UNIVERSITY of GLASGOW

Computing at Glasgow University
 

Publications for '- no address book entry -' ordered by Year. (84)

2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1996 1995 1994 1993 1992 1990 1989 1987 1984

2008

BioNessie - A Grid Enabled Biochemical Network Simulator
Liu,X.
Ajayi,O. Gu,X. Gilbert,D. Jiang,J. Sinnott,R.O. Proceedings of the 6th International HealthGrid conference, Chicago, USA, June 2008. [More Details].

A Case Study in Model-driven Synthetic Biology
Gilbert,D.R. Heiner,M. Rosser,S. Fulton,F. Gu,X. Trybilo,M. Biologically Inspired Cooperative Computing: BICC 2008 IFIP [More Details].

Petri Nets for Systems and Synthetic Biology.
Heiner,M. Gilbert,D.R. Donaldson,R. In M Bernardo, P Degano, and G Zavattaro (Eds.): SFM 2008, Springer LNCS 5016, 2008. pp 215–264 Springer [More Details].

Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions
Reyes,J.A. Gilbert,D.R. Proc Data Integration and the Life Sciences DILS 2008. LNCS/LNBI LNCS, Springer [More Details].

2007

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets
Gilbert,D.R. Heiner,M. Lehrack,S. In proceedings CMSB 2007 (Computational Methods in Systems Biology), Springer-Verlag in LNCS/LNBI Volume 4695 Springer Verlag
[More Details].

A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets
Gilbert,D.R. Heiner,M. Lehrack,S. DCS Technical Report Series pp 36 Dept of Computing Science, University of Glasgow [More Details].

Prediction of protein-protein interactions using one-class classification methods and integrating diverse data.
Rayes,J.A. Gilbert,D. Journal of Integrative Bioinformatics, 4(3):77, 2007. [More Details].

Assessment of the probabilities for evolutionary structural changes in protein folds
Viksna,J. Gilbert,D.R. Bioinformatics 23(7):832-841; doi:10.1093/bioinformatics/btm022 pp 832-841 Oxford University Press [More Details].

MetaNetter: inference and visualization of high-resolution metabolomic networks
Jourdan,F. Breitling,R. Barrett,M.P. Gilbert,D.R. Bioinformatics 2007; doi: 10.1093/bioinformatics/btm536 Oxford University Press [More Details].

Automatic generation of 3D motifs for classification of protein binding sites
Nebel,J.C. Herzyk,P. Gilbert,D. BMC Bioinformatics 2007, 8:321 (30 Aug 2007) [More Details].

2006

A Lock-and-Key model for Protein-Protein interactions
Morrison,J.L. Breitling,R. Higham,D.J. Gilbert,D.R. Bioinformatics, 2006 Aug 15;22(16) pp 2012-9 Oxford University Press [More Details].

Bioinformatics and Constraints
Backofen,R. Gilbert,D. Handbook of Constraint Programming, Editors Francesca Rossi, Peter van Beek and Toby Walsh, Chapter 26 pp 905-944 Elsevier Science [More Details].

From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis
Gilbert,D. Heiner,M. International Conference on the Applications and Theory of Petri Nets (ICAPTN) 2006, LNCS 4024 / 2006 pp 181-200 Springer [More Details].

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

Computational methodologies for modelling, analysis and simulation of signalling networks
Gilbert,D. Fuß,H. Gu,X. Orton,R. Robinson,S. Vyshemirsky,V. Kurth,M.J. Downes,C.S. Dubitzky,W. Briefings in Bioinformatics Oxford University Press [More Details].

Computational methodologies for modelling, analysis and simulation of signalling networks
Gilbert,D. Fuss,H. Gu,X. Orton,R. Robinson,S. Vyshemisrsky,V. Kurth,M.J. Downes,C.S. Dubitzky,W. Briefings in Bioinformatics, doi:10.1093/bib/bbl043 pp doi:10.1093/bib/bbl043 Oxford University Press [More Details].

2005

From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis
Gilbert,D. Heiner,M. DCS Technical Report Series pp 23 Dept of Computing Science, University of Glasgow [More Details].

GeneRank: Using search engine technology for the analysis of microarray experiments
Morrison,J. Breitling,R. Higham,D.J. Gilbert,D. BMC Bioinformatics 2005, 6:233 [More Details].

Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence
Al-Shahib,A. Breitling,B. Gilbert,D. Applied Bioinformatics [More Details].

Computational Modelling of the Receptor Tyrosine Kinase Activated MAPK Pathway
Orton,R.J. Sturm,O. Vyshemirsky,V. Calder,M. Gilbert,D.R. Kolch,W. Biochemical Journal, Volume 392 pp 249--261 [More Details].

