David R. Gilbert

According to our database1, David R. Gilbert authored at least 107 papers between 1987 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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PhD thesis 
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Bibliography

2019
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking.
BMC Bioinformatics, 2019

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems.
Briefings in Bioinformatics, 2019

Towards dynamic genome-scale models.
Briefings in Bioinformatics, 2019

2018
Petri-net-based 2D design of DNA walker circuits.
Natural Computing, 2018

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes.
BMC Bioinformatics, 2018

Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models.
Proceedings of the Computational Methods in Systems Biology, 2018

2016
Reflexive-Insensitive Modal Logics.
Rev. Symb. Log., 2016

2015
Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes.
ACM Trans. Model. Comput. Simul., 2015

Advances in Computational Methods in Systems Biology.
Theor. Comput. Sci., 2015

Modular Sequent Calculi for Classical Modal Logics.
Studia Logica, 2015

Computational models for inferring biochemical networks.
Neural Computing and Applications, 2015

2014
Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481).
Dagstuhl Reports, 2014

Speeding up systems biology simulations of biochemical pathways using condor.
Concurrency and Computation: Practice and Experience, 2014

Automatic validation of computational models using pseudo-3D spatio-temporal model checking.
BMC Systems Biology, 2014

Investigating the speedup of systems biology simulation using the sztaki desktop grid.
Proceedings of the 2014 Winter Simulation Conference, 2014

2013
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing.
IEEE/ACM Trans. Comput. Biology Bioinform., 2013

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei.
PLoS Computational Biology, 2013

Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling.
Proceedings of the Nature Inspired Cooperative Strategies for Optimization (NICSO 2013), 2013

Modelling and Analysis of Phase Variation in Bacterial Colony Growth.
Proceedings of the Computational Methods in Systems Biology, 2013

Evolving biochemical systems.
Proceedings of the IEEE Congress on Evolutionary Computation, 2013

Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology.
Proceedings of the Application and Theory of Petri Nets and Concurrency, 2013

2012
Completeness Results for some two-Dimensional Logics of actuality.
Rev. Symb. Log., 2012

A machine learning approach for generating temporal logic classifications of complex model behaviours.
Proceedings of the Winter Simulation Conference, 2012

A Hybrid Approach to Piecewise Modelling of Biochemical Systems.
Proceedings of the Parallel Problem Solving from Nature - PPSN XII, 2012

Towards an Ontology of Biomodelling.
Proceedings of the Computational Methods in Systems Biology, 2012

2011
Bootstrapping Parameter Estimation in Dynamic Systems.
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.
Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

How Might Petri Nets Enhance Your Systems Biology Toolkit.
Proceedings of the Applications and Theory of Petri Nets - 32nd International Conference, 2011

2010
Biomodel Engineering - From Structure to Behavior.
Trans. Computational Systems Biology, 2010

An optimized TOPS+ comparison method for enhanced TOPS models.
BMC Bioinformatics, 2010

Formal Models of Virtual Enterprise Architecture: Motivations and Approaches.
Proceedings of the Pacific Asia Conference on Information Systems, 2010

Target driven biochemical network reconstruction based on petri nets and simulated annealing.
Proceedings of the Computational Methods in Systems Biology, 8th International Conference, 2010

2009
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments.
Trans. Computational Systems Biology, 2009

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway.
BMC Systems Biology, 2009

Prediction of protein-protein interaction types using association rule based classification.
BMC Bioinformatics, 2009

Towards formalizing Virtual Enterprise Architecture.
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.
Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

09091 Executive Summary - Formal Methods in Molecular Biology.
Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

09091 Abstracts Collection - Formal Methods in Molecular Biology.
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.
Nucleic Acids Research, 2008

A novel method for comparing topological models of protein structures enhanced with ligand information.
Bioinformatics, 2008

MetaNetter: inference and visualization of high-resolution metabolomic networks.
Bioinformatics, 2008

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.
Briefings in Bioinformatics, 2008

Petri Nets for Systems and Synthetic Biology.
Proceedings of the Formal Methods for Computational Systems Biology, 2008

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways.
Proceedings of the Membrane Computing - 9th International Workshop, 2008

A Case Study in Model-driven Synthetic Biology.
Proceedings of the Biologically-Inspired Collaborative Computing, 2008

BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment.
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.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

A Model Checking Approach to the Parameter Estimation of Biochemical Pathways.
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.
J. Integrative Bioinformatics, 2007

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs.
BMC Systems Biology, 2007

Automatic generation of 3D motifs for classification of protein binding sites.
BMC Bioinformatics, 2007

Assessment of the probabilities for evolutionary structural changes in protein folds.
Bioinformatics, 2007

Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2007

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2007

Fast Structural Similarity Search Based on Topology String Matching.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006
Bioinformatics and Constraints.
Proceedings of the Handbook of Constraint Programming, 2006

Analysis of Signalling Pathways Using Continuous Time Markov Chains.
, 2006

A lock-and-key model for protein-protein interactions.
Bioinformatics, 2006

Computational methodologies for modelling, analysis and simulation of signalling networks.
Briefings in Bioinformatics, 2006

From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis.
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.
Int. J. Neural Syst., 2005

Franksum: new feature selection method for protein function prediction.
Int. J. Neural Syst., 2005

GeneRank: Using search engine technology for the analysis of microarray experiments.
BMC Bioinformatics, 2005

Protein structure topological comparison, discovery and matching service.
Bioinformatics, 2005

2004
TOPS: an enhanced database of protein structural topology.
Nucleic Acids Research, 2004

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

ISMB/ECCB 2004.
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.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2004

2003
Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming.
Electr. Notes Theor. Comput. Sci., 2003

An overview of data models for the analysis of biochemical pathways.
Briefings in Bioinformatics, 2003

Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples.
Proceedings of the German Conference on Bioinformatics, 2003

Integrative machine learning approach for multi-class SCOP protein fold classification.
Proceedings of the German Conference on Bioinformatics, 2003

An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics.
Proceedings of the First Asia-Pacific Bioinformatics Conference (APBC 2003), 2003

2002
A Computer System to Perform Structure Comparison using Representations of Protein Structure.
Computers & Chemistry, 2002

Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes.
Computers and Artificial Intelligence, 2002

2001
Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer.
Inf. Sci., 2001

Introduction to the Special Issue on Bioinformatics.
Constraints, 2001

A Constraint Based Structure Description Language for Biosequences.
Constraints, 2001

Bioinformatics and Constraints.
Constraints, 2001

Pattern Matching and Pattern Discovery Algorithms for Protein Topologies.
Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Multi-agent Systems as Concurrent Constraint Processes.
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.
Proceedings of the Computational Biology, 2000

Une technique déclarative pour filtrer des motifs topologiques de protéines.
Proceedings of the Programmation en logique avec contraintes, 2000

Tutoriel I: Bioinformatique et contraintes.
Proceedings of the Programmation en logique avec contraintes, 2000

Concurrent Constraint Programming with Process Mobility.
Proceedings of the Computational Logic, 2000

FURY: Fuzzy Unification and Resolution Based on Edit Distance.
Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering, 2000

1999
The development of interactive algorithms for the Mathematical Environment.
Proceedings of the Systems for Integrated Computation and Deduction, 1999

Motif-based searching in TOPS protein topology databases.
Bioinformatics, 1999

A Model for Interaction of Agents and Environments.
Proceedings of the Recent Trends in Algebraic Development Techniques, 1999

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database.
Proceedings of the German Conference on Bioinformatics, 1999

Pattern discovery methods for protein topology diagrams.
Proceedings of the German Conference on Bioinformatics, 1999

1998
Approaches to the Automatic Discovery of Patterns in Biosequences.
Journal of Computational Biology, 1998

1997
FlyBase: a Drosophila database. The FlyBase consortium.
Nucleic Acids Research, 1997

1996
Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems?
ACM Comput. Surv., 1996

A General Framework for Integrating HCLP and PCSP (Poster Abstract).
Proceedings of the Logic Programming, 1996

Transformations Between HCLP and PCSP.
Proceedings of the Second International Conference on Principles and Practice of Constraint Programming, 1996

A Process Algebra for Synchronous Concurrent Constraint Programming.
Proceedings of the Algebraic and Logic Programming, 5th International Conference, 1996

1995
Synchronisation in Scc.
Proceedings of the Logic Programming, 1995

1994
Transforming Specifications of Observable Behaviour into Programs.
Proceedings of the Logic Programming Synthesis and Transformation, 1994

1992
Logic for Representing and Implementing Knowledge about System Behaviour.
Proceedings of the Advanced Topics in Artificial Intelligence, 1992

1991
Deriving Logic Programs from Observations.
Proceedings of the Constructing Logic Programs, 1991

1990
Specifying and reasoning about concurrent systems in logic.
PhD thesis, 1990

1989
Specifying Concurrent Systems Using Logic.
Proceedings of the Formal Description Techniques, 1989

1988
A LOTOS to PARLOG Translator.
Proceedings of the Formal Description Techniques, 1988

Specification and Implementation of Concurrent Systems using PARLOG.
Proceedings of the Specification and Verification of Concurrent Systems [BCS-FACS Workshop, 1988

1987
Executable LOTOS: Using PARLOG to Implement an FDT.
Proceedings of the Protocol Specification, 1987


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