David R. Gilbert

According to our database, David R. Gilbert authored at least 116 papers between 1987 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

A Logic of Isolation.

Can Baskent, David R. Gilbert, Giorgio Venturi

Proceedings of the Logic, Language, Information, and Computation, 2024

2022

Logics of Ignorance and Being Wrong.

David R. Gilbert, Ekaterina Kubyshkina, Mattia Petrolo, Giorgio Venturi

Log. J. IGPL, 2022

Hybrid modelling of biological systems: current progress and future prospects.

Fei Liu, Monika Heiner, David R. Gilbert

Briefings Bioinform., 2022

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

From Epidemic to Pandemic Modelling.

Shannon Connolly, David R. Gilbert, Monika Heiner

CoRR, 2021

Hybrid modelling of biological systems using fuzzy continuous Petri nets.

Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert

Briefings Bioinform., 2021

2020

A note on logics of essence and accident.

David R. Gilbert, Giorgio Venturi

Log. J. IGPL, 2020

Fuzzy Petri nets for modelling of uncertain biological systems.

Fei Liu, Monika Heiner, David R. Gilbert

Briefings Bioinform., 2020

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

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems.

Fei Liu, Monika Heiner, David R. Gilbert

Briefings Bioinform., 2019

Towards dynamic genome-scale models.

David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr

Briefings Bioinform., 2019

2018

Petri-net-based 2D design of DNA walker circuits.

David R. Gilbert, Monika Heiner, Christian Rohr

Nat. Comput., 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

Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models.

Timothy Self, David R. Gilbert, Monika Heiner

Proceedings of the Computational Methods in Systems Biology, 2018

2016

Reflexive-Insensitive Modal Logics.

David R. Gilbert, Giorgio Venturi

Rev. Symb. Log., 2016

Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure.

Juris Viksna, David R. Gilbert

Balt. J. Mod. Comput., 2016

2015

Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes.

Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders, Simon Shaw

ACM Trans. Model. Comput. Simul., 2015

Advances in Computational Methods in Systems Biology.

David R. Gilbert, Monika Heiner

Theor. Comput. Sci., 2015

Modular Sequent Calculi for Classical Modal Logics.

David R. Gilbert, Paolo Maffezioli

Stud Logica, 2015

Computational models for inferring biochemical networks.

Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, Ramona Stoica, David R. Gilbert

Neural Comput. Appl., 2015

2014

Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481).

David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher

Dagstuhl Reports, 2014

Speeding up systems biology simulations of biochemical pathways using condor.

Xuan Liu, Simon J. E. Taylor, Navonil Mustafee, Jun Wang, Qian Gao, David R. Gilbert

Concurr. Comput. Pract. Exp., 2014

Automatic validation of computational models using pseudo-3D spatio-temporal model checking.

Ovidiu Parvu, David R. Gilbert

BMC Syst. Biol., 2014

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

Proceedings of the 2014 Winter Simulation Conference, 2014

2013

Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing.

Qian Gao, David R. Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in <i>Trypanosoma brucei</i>.

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

Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling.

Zujian Wu, Crina Grosan, David R. Gilbert

Proceedings of the Nature Inspired Cooperative Strategies for Optimization (NICSO 2013), 2013

Modelling and Analysis of Phase Variation in Bacterial Colony Growth.

Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders

Proceedings of the Computational Methods in Systems Biology, 2013

Evolving biochemical systems.

Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, David R. Gilbert

Proceedings of the IEEE Congress on Evolutionary Computation, 2013

Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology.

David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders

Proceedings of the Application and Theory of Petri Nets and Concurrency, 2013

2012

Completeness Results for some two-Dimensional Logics of actuality.

David R. Gilbert, Edwin D. Mares

Rev. Symb. Log., 2012

A machine learning approach for generating temporal logic classifications of complex model behaviours.

Daniele Maccagnola, Enza Messina, Qian Gao, David R. Gilbert

Proceedings of the Winter Simulation Conference, 2012

A Hybrid Approach to Piecewise Modelling of Biochemical Systems.

Zujian Wu, Shengxiang Yang, David R. Gilbert

Proceedings of the Parallel Problem Solving from Nature - PPSN XII, 2012

Towards an Ontology of Biomodelling.

Larisa N. Soldatova, Qian Gao, David R. Gilbert

Proceedings of the Computational Methods in Systems Biology, 2012

2011

Bootstrapping Parameter Estimation in Dynamic Systems.

Huma Lodhi, David R. Gilbert

Proceedings of the Discovery Science - 14th International Conference, 2011

A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets.

Qian Gao, Fei Liu, David R. Gilbert, Monika Heiner, David Tree

Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

How Might Petri Nets Enhance Your Systems Biology Toolkit.

