Selected publications by David Gilbert

[Papers] [Contributions to books] [Brunel Archive: BURA] [Google Scholar] [ResearcherID]



F. Liu, W. Sun, M. Heiner and D. Gilbert: Hybrid modelling of biological systems using fuzzy continuous Petri nets. Briefings in Bioinformatics, 2019 (accepted for publication: 07 August 2019)

D. Gilbert, M. Heiner, L. Ghanbar and J. Chodak (2019): Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking. BMC Bioinformatics 20, Article number 173, Supplement 4 (2019) (Accepted for publication: July, 26 2018, published April 2019).


F. Liu, M. Heiner, D. Gilbert (2018). Fuzzy Petri nets for modelling of uncertain biological systems. Briefings in Bioinformatics, bby118,

R. Colombo, C. Damiani, D. Gilbert, M. Heiner, G. Mauri, D. Pescini (2018). Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinformatics, 19:7

T. Self, D. Gilbert and M. Heiner (2018). Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models; CMSB 2018 (16th International Conference on Computational Methods in Systems Biology). Springer LNCS 11095.

D. Gilbert, M. Heiner and C. Rohr (2018): Petri-net-based 2D Design of DNA Walker Circuits; Natural Computing, 201.

H. Xu, TY. Curtis, SJ. Powers, S. Raffan, R. Gao, J. Huang, M. Heiner, D. Gilbert, N.G. Halford (2018): Genomic, biochemical and modelling analyses of asparagine synthetases from wheat; Frontiers in Plant Science, section Plant Physiology, 15 Jan 2018,


A. Bracciali, G. Caravagna, D. Gilbert, R. Tagliaferri [Eds] (2017): Computational Intelligence Methods for Bioinformatics and Biostatistics 13th International Meeting, CIBB 2016, Stirling, UK, September 1-3, 2016, Revised Selected Papers. Springer LNBI 10477 ISBN 978-3-319-67834-4

F. Liu, M. Heiner, D. Gilbert (2017): Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems, Briefings in Bioinformatics, Volume 20, Issue 3, May 2019, Pages 877 - 886. Published November 2017.

D. Gilbert, M. Heiner, Y. Jayaweera, C. Rohr (2017): Towards dynamic genome scale models. Briefings in Bioinformatics, October 2017.

D. Gilbert, M.Heiner, L.Ghanbar (2017): Personalised models for human - gut microbiota interaction. In Methods, tools & platforms for Personalised Medicine in the Big Data Era, NETTAB 2017 Workshop Collection, PeerJ, volume Preprints 5:e3267v1, pages 1-4, September 2017


O. Parvu, D. Gilbert (2016): A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking. PloS one 11 (5), e0154847

O. Parvu, D. Gilbert (2016): Implementation of linear minimum area enclosing triangle algorithm. Computational and Applied Mathematics 35:2 pp 423-438

J. Viksna, D.Gilbert (2016): Gene duplication models and reconstruction of gene regulatory network evolution from network structure Baltic Journal of Modern Computing 4 (4), 876


O. Parvu, D. Gilbert, M. Heiner, F. Liu, N. Saunders, S. Shaw (2015): Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. ACM Trans. Model. Comput. Simul. 25, 2, Article 13 (May 2015), 25 pages. DOI=10.1145/2742546


O. Parvu, D. Gilbert (2014): Automatic validation of computational models using pseudo-3D spatio-temporal model checking. BMC Systems Biology 2014, 8:124

S. Rausanu, C. Grosan, Z. Wu, O. Parvu, R. Stoica, D. Gilbert (2014). Computational models for inferring biochemical networks. Neural Computing and Applications, Springer 1-13. [Paper]


X. Liu, S. J. E. Taylor, N. Mustafee, J. Wang, Q. Gao, D. Gilbert (2013): Speeding up systems biology simulations of biochemical pathways using condor. Concurrency and Computation: Practice and Experience. Volume 26, Issue 17, pages 2727-2742.

E. J. Kerkhoven, F. Achcar, V. P. Alibu, R. J. Burchmore, I. H. Gilbert, M. Trybiło, N. N. Driessen, D. Gilbert, R. Breitling, B. M. Bakker, M. P. Barrett (2013): Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Computational Biology 9:12

Z. Wu, C. Grosan and D. Gilbert (2013): Empirical study of computational intelligence strategies for biochemical systems modelling. In Proceedings VI International Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2013). Springer LNCS, Studies in Computational Intelligence 512, pp 245-260 [Preprint]

S. Rausanu, C. Grosan, Zujian Wu, O. Parvu and D. Gilbert (2013): Evolving biochemical systems. In Proceedings IEEE Congress on Evolutionary Computation pp 1602-1609. [Preprint]

O. Parvu, D. Gilbert, M. Heiner, F. Liu, and N. Saunders (2013): Modelling and Analysis of Phase Variation in Bacterial Colony Growth. In Proceedings Computational Methods in Systems Biology; 11th International Conference CMSB 2013, Springer LNCS, Volume 8130, pp 78-91 [Preprint].

