David Gilbert

Larisa N. Soldatova, Qian Gao, David Gilbert: Towards an Ontology of Biomodelling. CMSB 2012: 390-393

Zujian Wu, Shengxiang Yang, David Gilbert: A Hybrid Approach to Piecewise Modelling of Biochemical Systems. PPSN (1) 2012: 519-528

Daniele Maccagnola, Enza Messina, Qian Gao, David Gilbert: A machine learning approach for generating temporal logic classifications of complex model behaviours. Winter Simulation Conference 2012: 294

David Gilbert, Monika Heiner (Eds.): Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Lecture Notes in Computer Science 7605, Springer 2012, isbn 978-3-642-33635-5

Monika Heiner, David Gilbert: How Might Petri Nets Enhance Your Systems Biology Toolkit. Petri Nets 2011: 17-37

Qian Gao, Fei Liu, David Gilbert, Monika Heiner, David Tree: A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets. CMSB 2011: 209-218

Huma Lodhi, David Gilbert: Bootstrapping Parameter Estimation in Dynamic Systems. Discovery Science 2011: 194-208

Mallika Veeramalai, David Gilbert, Gabriel Valiente: An optimized TOPS+ comparison method for enhanced TOPS models. BMC Bioinformatics 11: 138 (2010)

Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner: Biomodel Engineering - From Structure to Behavior. T. Comp. Sys. Biology 12: 1-12 (2010)

Zujian Wu, Qian Gao, David Gilbert: Target driven biochemical network reconstruction based on petri nets and simulated annealing. CMSB 2010: 33-42

Amit Goel, Heinz Schmidt, David R. Gilbert: Formal Models of Virtual Enterprise Architecture: Motivations and Approaches. PACIS 2010: 117

Corrado Priami, Rainer Breitling, David Gilbert, Monika Heiner, Adelinde M. Uhrmacher (Eds.): Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies. Lecture Notes in Computer Science 5945, Springer 2010, isbn 978-3-642-11711-4

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 Bioinformatics 10 (2009)

Monika Heiner, Sebastian Lehrack, David Gilbert, Wolfgang Marwan: Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments. T. Comp. Sys. Biology 11: 138-163 (2009)

Amit Goel, Heinz Schmidt, David Gilbert: Towards formalizing Virtual Enterprise Architecture. EDOCW 2009: 238-242

Rainer Breitling, David Gilbert, Monika Heiner, Richard J. Orton: A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics 9(5): 404-421 (2008)

Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David Gilbert: MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics 24(1): 143-145 (2008)

Mallika Veeramalai, David Gilbert: A novel method for comparing topological models of protein structures enhanced with ligand information. Bioinformatics 24(23): 2698-2705 (2008)

Sebastian Oehm, David 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 Research 36(Web-Server-Issue): 433-437 (2008)

Robin Donaldson, David Gilbert: A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. CMSB 2008: 269-287

José A. Reyes, David Gilbert: Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. DILS 2008: 177-191

David Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson: An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing 2008: 13-28

Monika Heiner, David Gilbert, Robin Donaldson: Petri Nets for Systems and Synthetic Biology. SFM 2008: 215-264

Juris Viksna, David Gilbert: Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinformatics 23(7): 832-841 (2007)

Jean-Christophe Nebel, Pawel Herzyk, David R. Gilbert: Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 8 (2007)

José A. Reyes, David Gilbert: Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data. J. Integrative Bioinformatics 4(3) (2007)

Sung-Hee Park, David Gilbert, Keun Ho Ryu: Fast Structural Similarity Search Based on Topology String Matching. APBC 2007: 341-351

David Gilbert, Monika Heiner, Sebastian Lehrack: A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets. CMSB 2007: 200-216

Ali Al-Shahib, David Gilbert, Rainer Breitling: Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL 2007: 890-897

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 in Bioinformatics 7(4): 339-353 (2006)

Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert: A lock-and-key model for protein-protein interactions. Bioinformatics 22(16): 2012-2019 (2006)

Muffy Calder, Vladislav Vyshemirsky, David Gilbert, Richard J. Orton: Analysis of Signalling Pathways Using Continuous Time Markov Chains. : 44-67 (2006)

David Gilbert, Monika Heiner: From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis. ICATPN 2006: 181-200

Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead: Protein structure topological comparison, discovery and matching service. Bioinformatics 21(10): 2537-2538 (2005)

Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert: GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinformatics 6: 233 (2005)

Ali Al-Shahib, Rainer Breitling, David Gilbert: Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. 15(4): 259-275 (2005)

Sung-Hee Park, Keun Ho Ryu, David Gilbert: Fast similarity search for protein 3d structures using topological pattern matching based on spatial relations. Int. J. Neural Syst. 15(4): 287-296 (2005)

Dominique Turnbow, Kris Kasianovitz, Lise Snyder, David Gilbert, David Yamamoto: Usability testing for web redesign: a UCLA case study. OCLC Systems & Services 21(3): 226-234 (2005)

Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead: TOPS: an enhanced database of protein structural topology. Nucleic Acids Research 32(Database-Issue): 251-254 (2004)

Ali Al-Shahib, Chao He, Aik Choon Tan, Mark Girolami, David Gilbert: An Assessment of Feature Relevance in Predicting Protein Function from Sequence. IDEAL 2004: 52-57

Janet M. Thornton, David Gilbert, Catherine Brooksbank: ISMB/ECCB 2004. ISMB/ECCB (Supplement of Bioinformatics) 2004: 1-2

Janet M. Thornton, David Gilbert, Catherine Brooksbank: ISMB/ECCB 2004 Organization. ISMB/ECCB (Supplement of Bioinformatics) 2004: 3-5

Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4(3): 246-259 (2003)