Monika Heiner, David R. Gilbert

Proceedings of the Applications and Theory of Petri Nets - 32nd International Conference, 2011

2010

Biomodel Engineering - From Structure to Behavior.

Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner

Trans. Comp. Sys. Biology, 2010

An optimized TOPS+ comparison method for enhanced TOPS models.

Mallika Veeramalai, David R. Gilbert, Gabriel Valiente

BMC Bioinform., 2010

Formal Models of Virtual Enterprise Architecture: Motivations and Approaches.

Amit Goel, Heinz Schmidt, David R. Gilbert

Proceedings of the Pacific Asia Conference on Information Systems, 2010

Target driven biochemical network reconstruction based on petri nets and simulated annealing.

Zujian Wu, Qian Gao, David R. Gilbert

Proceedings of the Computational Methods in Systems Biology, 8th International Conference, 2010

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

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

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

Towards formalizing Virtual Enterprise Architecture.

Amit Goel, Heinz Schmidt, David R. Gilbert

Proceedings of the Workshops Proceedings of the 12th IEEE International Enterprise Distributed Object Computing Conference, 2009

BioModel Engineering: Its role in Systems Biology and Synthetic Biology.

David Roger Gilbert, Rainer Breitling, Monika Heiner

Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

09091 Executive Summary - Formal Methods in Molecular Biology.

Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami

Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

09091 Abstracts Collection - Formal Methods in Molecular Biology.

Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami

Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

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

A novel method for comparing topological models of protein structures enhanced with ligand information.

Mallika Veeramalai, David R. Gilbert

Bioinform., 2008

MetaNetter: inference and visualization of high-resolution metabolomic networks.

Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert

Bioinform., 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

Petri Nets for Systems and Synthetic Biology.

Monika Heiner, David R. Gilbert, Robin Donaldson

Proceedings of the Formal Methods for Computational Systems Biology, 2008

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways.

David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson

Proceedings of the Membrane Computing - 9th International Workshop, 2008

A Case Study in Model-driven Synthetic Biology.

David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo

Proceedings of the Biologically-Inspired Collaborative Computing, 2008

BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment.

Xuan Liu, Jipu Jiang, Oluwafemi O. Ajayi, Xu Gu, David R. Gilbert, Richard O. Sinnott

Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008

Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions.

José A. Reyes, David R. Gilbert

Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

A Model Checking Approach to the Parameter Estimation of Biochemical Pathways.

Robin Donaldson, David R. Gilbert

Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

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

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

Automatic generation of 3D motifs for classification of protein binding sites.

Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert

BMC Bioinform., 2007

Assessment of the probabilities for evolutionary structural changes in protein folds.

Juris Viksna, David R. Gilbert

Bioinform., 2007

Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning.

Ali Al-Shahib, David R. Gilbert, Rainer Breitling

Proceedings of the Intelligent Data Engineering and Automated Learning, 2007

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets.

David R. Gilbert, Monika Heiner, Sebastian Lehrack

Proceedings of the Computational Methods in Systems Biology, International Conference, 2007

Fast Structural Similarity Search Based on Topology String Matching.

Sung-Hee Park, David R. Gilbert, Keun Ho Ryu

Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006

Bioinformatics and Constraints.

Rolf Backofen, David R. Gilbert

Proceedings of the Handbook of Constraint Programming, 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

A lock-and-key model for protein-protein interactions.

Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert

Bioinform., 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

From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis.

David R. Gilbert, Monika Heiner

Proceedings of the Petri Nets and Other Models of Concurrency, 2006

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

Franksum: new feature selection method for protein function prediction.

Ali Al-Shahib, Rainer Breitling, David R. Gilbert

Int. J. Neural Syst., 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

Protein structure topological comparison, discovery and matching service.

Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead

Bioinform., 2005

2004

TOPS: an enhanced database of protein structural topology.

Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead

Nucleic Acids Res., 2004

ISMB/ECCB 2004 Organization.

Janet M. Thornton, David R. Gilbert, Catherine Brooksbank

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

ISMB/ECCB 2004.

Janet M. Thornton, David R. Gilbert, Catherine Brooksbank

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

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

Proceedings of the Intelligent Data Engineering and Automated Learning, 2004

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

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

Proceedings of the German Conference on Bioinformatics, 2003

Integrative machine learning approach for multi-class SCOP protein fold classification.

Aik Choon Tan, David R. Gilbert, Yves Deville

Proceedings of the German Conference on Bioinformatics, 2003

An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics.

Aik Choon Tan, David R. Gilbert

Proceedings of the First Asia-Pacific Bioinformatics Conference (APBC 2003), 2003

2002

Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming.

Jean-Marie Jacquet, Lubos Brim, David R. Gilbert, Mojmír Kretínský

Proceedings of the Foundations of Coordination Languages and Software Architectures, 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

Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes.