D. Gilbert, M. Heiner, F. Liu and N. Saunders (2013): Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. In Proc. PETRI NETS 2013. Springer LNCS, volume 7927, pages 230-249, June 2013 [Preprint].

X. Gu, D. Reid, D. J. Higham, D. Gilbert, (2013): Mathematical Modelling of Polyamine Metabolism in Bloodstream-form Trypanosoma brucei: An Application to Drug Target Identification. PLOS ONE, 8:1, e5374, doi:10.1371/journal.pone.0053734

M. Heiner and D. Gilbert, (2013): BioModel Engineering for Multiscale Systems Biology; Progress in Biophysics and Molecular Biology, 11:2-3, 119-128. DOI 10.1016/j.pbiomolbio.2012.10.001


Q. Gao, D. Gilbert, M. Heiner, F. Liu, D. Maccagnola and D. Tree, (2012). Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10:2. DOI 10.1109/TCBB.2012.101 [Preprint]

D. Gilbert and M. Heiner (eds.): (2012) Computational Methods in Systems Biology; Proc. 10th International Conference CMSB 2012; LNCS/LNBI 7605 DOI: 10.1007/978-3-642-33636-2, Springer

L. Soldatova, Q. Gao and D. Gilbert, (2012). Towards an Ontology of Biomodelling, (Flash Poster - short paper). In Proceedings of Computational Methods in Systems Biology; Proc. 10th International Conference CMSB 2012; LNCS/LNBI 7605 DOI: 10.1007/978-3-642-33636-2_28 pp 390-393, Springer [Preprint], [OBM website].

D. Maccagnola, E. Messina, Q. Gao and D. Gilbert, (2012). A Machine Learning Approach for Generating Temporal Logic Classifications of Complex Model Behaviours, in Proceedings of WSC 2012 (Winter Simulation Conference December 9-12, 2012, Berlin). [Preprint]

Zujian Wu, Shengxian Wang and David Gilbert. (2012). A Hybrid Approach to Piece-wise Modelling of Biochemical Systems, in PPSN XII (12th International Conference on Parallel Problem Solving From Nature). LNCS 7491/2012, pages 519-528, DOI: 10.1007/978-3-642-32937-1_52. [Preprint].


M Heiner and D Gilbert: How Might Petri Nets Enhance Your Systems Biology Toolkit; (2011). In Proc. PETRI NETS 2011, LNCS 6709/2011, Springer, pages 17-37, DOI: 10.1007/978-3-642-21834-7_2. [Preprint]

Vijayakrishnan, S., Callow, P., Nutley, M.A., McGow, D., Gilbert, D., Kropholler, P., Cooper, A., Byron, O. and Lindsay, J.G. (2011). Variation in the organisation and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly, Biochemical Journal 437 (3) : 565- 574 [Pre-publication version: Paper, Supplementary Information ]

Huma Lodhi and David Gilbert (2011). Bootstrapping Parameter Estimation in Dynamic Systems, Discovery Science 2011. Lecture Notes in Computer Science, 2011, Volume 6926/2011, 194-208, DOI: 10.1007/978-3-642-24477-3_17

Qian Gao, Fei Liu, David Gilbert, Monika Heiner, David Tree (2011). A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets, CMSB 2011 9th International Conference on Computational Methods in Systems Biology. Published in the ACM Digital Library, pp 209-218. Pre-publication version.

Qian Gao, Fei Liu, David Tree, David Gilbert (2011). Multi-cell Modelling Using Coloured Petri Nets Applied to Planar Cell Polarity, BioPPN-2011 International Workshop on Biological Processes & Petri Nets. ISBN: 978-1-4503-0817-5; doi: 10.1145/2037509.2037538


Oliver E. Sturm, Richard Orton, Vlad Vyshemirsky, Joan Grindlay, Marc Birtwistle, David Gilbert, Muffy Calder, Andrew Pitt, Boris Kholodenko and Walter Kolch (2010). The mammalian MAPK/ERK pathway functions as negative feedback amplifier Science Signalling Dec 21;3(153).

X.Gu, M.Trybiło, S.Ramsay, M.Jensen, R.Fulton, S. Rosser and D. Gilbert (2010), Engineering a novel self-powering electrochemical biosensor, in Journal for Systems and Synthetic Biology, Springer, Special Issue:Top-down and bottom-up approaches to the design of biological systems - papers arising from the Second European Conference on Synthetic Biology 1:4, 203-214, DOI: 10.1007/s11693-010-9063.

