. IGPL, 2022)

A Logic of Isolation. - Can Baskent; David R. Gilbert; Giorgio Venturi (WoLLIC, 2024)

Insensitive Games: Game Semantics for Modal Insensitivity. - Can Baskent; David R. Gilbert; Giorgio Venturi (WoLLIC, 2025)