David R. Gilbert

Publication Activity (10 Years)

Years Active: 1987-2024
Publications (10 Years): 16

Top Venues

Briefings Bioinform.

BMC Bioinform.

Log. J. IGPL

CoRR

Publications

Can Baskent, David R. Gilbert, Giorgio Venturi
A Logic of Isolation. WoLLIC (2024)
Fei Liu, Monika Heiner, David R. Gilbert
Hybrid modelling of biological systems: current progress and future prospects. Briefings Bioinform. 23 (3) (2022)
David R. Gilbert, Ekaterina Kubyshkina, Mattia Petrolo, Giorgio Venturi
Logics of Ignorance and Being Wrong. Log. J. IGPL 30 (5) (2022)
Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert
Hybrid modelling of biological systems using fuzzy continuous Petri nets. Briefings Bioinform. 22 (1) (2021)
Shannon Connolly, David R. Gilbert, Monika Heiner
From Epidemic to Pandemic Modelling. CoRR (2021)
David R. Gilbert, Giorgio Venturi
Reflexive-Insensitive Logics, the Boxdot Translation, and the Modal Logic of Generic Absoluteness. Notre Dame J. Formal Log. 62 (2) (2021)
David R. Gilbert, Giorgio Venturi
A note on logics of essence and accident. Log. J. IGPL 28 (5) (2020)
Fei Liu, Monika Heiner, David R. Gilbert
Fuzzy Petri nets for modelling of uncertain biological systems. Briefings Bioinform. 21 (1) (2020)
Fei Liu, Monika Heiner, David R. Gilbert
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. Briefings Bioinform. 20 (3) (2019)
David R. Gilbert, Monika Heiner, Leila Ghanbar, Jacek Chodak
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinform. (4) (2019)
David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
Towards dynamic genome-scale models. Briefings Bioinform. 20 (4) (2019)
Timothy Self, David R. Gilbert, Monika Heiner
Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models. CMSB (2018)
David R. Gilbert, Monika Heiner, Christian Rohr
Petri-net-based 2D design of DNA walker circuits. Nat. Comput. 17 (1) (2018)
Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinform. (7) (2018)
David R. Gilbert, Giorgio Venturi
Reflexive-Insensitive Modal Logics. Rev. Symb. Log. 9 (1) (2016)
Juris Viksna, David R. Gilbert
Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure. Balt. J. Mod. Comput. 4 (4) (2016)
Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, Ramona Stoica, David R. Gilbert
Computational models for inferring biochemical networks. Neural Comput. Appl. 26 (2) (2015)
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders, Simon Shaw
Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. ACM Trans. Model. Comput. Simul. 25 (2) (2015)
David R. Gilbert, Paolo Maffezioli
Modular Sequent Calculi for Classical Modal Logics. Stud Logica 103 (1) (2015)
David R. Gilbert, Monika Heiner
Advances in Computational Methods in Systems Biology. Theor. Comput. Sci. 599 (2015)
Xuan Liu, Simon J. E. Taylor, Navonil Mustafee, Jun Wang, Qian Gao, David R. Gilbert
Speeding up systems biology simulations of biochemical pathways using condor. Concurr. Comput. Pract. Exp. 26 (17) (2014)
David R. Gilbert, Monika Heiner, Koichi Takahashi, Adelinde M. Uhrmacher
Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Dagstuhl Reports 4 (11) (2014)
Simon J. E. Taylor, Mohammadmersad Ghorbani, Navonil Mustafee, Tamás Kiss, Péter Borsody, Annette M. Payne, David R. Gilbert
Investigating the speedup of systems biology simulation using the sztaki desktop grid. WSC (2014)
Ovidiu Parvu, David R. Gilbert
Automatic validation of computational models using pseudo-3D spatio-temporal model checking. BMC Syst. Biol. 8 (2014)
Zujian Wu, Crina Grosan, David R. Gilbert
Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling. NICSO (2013)
Ovidiu Parvu, David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
Modelling and Analysis of Phase Variation in Bacterial Colony Growth. CMSB (2013)
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. 9 (12) (2013)
David R. Gilbert, Monika Heiner, Fei Liu, Nigel J. Saunders
Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. Petri Nets (2013)
Silvia Rausanu, Crina Grosan, Zujian Wu, Ovidiu Parvu, David R. Gilbert
Evolving biochemical systems. IEEE Congress on Evolutionary Computation (2013)
Qian Gao, David R. Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (2) (2013)
Larisa N. Soldatova, Qian Gao, David R. Gilbert
Towards an Ontology of Biomodelling. CMSB (2012)
Zujian Wu, Shengxiang Yang, David R. Gilbert
A Hybrid Approach to Piecewise Modelling of Biochemical Systems. PPSN (1) (2012)
David R. Gilbert, Edwin D. Mares
Completeness Results for some two-Dimensional Logics of actuality. Rev. Symb. Log. 5 (2) (2012)