David Gilbert, Alfonso Jaramillo, Natalio Krasnogor and Victor de Lorenzo (2010), Synthetic biology gains momentum in Europe, in Journal for Systems and Synthetic Biology, Springer, Special Issue:Top-down and bottom-up approaches to the design of biological systems - papers arising from the Second European Conference on Synthetic Biology 1:4, pp 145-147, DOI: 10.1007/s11693-010-9065-0

D. Gilbert, M. Heiner, R. Breitling, R. Orton (2010). Computational modelling of kinase signalling cascades in MAP Kinase Signaling Protocols, Rony Seger (Ed), Methods in Molecular Biology, 2010, Volume 661, Part 4, 369-384, DOI: 10.1007/978-1-60761-795-2_22. [PubMed]

Zujian Wu, Qian Gao and David Gilbert (2010), Target Driven Biochemical Network Reconstruction Based on Petri nets and Simulated Annealing, CMSB 2010, Trento, September 29 - October 1, 2010. Published by the ACM Digital Library.

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

Corrado Priami, Rainer Breitling, David Gilbert, Monika Heiner, Adelinde M. Uhrmacher (Eds.) (2010). Transactions on Computational Systems Biology XII: Special Issue on Modeling Methodologies. Springer LNCS 5945, ISSN 0302-9743 (Print), 1611-3349 (Online).

Rainer Breitling, Robin Donaldson, David Gilbert, Monika Heiner (2010): Biomodel Engineering - From Structure to Behavior; (position paper) in C Priami et al. (eds.): Trans. on Computational Systems Biology XII, Springer LNCS 5945, pp. 1-12. [Preprint].

Monika Heiner, Robin Donaldson and David Gilbert (2010): Petri Nets for Systems Biology; In Symbolic Systems Biology: Theory and Methods, (MS Iyengar, Ed.), Jones & Bartlett Learning, LCC, pages 61-97. [Preprint]


von Kriegsheim A, Baiocchi D, Birtwistle M, Sumpton D, Bienvenut W, Morrice N, Yamada K, Lamond A, Kalna G, Orton R, Gilbert D, Kolch W. (2009) Cell fate decisions are specified by the dynamic ERK interactome. Nat Cell Biol. 2009 Dec;11(12):1458-64

Richard Orton, Michiel Adriaens, Amelie Gormand, Oliver Sturm, Walter Kolch, David Gilbert (2009). Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Syst Biol. 2009 Oct 5;3(1):100. PMID: 19804630

Jun Wang, Xuan Liu, Navonil Mustafee, Qian Gao, Simon J E Taylor and David Gilbert (2009) Grid-enabled SIMAP Utility: Motivation, Integration Technology and Performance Results AHM 2009. [Preprint]

Monika Heiner, Sebastian Lehrack, David Gilbert and Wolfgang Marwan (2009), Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments in C Priami, RJ Back, I Petre (eds.): Computational models for cell processes; Trans. on Computational Systems Biology XI, Springer LNCS 5750, pp. 138-163. [Preprint]

Sung Hee Park, Jose A Reyes, David Gilbert, Ji Woong Kim and Sangsoo Kim (2009). Prediction of Protein-Protein Interaction Types using Association Rule based Classification. BMC Bioinformatics 2009 Jan 28;10:36.

Gilleain Torrance, David Leader, David Gilbert and James Milner-White. A novel main chain motif in proteins bridged by cationic groups: the niche. J Mol Biol. 2009 Jan 30;385(4):1076-86.

David Gilbert, Rainer Breitling, Monika Heiner, and Robin Donaldson (2009). An introduction to BioModel Engineering, illustrated for signal transduction pathways, 9th International Workshop, WMC 2008, Edinburgh, UK, July 28-31, 2008, Revised Selected and Invited Papers, Corne, D.; Frisco, P.; Paun, G.; Rozenberg, G.; Salomaa, A. (Eds.) LNCS Volume 5391, pp13-28 ISBN: 978-3-540-95884-0. [Preprint].


Mallika Veeramalai and David Gilbert (2008). A novel method for comparing topological models of protein structures enhanced with ligand information Bioinformatics 2008 24(23):2698-2705; doi:10.1093/bioinformatics/btn518

Robin Donaldson and David Gilbert (2008). A Monte Carlo Model Checker for Probabilistic LTL with Numerical Constraints.  Technical Report TR-2008-282 at the Department of Computer Science at University of Glasgow.

Robin Donaldson and David Gilbert (2008). A Model Checking Approach to the Parameter Estimation of Biochemical Pathways. In proceedings CMSB 2008 (Computational Methods in Systems Biology). Heiner, Monika; Uhrmacher, Adelinde M. (Eds.) LNCS 5307/2008, pp269-287. ISBN: 978-3-540-88561-0. [Preprint]

Richard Orton, Oliver Sturm, Amelie Gormand, Walter Kolch and David Gilbert (2008). Computational modelling reveals feedback redundancy within the EGFR/ERK signalling pathway. IET Systems Biology Vol. 2, No. 4, pp. 173 - 183, doi: 10.1049/iet-syb:20070066.

Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann (2008). Comparative Pathway Analyzer - CPA - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms Nucleic Acids Research, Jul 1;36(Web Server issue):W433-7, doi:10.1093/nar/gkn284

Jose Antonio Reyes and David Gilbert (2008). Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions. Proc Data Integration and the Life Sciences DILS 2008. LNCS/LNBI 5109/2008, pp177-191.

Rainer Breitling, David Gilbert, Monika Heiner, Richard Orton (2008). A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics, 2008 9(5):404-42, doi:10.1093/bib/bbn026 [preprint]

Monika Heiner, David Gilbert, and Robin Donaldson (2008), Petri Nets for Systems and Synthetic Biology. In M Bernardo, P Degano, and G Zavattaro (Eds.): Formal Methods for Systems Biology SFM 2008, Springer LNCS 5016, pp. 215-264, 2008. [Pre-publication version]

Xuan Liu, Jipu Jiang, Oluwafemi Ajayi, Xu Gu, David Gilbert, Richard Sinnott (2008), 'BioNessie(G) - A Grid Enabled Biochemical Networks Simulation Environment'. Studies in Health Technology and Informatics IOS Press, 2008, 138: 147-157. Global Healthgrid: e-Science Meets Biomedical Informatics - Proceedings of HealthGrid 2008 Edited by Tony Solomonides, Jonathan C. Silverstein, Joel Saltz, Yannick Legre, Mary Kratz, Ian Foster, Vincent Breton, J. Robert Beck ISBN 978-1-58603-874-8 [preprint]

David Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu and Maciej Trybiło (2008), A Case Study in Model-driven Synthetic Biology. In Biologically Inspired Cooperative Computing: BICC 2008. IFIP Springer ISSN 1571-5736 (Print) 1861-2288 (Online). Volume 268/2008. DOI 10.1007/978-0-387-09655-1. ISBN 978-0-387-09654-4. pp 163-175. [Preprint]

Fabien Jourdan, Rainer Breitling, Mike Barrett and David Gilbert. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2008). Abstract, PDF. Bioinformatics 2008 24(1):143-145; doi:10.1093/bioinformatics/btm536


Jean-Christophe Nebel, Pawel Herzyk and David R Gilbert (2007). Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 2007, 8:321 (30 Aug 2007) [PubMed]

Jose Antonio Reyes and David Gilbert (2007). Prediction of protein-protein interactions using one-class classification methods and integrating diverse data. (Proc 4th Integrative Bioinformatics Workshop, September 2007), Journal of Integrative Bioinformatics, 4(3):77, 2007. (Online Journal). [Preprint, Supplementary Data]

David Gilbert, Monika Heiner and Sebastian Lehrack (2007). A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets Technical Report TR-2007-253 at the Department of Computer Science at University of Glasgow, and Techn. Report I-02/2007, Brandenburg University of Technology Cottbus, Germany. This paper is an extended version of Gilbert et al., CMSB 2007.

David Gilbert, Monika Heiner and Sebastian Lehrack (2007). A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets In proceedings CMSB 2007 (Computational Methods in Systems Biology), Editors: M.Calder and S.Gilmore, Springer LNCS/LNBI 4695, pp. 200-216.

Ali Al-Shahib, Rainer Breitling and David Gilbert, (2007). Predicting protein function by machine learning on amino acid sequences - A critical evaluation, BMC Genomics 2007, 8:78

David Gilbert, Francesco Rossello and Gabriel Valiente and Mallika Veeramalai (2007) Alignment-Free Comparison of TOPS Strings, London Algorithmics and Stringology 2007, In J. Daykin, M. Mohamed, K. Steinhofel (Ed.), London Algorithmics and Stringology, volume 8 of Texts in Algorithmics, College Publications (2007), ch. 11, pp. 177-197.

Juris Viksna and David Gilbert. (2007). Assessment of the probabilities for evolutionary structural changes in protein folds, Bioinformatics 2007 23(7):832-841; doi:10.1093/bioinformatics/btm022

Sung Hee Park, David Gilbert and Keun Ho-Ryu (2007) Fast structural similarity search based on topology string matching in Proceedings of the Fifth Asia Pacific Bioinformatics Conference (APBC2007), Imperial College Press.


David Gilbert, Hendrik Fuß, Xu Gu, Richard Orton, Steve Robinson, Vladislav Vyshemirsky, Mary Jo Kurth, C. Stephen Downes and Werner Dubitzky. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks, Briefings in Bioinformatics 2006 7(4):339-353; doi: 10.1093/bib/bbl043 Special Issue: Computational Methodologies for Systems Biology.