Lubos Brim, Mojmír Kretínský, Jean-Marie Jacquet, David R. Gilbert

Comput. Artif. Intell., 2002

2001

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer.

Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy

Inf. Sci., 2001

Introduction to the Special Issue on Bioinformatics.

David R. Gilbert, Rolf Backofen, Roland H. C. Yap

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

Bioinformatics and Constraints.

Rolf Backofen, David R. Gilbert

Constraints An Int. J., 2001

Pattern Matching and Pattern Discovery Algorithms for Protein Topologies.

Juris Viksna, David R. Gilbert

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Multi-agent Systems as Concurrent Constraint Processes.

Lubos Brim, David R. Gilbert, Jean-Marie Jacquet, Mojmír Kretínský

Proceedings of the SOFSEM 2001: Theory and Practice of Informatics, 28th Conference on Current Trends in Theory and Practice of Informatics Piestany, Slovak Republic, November 24, 2001

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, Shoshana J. Wodak

Proceedings of the Computational Biology, 2000

Une technique déclarative pour filtrer des motifs topologiques de protéines.

David R. Gilbert, David R. Westhead, Janet M. Thornton, Karine Yvon

Proceedings of the Programmation en logique avec contraintes, 2000

Tutoriel I: Bioinformatique et contraintes.

David R. Gilbert

Proceedings of the Programmation en logique avec contraintes, 2000

Concurrent Constraint Programming with Process Mobility.

David R. Gilbert, Catuscia Palamidessi

Proceedings of the Computational Logic, 2000

FURY: Fuzzy Unification and Resolution Based on Edit Distance.

David R. Gilbert, Michael Schroeder

Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering, 2000

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

Proceedings of the Systems for Integrated Computation and Deduction, 1999

Motif-based searching in TOPS protein topology databases.

David R. Gilbert, David R. Westhead, Nozomi Nagano, Janet M. Thornton

Bioinform., 1999

A Model for Interaction of Agents and Environments.

Alexander A. Letichevsky, David R. Gilbert

Proceedings of the Recent Trends in Algebraic Development Techniques, 1999

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database.

Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak

Proceedings of the German Conference on Bioinformatics, 1999

Pattern discovery methods for protein topology diagrams.

David R. Gilbert, Juris Viksna

Proceedings of the German Conference on Bioinformatics, 1999

1998

Approaches to the Automatic Discovery of Patterns in Biosequences.

Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David R. Gilbert

J. Comput. Biol., 1998

1997

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, Thomas C. Kaufman, K. Matthews, David R. Gilbert, Victor B. Strelets, C. Tolstoshev

Nucleic Acids Res., 1997

1996

Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems?

David R. Gilbert

ACM Comput. Surv., 1996

A General Framework for Integrating HCLP and PCSP (Poster Abstract).

Michael Jampel, Jean-Marie Jacquet, David R. Gilbert

Proceedings of the Logic Programming, 1996

Transformations Between HCLP and PCSP.

Michael Jampel, Jean-Marie Jacquet, David R. Gilbert, Sebastian Hunt

Proceedings of the Second International Conference on Principles and Practice of Constraint Programming, 1996

A Process Algebra for Synchronous Concurrent Constraint Programming.

Lubos Brim, Jean-Marie Jacquet, David R. Gilbert, Mojmír Kretínský

Proceedings of the Algebraic and Logic Programming, 5th International Conference, 1996

1995

Synchronisation in Scc.

Lubos Brim, David R. Gilbert, Jean-Marie Jacquet, Mojmír Kretínský

Proceedings of the Logic Programming, 1995

1994

Transforming Specifications of Observable Behaviour into Programs.

David R. Gilbert, Christopher J. Hogger, Jirí Zlatuska

Proceedings of the Logic Programming Synthesis and Transformation, 1994

1992

Logic for Representing and Implementing Knowledge about System Behaviour.

David R. Gilbert, Christopher J. Hogger

Proceedings of the Advanced Topics in Artificial Intelligence, 1992

1991

Deriving Logic Programs from Observations.

David R. Gilbert, Christopher J. Hogger

Proceedings of the Constructing Logic Programs, 1991

1990

Specifying and reasoning about concurrent systems in logic.

David Roger Gilbert

PhD thesis, 1990

1989

Specifying Concurrent Systems Using Logic.

David R. Gilbert

Proceedings of the Formal Description Techniques, 1989

1988

A LOTOS to PARLOG Translator.

David R. Gilbert

Proceedings of the Formal Description Techniques, 1988

Specification and Implementation of Concurrent Systems using PARLOG.

David R. Gilbert

Proceedings of the Specification and Verification of Concurrent Systems [BCS-FACS Workshop, 1988

1987

Executable LOTOS: Using PARLOG to Implement an FDT.

David R. Gilbert

Proceedings of the Protocol Specification, 1987