When kinases meet mathematics: the systems biology of MAPK signalling
Kolch,W. Calder,M. Gilbert,D. FEBS Lett 579 pp 1891-1895 [More Details].

Protein Structure Topological Comparison, Discovery and Matching Service
Torrance,G.M. Gilbert,D.R. Michalopoulos,I. Westhead,D.R. Bioinformatics, 21(10):2537-2538 [More Details].

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

Fast Similarity Search for 3D Protein Structures using Topological Pattern Matching based on Spatial Relations
Park,S.H. Ho-Ryu,K. Gilbert,D. International Journal of Neural Systems, 15:4 pp 287-296 [More Details].

FrankSum: New Feature Selection Method for Protein Function Prediction
Al-Shahib,A. Breitling,R. Gilbert,D. International Journal of Neural Systems, 15:4 pp 259-275 World Scientific [More Details].

2004

Isolation and expression of the reverse transcriptase component of the canis familiaris telomerase ribonucleoprotein (canTERT) Gene
Nasir,L. Gault,E. Campbell,S.
Veeramalai,M. Gilbert,D. McFarlane,R. Munro,A. Argyle,D.J. Gene. 2004 Jul 7;336(1):105-13. [More Details].

TOPS: an enhanced database of protein structural topology,
Michalopoulos,I. Torrance,G.M. Gilbert,D.R. Westhead,D.R. Nucleic Acids Research 2004 pp v 32, Database issue D251-D254 Oxford University Press [More Details].

Grid Services Supporting the Usage of Secure Federated, Distributed Biomedical Data
Sinnott,R.O. Atkinson,M. Bayer,M. Berry,D. Dominiczak,A. Ferrier,M. Gilbert,D. Hanlon,N. Houghton,D. Hunt,E. White,D. Proceedings of UK e-Science All Hands Meeting, 31st August to 3rd September 2004, Nottingham, UK pp 135-138 EPSRC, UK [More Details].

MSAT: a Multiple Sequence Alignment tool based on TOPS
Ren,T. Veeramalai,M. Tan,A.C. Gilbert,D.R. Journal of Applied Bioinformatics, 3 (2-3): 149-158 [More Details].

Domain discovery method for topological profile searches in protein structures
Viksna,J. Gilbert,D. Torrance,G. Proceedings of the 15th International Conference on Genome Informatics GIW 2004 [More Details].

An Assessment of Feature Relevance in Predicting Protein Function from Sequence
Al-Shahib,A. He,C. Tan,A.C. Girolami,G. Gilbert,D.R. Proceedings of the Fifth International Conference on Intelligent Data Proceedings of the Fifth International Conference on Intelligent Data Engineering and Automated Learning (IDEAL'04). LNCS 3177 LNCS, Springer [More Details].

2003

MSAT: a Multiple Sequence Alignment tool based on TOPS
Ren,T. Veeramalai,M. Tan,A.C. Gilbert,D. Proceedings of the Biological Language Confernece 2003. Editors, J.Klein-Seetharaman, R.rosenfeld, R.Reddy pp 286-301 [More Details].

Ensemble machine learning on gene expression data from cancer classification
Tan,A.C. Gilbert,D. Applied Bioinformatics 2 (Supplement of the Proceedings of New Zeland Bioinformatics Conference Te Papa, Wellington, New Zeland. pp S75-S83 [More Details].

Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing.
Williams,A. Gilbert,D.R. Westhead,D.R. Protein Engineering 2003 Dec;16(12):913-23. pp v16, no.12 [More Details].

An empirical comparison of supervised machine learning techniques in bioinformatics
Tan,A.C. Gilbert,D. Proceedings of First Asia Pacific Bioinformatics Conference (APBC 2003) Adelaide Australia. Australian Computer Society. P.Chen (editor) Conferences in Research and Practice in Infomation Technology pp v.19 219-222 [More Details].

Multi-class Protein Fold Classification using a New Ensemble Machine Learning Approach
Tan,A.C. Gilbert,D. Deville,Y. Proceeding of the 14th International Conference on Genome Informatics (GIW 2003) editors M.Gribskov, M.Kanehisa, S.Miyano, T.Takagi pp 206-217 [More Details].

Integrative machine learning approach for multi-class SCOP protien fold classification
Tan,A.C. Gilbert,D. Deville,Y. GCB03: German Conference on Bioinformatics. (Editors) H.W.Mews, D.Frishman, V.Heun, S.Kramer pp 153-159 [More Details].