Rolf Backofen and David Gilbert. (2006). Bioinformatics and Constraints, in Handbook of Constraint Programming, Editors: Francesca Rossi, Peter van Beek and Toby Walsh, Chapter 26, pp 905-944, ISBN: 0-444-52726-5, Elsevier, 2006

Julie Morrison, Rainer Breitling, Des Higham and David Gilbert. (2006). A Lock-and-Key model for Protein-Protein interactions, Bioinformatics, 2006 Aug 15;22(16):2012-9. ISSN 1367-4803. Epub 2006 Jun 20. [Abstract] [PDF]

M. Calder, V. Vyshemirsky, D. Gilbert and R. Orton. (2006). Analysis of Signalling Pathways using Continuous Time Markov Chains, Trans.on Computat. Syst. Biol. VI, volume 4220 pp 44-67 Springer Verlag

David Gilbert and Monika Heiner, (2006). From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis, 27th International Conference on Application and Theory of Petri Nets and other models of concurrency (ATPN06), Turku, Finland, June 26-30, 2006. Proceedings; Editors: Susanna Donatelli, P. S. Thiagarajan; LNCS 4024 / 2006, pp. 181-200, ISBN: 3-540-34699-6 DOI: 10.1007/11767589


David Gilbert and Monika Heiner, (2005) From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis, Technical Report TR-2005-208 at the Department of Computer Science at University of Glasgow, and I-04/2005 at the Brandenburg University of Technology Cottbus, Germany.

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

Ali Al-Shahib, Rainer Breitling and David Gilbert, (2005) FrankSum: New Feature Selection Method for Protein Function Prediction International Journal of Neural Systems, 15:4 259-275, 2005.

Sung Hee Park, Keun Ho-Ryu and David Gilbert, (2005) Fast Similarity Search for 3D Protein Structures using Topological Pattern Matching based on Spatial Relations International Journal of Neural Systems, 15:4 287-296, 2005.

Richard Orton, Oliver Sturm, Vladislav Vyshemirsky, Muffy Calder, David Gilbert, and Walter Kolch, (2005) Computational Modelling of the Tyrosine Receptor Kinase Activated MAPK Pathway , Biochemical Journal, Volume 392 pp 249-261, 2005

Walter Kolch, Muffy Calder and David Gilbert, (2005) When kinases meet mathematics: the systems biology of MAPK signalling, FEBS Letters, 579:8, 1891--5, 2005.

M. Calder, V. Vyshemirsky, D. Gilbert and R. Orton, (2005) Analysis of Signalling Pathways using the Prism Model Checker. In Proceedings of Third International CMSB 2005 (Computational Methods in Systems Biology), pp 179-190 University of Edinburgh, 2005

Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos and David R. Westhead (2005). Protein Structure Topological Comparison, Discovery and Matching Service, Bioinformatics 2005 21(10):2537-2538. On-line version.

Ali Al-Shahib, Rainer Breitling and David Gilbert (2005). Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence. Applied Bioinformatics. 2005;4(3):195-203 [PUBMED]


Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert (2004). MSAT: a Multiple Sequence Alignment tool based on TOPS. Applied Bioinformatics 2004 3 (2-3): 149-158

Juris Viksna, David Gilbert and Gilleain Torrance, (2004). Domain discovery method for topological profile searches in protein structures. 15th International Conference on Genome Informatics GIW 2004, Tatsuya Akutsu Vladimir Brusic, co-chairs. Genome Informatics 15(2):72-81.

Sinnott,R.0. Atkinson,M. Bayer,M. Berry,D. Dominiczak,A. Ferrier,M. Gilbert,D. Hanlon,N. Houghton,D. Hunt,E. White,D. (2004) Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data Proceedings of UK e-Science All Hands Meeting, pp 135-138, EPSRC, September 2004

Ali Al-Shahib, Chao He, Aik Choon Tan, Mark Girolami, David Gilbert, (2004). An Assessment of Feature Relevance in Predicting Protein Function from Sequence. In the Proceedings of the Fifth International Conference on Intelligent Data Engineering and Automated Learning (IDEAL'04). Published by Springer-Verlag in the Lecture Notes in Computer Science series. ISSN: 0302-9743, ISBN: 3-540-22881-0, Volume 3177 / 2004, p52. On-line version.

Lubna Nasir, Elizabeth Gault, Sarah Campbell, Mallika Veeramalai, David Gilbert, Robert McFarlane, Alison Munro and David J Argyle. Isolation and expression of the reverse transcriptase component of the canis familiaris telomerase ribonucleoprotein (canTERT), Gene 2004 Jul 7;336(1):105-13. [PUBMED]

Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert and David R. Westhead (2004). TOPS: an enhanced database of protein structural topology, Nucleic Acids Research, 2004, Vol. 32, Database issue D251-D254. Abstract, Full Text, [PubMed]


A. Williams, D.R. Gilbert, and D.R. Westhead, Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing, Protein Eng. 2003 Dec;16(12):913-23. [PubMed]

Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert (2003). MSAT : a Multiple Sequence Alignment tool based on TOPS, Proceedings of the Biological Language Conference 2003. J. Klein-Seetharaman, R. Rosenfeld and R. Reddy (editors) p.286-301. Pre-publication version. MSAT webserver.