Daniele Maccagnola, Enza Messina, Qian Gao, David R. Gilbert
A machine learning approach for generating temporal logic classifications of complex model behaviours. WSC (2012)
Monika Heiner, David R. Gilbert
How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets (2011)
Qian Gao, Fei Liu, David R. Gilbert, Monika Heiner, David Tree
A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. CMSB (2011)
Huma Lodhi, David R. Gilbert
Bootstrapping Parameter Estimation in Dynamic Systems. Discovery Science (2011)
Amit Goel, Heinz Schmidt, David R. Gilbert
Formal Models of Virtual Enterprise Architecture: Motivations and Approaches. PACIS (2010)
Mallika Veeramalai, David R. Gilbert, Gabriel Valiente
An optimized TOPS+ comparison method for enhanced TOPS models. BMC Bioinform. 11 (2010)
Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology 12 (2010)
Zujian Wu, Qian Gao, David R. Gilbert
Target driven biochemical network reconstruction based on petri nets and simulated annealing. CMSB (2010)
Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim
Prediction of protein-protein interaction types using association rule based classification. BMC Bioinform. 10 (2009)
Richard J. Orton, Michiel E. Adriaens, Amelie Gormand, Oliver E. Sturm, Walter Kolch, David R. Gilbert
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Syst. Biol. 3 (2009)
Amit Goel, Heinz Schmidt, David R. Gilbert
Towards formalizing Virtual Enterprise Architecture. EDOCW (2009)
Monika Heiner, Sebastian Lehrack, David R. Gilbert, Wolfgang Marwan
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. Trans. Comp. Sys. Biology 11 (2009)
Xuan Liu, Jipu Jiang, Oluwafemi O. Ajayi, Xu Gu, David R. Gilbert, Richard O. Sinnott
BioNessieG - A Grid Enabled Biochemical Networks Simulation Environment. HealthGrid (2008)
Mallika Veeramalai, David R. Gilbert
A novel method for comparing topological models of protein structures enhanced with ligand information. Bioinform. 24 (23) (2008)
David R. Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu, Maciej Trybilo
A Case Study in Model-driven Synthetic Biology. BICC (2008)
Robin Donaldson, David R. Gilbert
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. CMSB (2008)
David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing (2008)
Monika Heiner, David R. Gilbert, Robin Donaldson
Petri Nets for Systems and Synthetic Biology. SFM (2008)
Sebastian Oehm, David R. Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert
MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinform. 24 (1) (2008)
José A. Reyes, David R. Gilbert
Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. DILS (2008)
Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings Bioinform. 9 (5) (2008)
Xu Gu, David R. Gilbert, Desmond J. Higham, Miles Houslay
Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs. BMC Syst. Biol. 1 (S-1) (2007)
David R. Gilbert, Monika Heiner, Sebastian Lehrack
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB (2007)
Ali Al-Shahib, David R. Gilbert, Rainer Breitling
Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL (2007)
Juris Viksna, David R. Gilbert
Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinform. 23 (7) (2007)
Sung-Hee Park, David R. Gilbert, Keun Ho Ryu
Fast Structural Similarity Search Based on Topology String Matching. APBC (2007)
Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert
Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinform. 8 (2007)
José A. Reyes, David R. Gilbert
Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data. J. Integr. Bioinform. 4 (3) (2007)
David R. Gilbert, Monika Heiner
From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN (2006)
Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
A lock-and-key model for protein-protein interactions. Bioinform. 22 (16) (2006)
David R. Gilbert, Hendrik Fuß, Xu Gu, Richard J. Orton, Steve Robinson, Vladislav Vyshemirsky, Mary Jo Kurth, C. Stephen Downes, Werner Dubitzky
Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings Bioinform. 7 (4) (2006)
Muffy Calder, Vladislav Vyshemirsky, David R. Gilbert, Richard J. Orton
Analysis of Signalling Pathways Using Continuous Time Markov Chains. Trans. Comp. Sys. Biology 6 (2006)
Sung-Hee Park, Keun Ho Ryu, David R. Gilbert
Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations. Int. J. Neural Syst. 15 (4) (2005)
Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinform. 6 (2005)
Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead
Protein structure topological comparison, discovery and matching service. Bioinform. 21 (10) (2005)
Ali Al-Shahib, Rainer Breitling, David R. Gilbert
Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. 15 (4) (2005)
Janet M. Thornton, David R. Gilbert, Catherine Brooksbank
ISMB/ECCB 2004. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Janet M. Thornton, David R. Gilbert, Catherine Brooksbank
ISMB/ECCB 2004 Organization. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Ali Al-Shahib, Chao He, Aik Choon Tan, Mark A. Girolami, David R. Gilbert
An Assessment of Feature Relevance in Predicting Protein Function from Sequence. IDEAL (2004)
Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead
TOPS: an enhanced database of protein structural topology. Nucleic Acids Res. 32 (Database-Issue) (2004)
Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
An overview of data models for the analysis of biochemical pathways. Briefings Bioinform. 4 (3) (2003)
Aik Choon Tan, David R. Gilbert
An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. APBC (2003)
Juris Viksna, David R. Gilbert, Gilleain M. Torrance
Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples. German Conference on Bioinformatics (2003)
Aik Choon Tan, David R. Gilbert, Yves Deville
Integrative machine learning approach for multi-class SCOP protein fold classification. German Conference on Bioinformatics (2003)
Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB (2003)
Jean-Marie Jacquet, Lubos Brim, David R. Gilbert, Mojmír Kretínský
Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming. Electron. Notes Theor. Comput. Sci. 68 (3) (2003)
Lubos Brim, Mojmír Kretínský, Jean-Marie Jacquet, David R. Gilbert
Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes. Comput. Artif. Intell. 21 (6) (2002)
David R. Gilbert, David R. Westhead, Juris Viksna, Janet M. Thornton
A Computer System to Perform Structure Comparison using Representations of Protein Structure. Comput. Chem. 26 (1) (2002)
Ingvar Eidhammer, Inge Jonassen, Svenn Helge Grindhaug, David R. Gilbert, Madu Ratnayake
A Constraint Based Structure Description Language for Biosequences. Constraints An Int. J. 6 (2/3) (2001)
Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy
Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. 139 (1-2) (2001)
David R. Gilbert, Rolf Backofen, Roland H. C. Yap
Introduction to the Special Issue on Bioinformatics. Constraints An Int. J. 6 (2/3) (2001)
Lubos Brim, David R. Gilbert, Jean-Marie Jacquet, Mojmír Kretínský
Multi-agent Systems as Concurrent Constraint Processes. SOFSEM (2001)
Rolf Backofen, David R. Gilbert
Bioinformatics and Constraints. Constraints An Int. J. 6 (2/3) (2001)
Juris Viksna, David R. Gilbert
Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. WABI (2001)
Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak
Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. JOBIM (2000)
David R. Gilbert, David R. Westhead, Janet M. Thornton, Karine Yvon
Une technique déclarative pour filtrer des motifs topologiques de protéines. JFPLC (2000)
David R. Gilbert, Catuscia Palamidessi
Concurrent Constraint Programming with Process Mobility. Computational Logic (2000)
David R. Gilbert
Tutoriel I: Bioinformatique et contraintes. JFPLC (2000)
David R. Gilbert, Michael Schroeder
FURY: Fuzzy Unification and Resolution Based on Edit Distance. BIBE (2000)
Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak
Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics (1999)
Alexander A. Letichevsky, Julia V. Kapitonova, Vladislav A. Volkov, A. Chugayenko, Victor Khomenko, David R. Gilbert
The development of interactive algorithms for the Mathematical Environment. Calculemus (1999)
David R. Gilbert, Juris Viksna
Pattern discovery methods for protein topology diagrams. German Conference on Bioinformatics (1999)
Alexander A. Letichevsky, David R. Gilbert
A Model for Interaction of Agents and Environments. WADT (1999)
David R. Gilbert, David R. Westhead, Nozomi Nagano, Janet M. Thornton
Motif-based searching in TOPS protein topology databases. Bioinform. 15 (4) (1999)
Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David R. Gilbert
Approaches to the Automatic Discovery of Patterns in Biosequences. J. Comput. Biol. 5 (2) (1998)
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
FlyBase: a Drosophila database. The FlyBase consortium. Nucleic Acids Res. 25 (1) (1997)

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Publication Activity (10 Years)

Top Topics

Top Venues

David R. Gilbert