Jean-Marie Jacquet, Lubos Brim, David Gilbert, Mojmír Kretínský: Coordination by Means of Synchronous and Asynchronous Communication in Concurrent Constraint Programming. Electr. Notes Theor. Comput. Sci. 68(3): 347-370 (2003)

Aik Choon Tan, David Gilbert: An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. APBC 2003: 219-222

Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak: An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB 2003: 174

Aik Choon Tan, David Gilbert, Yves Deville: Integrative machine learning approach for multi-class SCOP protein fold classification. German Conference on Bioinformatics 2003: 153-159

Juris Viksna, David 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: 159-165

Lubos Brim, Mojmír Kretínský, Jean-Marie Jacquet, David Gilbert: Modelling Multi-Agent Systems as Synchronous Concurrent Constraint Processes. Computers and Artificial Intelligence 21(6) (2002)

David Gilbert, David R. Westhead, Juris Viksna, Janet M. Thornton: A Computer System to Perform Structure Comparison using Representations of Protein Structure. Computers & Chemistry 26(1): 23-30 (2002)

David Gilbert, Rolf Backofen, Roland H. C. Yap: Introduction to the Special Issue on Bioinformatics. Constraints 6(2/3): 139 (2001)

Rolf Backofen, David Gilbert: Bioinformatics and Constraints. Constraints 6(2/3): 141-156 (2001)

Ingvar Eidhammer, Inge Jonassen, Svenn Helge Grindhaug, David Gilbert, Madu Ratnayake: A Constraint Based Structure Description Language for Biosequences. Constraints 6(2/3): 173-200 (2001)

Michael Schroeder, David Gilbert, Jacques van Helden, Penny Noy: Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. 139(1-2): 19-57 (2001)

Lubos Brim, David Gilbert, Jean-Marie Jacquet, Mojmír Kretínský: Multi-agent Systems as Concurrent Constraint Processes. SOFSEM 2001: 201-210

Juris Viksna, David Gilbert: Pattern Matching and Pattern Discovery Algorithms for Protein Topologies. WABI 2001: 98-111

David Gilbert, Michael Schroeder: FURY: Fuzzy Unification and Resolution Based on Edit Distance. BIBE 2000: 330-336

David Gilbert, Catuscia Palamidessi: Concurrent Constraint Programming with Process Mobility. Computational Logic 2000: 463-477

David Gilbert: Tutoriel I: Bioinformatique et contraintes. JFPLC 2000: 13-

David Gilbert, David R. Westhead, Janet M. Thornton, Karine Yvon: Une technique déclarative pour filtrer des motifs topologiques de protéines. JFPLC 2000: 165-

Jacques van Helden, David 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: 147-164

David Gilbert, David R. Westhead, N. Nagano, Janet M. Thornton: Motif-based searching in TOPS protein topology databases. Bioinformatics 15(4): 317-326 (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. Electr. Notes Theor. Comput. Sci. 23(3): 352-369 (1999)

David Gilbert, Juris Viksna: Pattern discovery methods for protein topology diagrams. German Conference on Bioinformatics 1999: 194-196

Jacques van Helden, David Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew Eldridge, Kirill Degtyarenko, Shoshana J. Wodak: Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics 1999: 227-229

Alexander A. Letichevsky, David Gilbert: A Model for Interaction of Agents and Environments. WADT 1999: 311-328

Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert: Approaches to the Automatic Discovery of Patterns in Biosequences. Journal of Computational Biology 5(2): 279-305 (1998)

William M. Gelbart, Madeline A. Crosby, Beverley Matthews, W. P. Rindone, J. Chillemi, S. Russo Twombly, David Emmert, Michael Ashburner, Rachel A. Drysdale, E. Whitfield, Gillian H. Millburn, A. de Grey, T. Kaufman, K. Matthews, David Gilbert, Victor B. Strelets, C. Tolstoshev: FlyBase: a Drosophila database. The FlyBase consortium. Nucleic Acids Research 25(1): 63-66 (1997)

David Gilbert: Can Computational Logic Provide a Paradigm for Both the Specification and Implementation of Concurrent Systems? ACM Comput. Surv. 28(2): 303-305 (1996)

Lubos Brim, Jean-Marie Jacquet, David Gilbert, Mojmír Kretínský: A Process Algebra for Synchronous Concurrent Constraint Programming. ALP 1996: 165-178

Michael Jampel, Jean-Marie Jacquet, David Gilbert, Sebastian Hunt: Transformations Between HCLP and PCSP. CP 1996: 252-266

Michael Jampel, Jean-Marie Jacquet, David Gilbert: A General Framework for Integrating HCLP and PCSP (Poster Abstract). JICSLP 1996: 543

Lubos Brim, David Gilbert, Jean-Marie Jacquet, Mojmír Kretínský: Synchronisation in Scc. ILPS 1995: 641

David Gilbert, Christopher J. Hogger, Jirí Zlatuska: Transforming Specifications of Observable Behaviour into Programs. LOPSTR 1994: 88-103

David Gilbert, Christopher J. Hogger: Logic for Representing and Implementing Knwoledge about System Behaviour. Advanced Topics in Artificial Intelligence 1992: 42-49

David Gilbert, Christopher J. Hogger: Deriving Logic Programs from Observations. ICLP Workshop on Construction of Logic Programs 1991: 113-126

David Gilbert: Specifying Concurrent Systems Using Logic. FORTE 1989: 245-260

David Gilbert: Specification and Implementation of Concurrent Systems using PARLOG. Specification and Verification of Concurrent Systems 1988: 455-473

David Gilbert: A LOTOS to PARLOG Translator. FORTE 1988: 31-44

David Gilbert: Executable LOTOS: Using PARLOG to Implement an FDT. PSTV 1987: 281-294