Aik Choon Tan, David Gilbert and Yves Deville (2003). Multi-class Protein Fold Classification using a New Ensemble Machine Learning Approach. In the Proceedings of the 14th International Conference on Genome Informatics (GIW 2003)M. Gribskov, M. Kanehisa, S. Miyano, and T. Takagi (editors) p.206-217.[ PDF] Genome Informatics 2003;14:206-17.

Aik Choon Tan, David Gilbert and Yves Deville. Integrative machine learning approach for multi-class SCOP protein fold classification, GCB03: German Conference on Bioinformatics, 2003, H.-W. Mewes, D. Frishman, V. Heun and S. Kramer (editors) p. 153-159. ISBN 3-936-298-80-7. [Preprint]

Juris Viksna, David Gilbert and Gilleain Torrance. Protein structure comparison based on profiles of topological motifs: a feasible way to deal with information from negative examples, GCB03: German Conference on Bioinformatics, 2003, H.-W. Mewes, D. Frishman, V. Heun and S. Kramer (editors) p. 159-165. ISBN 3-936-298-80-7.

Yves Deville, David Gilbert, Jacques van Helden and Shoshana Wodak. An Overview of Data Models for the Analysis of Biochemical Pathways, Briefings in Bioinformatics, 2003 4:3, pp 246-259, ISSN 1467-5463. (pre-publication version) [PubMed].

David Gilbert, David Westhead and Juris Viksna. Techniques for comparison, pattern matching and pattern discovery: From sequences to protein topology, in "Artificial Intelligence and Heuristic Methods in Bioinformatics", Paolo Frasconi and Ron Shamir (Eds), IOS Press, ISBN 1-58603-294-1, pp 128-147, 2003 [Pre-publication version]

Aik Choon Tan and David Gilbert (2003). Ensemble machine learning on gene expression data for cancer classification. Applied Bioinformatics 2(3): S75-S83 (Supplement of the Proceedings of New Zealand Bioinformatics Conference Te Papa, Wellington, New Zealand) [PubMed], [ PDF]

Aik Choon Tan and David Gilbert (2003). An empirical comparison of supervised machine learning techniques in bioinformatics. Proceedings of First Asia Pacific Bioinformatics Conference (APBC 2003) Adelaide, Australia. Australian Computer Society. P. Chen (editor) Conferences in Research and Practice in Information Technology, 19: 219-222. ISSN: 1445-1336 ISBN: 0-909925-97-6 [Preprint PDF]


Russ Altman, David Gilbert and Thomas Lengauer, Computational Biology: the report of Dagstuhl Seminar 02471, 17-22 November 2002.

Jacques van Helden, Lorenz Wernisch, David Gilbert, and Shoshana Wodak. "Graph-based analysis of metabolic networks". in Ernst Schering Research Foundation Workshop Volume 38: Bioinformatics and Genome Analysis. Editors: H.-W. Mewes, B. Weiss, H. Seidel Springer-Verlag, ISBN 3-540-42893-3, pp245-274, Berlin Heidelberg 2002. [PubMed] [Preprint: article, figures].

Mallika Veeramalai and David Gilbert.,"Bioinformatics tools for Protein Structure", Bioinformatics World, Scientific Computing World, May/June 2002 Issue 64.

Aik Choon Tan, David Gilbert and Andrew Tuson (2002). Characterisation of FAD-family Folds using a Machine Learning Approach. Proceedings of International Conference on Bioinformatics, (InCOB 2002), Bangkok, Thailand. [Preprint PS] [Preprint PDF]


Lubos Brim, David Gilbert, Jean-Marie Jacquet, and Mojmir Kretinsky: "Multi-agent Systems as Concurrent Constraint Processes" in L.Pacholski, P.Ruzicka (eds.) SOFSEM 2001: Theory and Practice of Informatics, (28th Conference on Current Trends in Theory and Practice of Informatics Piestany, Slovak Republic,) Springer LNCS 2234, p. 201 - 210, ISBN 3-540-42912-3 ISSN 0302-9743 [Postscript] [PDF]

Juris Viksna and David Gilbert, Pattern matching and pattern discovery algorithms for protein topologies , Algorithms in Bioinformatics: First International Workshop, WABI 2001 Proceedings, LNCS 2149 pp 98-111, ISBN 3-540-42516-0, (pre-publication version)

David Gilbert, David Westhead, Juris Viksna and Janet Thornton, A computer system to perform structure comparison using TOPS representations of protein structure, Journal of Computers and Chemistry, 26:1, 23-30, 2001. [Pre- publication version], [PubMed]

David Gilbert, Rolf Backofen, Roland H. C. Yap, Introduction to the Special Issue on Bioinformatics, Constraints ISSN 1383-7133, 6(2/3): 139-139, June 2001 [Table of Contents]

Rolf Backofen and David Gilbert, Bioinformatics and Constraints, Constraints ISSN 1383-7133 6:2/3: 141-156, June 2001 [On-line abstract] [Preprint].

Ingvar Eidhammer, David Gilbert, Inge Jonassen, Madu Ratnayake and Svenn Helge Grindhaug, A Constraint Based Structure Description Language for Biosequences, Constraints ISSN 1383-7133 6:2/3: 173-200, June 2001 [On-line abstract] [Preprint].

Michael Schroeder, David Gilbert, Jacques van Helden, Penny Noy. Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Information Sciences 139 pp 19-57 2001 Elsevier


David Gilbert, Michael Schroeder and Jacques van Helden, Interactive visualisation and exploration of relationships between biological objects, Trends in Biotechnology, 18:12 [203] pp 487-494, 2000. ISSN 0167-7799, [PubMed].

David Gilbert and Michael Schroeder, FURY: Fuzzy unification and resolution based on edit distance, BIBE 2000: IEEE International Symposium on Bio-Informatics and Biomedical Engineering, November 8-10 2000.

Jacques van Helden, Avi Naim, Renato Mancuso, Mattew Eldridge, Lorenz Wernisch, David Gilbert, and Shoshana J. Wodak, Representing and analysing molecular and cellular function in the computer, Journal of Biological Chemistry, 381 (9-10):921-35, Sep-Oct 2000. [Abstract] [Pre-print version (pdf)] [Pre-print version (ps)] [PubMed].

David Gilbert and Catuscia Palamidessi, Concurrent Constraint Programming with Process Mobility, CL2000 (Computational Logic 2000), J Lloyd et al. (Eds), Springer LNAI 1861, ISBN 3-540-67797-6, pp 463-477, July 2000. [postscript] [Acrobat]

David Gilbert Bioinformatique et contraintes JFPLC2000: Neuvièmes Journées Francophones de Programmation Logique et Programmation par Contraintes, p 11, ISBN 2-7462-0147-X, (invited tutorial) [HTML] July 2000

David Gilbert, David Westhead, Janet Thornton and Karine Yvon, Une technique déclarative pour filtrer des motifs topologiques de protéines JFPLC2000: Neuvièmes Journées Francophones de Programmation Logique et Programmation par Contraintes, pp 165-185, ISBN 2-7462-0147-X, (in French) [HTML] [Postscript] [Transparentes] July 2000

Jacques van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, and Shoshana Wodak, Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data, in Computational Biology (Olivier Gascuel and Marie-France Sagot, Eds), LNCS 2006, pp147-163, ISBN 3-540-42242-0, 2001. [Pre-print version (pdf)] [Pre-print version (ps)]
This is a revised version of the paper presented at JOBIM'2000: Journées Ouvertes : Biologie, Informatique et Mathématiques, Montpellier 3-5 May 2000. Jacques van Helden, David Gilbert, Lorenz Wernisch and Shoshana Wodak, Application de l'analyse des mots et de l'analyse des graphes à l'interprétation des données d'expression génomique [Postscript] [HTML] (in French)

David Gilbert, David Westhead, Juris Viksna and Janet Thornton, Topology-based protein structure comparison using a pattern discovery technique, Proceedings of the AISB-00 Symposium on AI in Bioinformatics , Andrew Martin Dave Corne (Eds), ISBN 1 902956 12 X, pp 11-17, published by The Society for the Study of Artificial Intelligence and the Simulation of Behaviour, 19-20 April 2000.

David Gilbert, Michael Schroeder and Jacques van Helden, Interactive visualisation and exploration of biological data, Second International Workshop on Biomolecular Informatics in conjunction with Fifth Joint Conference on Information Sciences, Atlantic City, New Jersey, USA February 27 -- March 3, 2000. An HTML version is available here.


David Gilbert, David Westhead, Nozomi Nagano and Janet Thornton, Motif-based searching in TOPS protein topology databases. Bioinformatics, 15:4 1999, pp 317-326. ISSN 1367-4803 [Abstract]. An earlier version is available here, [PubMed].

A.A. Letichevsky, D.R. Gilbert, A model for interaction of agents and environments, WADT'99 (Workshop on Algebraic Development Techniques), 1999.
To be published in a special issue of LNCS.

A.A. Letichevsky, J.V. Kapitonva, V.A. Volkov, A. Chugayenko, V. Chomenko, D.R. Gilbert, The development of interactive algorithms for a mathematical environment, in Proceedings of CALCULEMUS 99, Electronic Notes in Theoretical Computer Science, 1999
An extended verson will be published in the Journal of Symbolic Computation.


A. Brazma, I. Jonassen, I. Eidhammer and D.R. Gilbert: Approaches to the automatic discovery of patterns in biosequences., Journal of Computational Biology. 5:2 1998, pp 277-303. ISSN 1066-5277. An earlier version is available as a PDF file and from the University of Bergen as Reports in Informatics no 113, [PubMed].

A. A. Letichevsky and D. R. Gilbert, `` A general theory of action languages'', Cybernetics and System Analysis, 1, 1998, pp 16-37. ISSN 0023-1274

A.A. Letichevsky and D.R. Gilbert, Agents and environments, In Proc. Conf. Ukrprog'98. Cybernetics Center, National Academy of Sciences of Ukraine, ISBN 966-02-0645-3, pp 225-232, Kiev, Ukraine, 1998.


David Gilbert, Can computational logic provide a paradigm for both the specification and implementation of concurrent systems?, Special Issue of ACM Computing Surveys, Volume 28, Number 2: Symposium on Models of Programming Languages and Computation. C. Hankin and HR Nielson, Eds, ISSN 0360-0300, 28:2 June 1996, pp 303-305

Maria Kambi and David Gilbert, Timetabling in Constraint Logic Programming, Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan 16-19 October 1996.

Archana Shankar, David Gilbert and Michael Jampel, Transient Analysis and Synthesis of Linear Circuits using Constraint Logic Programming, Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan 16-19 October 1996.

Nelson Donovon and David Gilbert, Economic Modelling using Constraint Logic Programming, Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan 16-19 October 1996.

L. Brim, D.R. Gilbert, J.-M. Jacquet, M. Kretinsky, A Process Algebra for Synchronous Concurrent Constraint Programming, Proceedings of ALP96: Fifth International Conference on Algebraic and Logic Programming, Michael Hanus and Mario Rodríguez-Artalejo (Editors), pp 165-178, Springer LNCS volume 1139, ISBN 3-540-61735-3, Aachen, Germany, September 24-27, 1996.

Michael Jampel, Jean-Marie Jacquet, David Gilbert and Sebastian Hunt, Transformations between HCLP and PCSP, Proceedings of CP96: Second International Conference on Principles and Practice of Constraint Programming, Eugene C. Freuder (Ed), Springer LNCS, ISBN 3-540-61551-2, pp 252-266, Cambridge, Massachusetts, USA, August 1996.

Archana Shankar, David Gilbert and Michael Jampel, Transient Analysis of Linear Circuits using Constraint Logic Programming, Proceedings of PACT96: Practical Application of Constraint Technology, The Practical Applications Company Ltd, pp 221-247, ISBN 0 9525554 2 5, 1996.


David Gilbert and Christopher Hogger and Jirí Zlatuska, Transforming specifications of observable behaviour into programs, Fourth International Workshop on Logic Programming Synthesis and Transformation (LOPSTR94), proceedings published by Springer-Verlag, L. Fribourg (ed), 1994.


David Gilbert and Chris Hogger, Logic for representing and implementing knowledge about system behaviour, Proceedings of the International Summer School on Advanced Topics in Artificial Intelligence, Springer-Verlag Lecture Notes in Artificial Intelligence No. 617, V Marik, O Stepankova and R Trappl (Eds), pp 42-49, Prague July 1992.


David Gilbert. Specifying Concurrent Systems using Logic, FORTE89 - Formal Description Techniques 1989, Vancouver, Canada, December 1989, published in Formal Description Techniques II, S. T. Vuong (Ed), pp 245-260, North-Holland 1990.

David Gilbert. Specification and Implementation of Concurrent Systems using PARLOG, Workshop on Specification and Verification of Concurrent Systems, organised by BCS-FACS, 6-8 July, 1988 Stirling, Scotland. Published by Springer Verlag 1990.


David Gilbert. A LOTOS to PARLOG Translator, FORTE88 - Formal Description Techniques 1988, Stirling August 1988, published in Formal Description Techniques, Ken Turner (Ed), pp 31-44, North-Holland 1989.


David Gilbert. PARLOG: a tutorial introduction, Current trends in Parallel Processing and Supercomputing, organised by the Belgian Institute for Automatic Control. November 19-20, Antwerp, 1987.

David Gilbert. Executable LOTOS: Using PARLOG to Implement an FDT, in Protocol Specification, Testing, and Verification VII, pp 281-295, H. Rudin and C.H. West (Eds), North-Holland 1987.

Contributions to edited books

David Gilbert, Curriculum development in Informatics in Lithuania, in Innovations in the Teaching of Computing 2: Improving the Quality of Teaching and Learning, Chapter 5, pp 43-50, ed M. Smith, SEDA, ISBN 0 946815 04 6, 1995.

David Gilbert and Chris Hogger, Deriving logic programs from observations, Constructing Logic Programs, ed Jean-Marie Jacquet, pp 113-126, ISBN 0 471 93789 4, John Wiley, 1993.

David Gilbert Multicultural Mathematics, in Education in a Multicultural Society, pp 97-104, M. Straker-Wells (Ed), Bell and Hyman 1984.