Techniques for comparison, pattern matching and pattern discovery: From sequences to protein topology
Gilbert,D. Westhead,D. Viksna,J. pp 128-147 IOS Press [More Details].

An Overview of Data Models for the Analysis of Biochemical Pathways, Briefings in Bioinformatics
Deville,Y. Gilbert,D. van Helden,J. Wodak,S. Briefings in Bioinformatics, pp 4:3 246-259 [More Details].

Protein structure comparison based on profiles of topological motifs: a feasible way to deal with information from negative examples
Visksna,J. Gilbert,D. Torrance,G. GCB03: German conference on Bioinformatics, 2003. Editors, H.W.Mews, D.Frishman, V.Heun, S.Kramer pp 159-165 [More Details].

2002

Computational Biology: the report of Dagstuhl Seminar 02471
Altman,R.
Gilbert,D. Lengauer,T. [More Details].

Graph-based analysis of metabolic networks
van Helden,J. Wernisch,L. Gilbert,D. Wodak,S. Foundation Workshop Volume 38: Bioinformatics and Genome Analysis. Editors: H.-W.Mewes, B.Weiss, H.Seidel Spriner-Verlag. [PubMed] pp 245-274 [More Details].

Bioinformatics tools for Protein Structure
Veeramalai,M. Gilbert,D. Bioinformatics World, Scientific Computing World,Issue 64. pp 12-15 [More Details].

Characterisation of FAD-family Folds using a Machine Learning Approach.
Tan,A.C. Gilbert,D. Tuson,A. [More Details].

2001

Characterisation of FAD-family Folds using a Machine Learning Approach
Tan,A.C. Gilbert,D. Tuson,A. To be appear in the Proceedings of International Conference on Bioinformatics, (InCOB 2002), Bangkok, Thailand. [Pre-print PS] [Pre-print PDF] [More Details].

Multi-agent Systems as Concurrent Constraint Processes
Brim,L. Gilbert,D. Jacquet,J.M. Kretinsky,M. 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,) pp 201 - 210 [More Details].

Pattern matching and pattern discovery algorithms for protein topologies, Algorithms in Bioinformatics
Viksna,J. Gilbert,D. First International Workshop, WABI 2001 Proceedings, LNCS 2149 (pre-publication version) pp 98-111 [More Details].

Topology-based protein structure comparison using a pattern discovery technique,
Gilbert,D. Westhead,D. Viksna,J. Thornton,J. Journal of Computers and Chemistry, 26:1 [Pre- publication version] [PubMed] pp 23-30 Academic Press [More Details].

Introduction to the Special Issue on Bioinformatics
Gilbert,D. Backofen,R. Roland,H. Yap,C. pp 139-139 [More Details].

Bioinformatics and Constraints
Backofen,R. Gilbert,D. [On-line abstract] [Pre-print]. pp 141-156 [More Details].

A Constraint Based Structure Description Language for Biosequences, Constraints
Eidhammer,I. Gilbert,D. Jonassen,I. Ratnayake,M. Grindhaug,S.H. pp 173-200 [More Details].

Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer
Schroeder,M. Gilbert,D. van Helden,J. Noy,P. Information Sciences 139 pp 19-57 Elsevier Science [More Details].

Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data, in Computational Biology
van Helden,J. Gilbert,D. Wernisch,L. Schroeder,M. Wodak,S. (Olivier Gascuel and Marie-France Sagot, Eds), LNCS 2006,[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) pp 147-163, [More Details].

2000

Topology-based protein structure comparison using a pattern discovery technique
Gilbert,D. Westhead,D. Viksna,J. Thornton,J. Proceedings of the AISB-00 Symposium on AI in Bioinformatics pp 11-17 Society for the Study of Artificial Intelligence and the Simulation of Behaviour [More Details].

Interactive visualisation and exploration of biological data,
Gilbert,D. Schroeder,M. van Helden,J. Second International Workshop on Biomolecular Informatics in conjunction with Fifth Joint Conference on Information Sciences, Atlantic City, New Jersey, USA. [More Details].

Interactive visualisation and exploration of relationships between biological objects,Trends in Biotechnology
Gilbert,D. Schroeder,M. van Helden,J. Trends in Biotechnology 18:12{203] [PubMed] pp 487-494 [More Details].

FURY: Fuzzy unification and resolution based on edit distance
Gilbert,D. Schroeder,M. BIBE: IEEE International Symposium on Bio-Informatics and Biomedical Engineering, November 8-10 2000. IEE Publications [More Details].

Concurrent Constraint Programming with Process Mobility
Gilbert,D. Palamidessi,C. CL2000 (Computational Logic 2000), J Lloyd et al. (Eds), Springer LNAI 1861,[postscript] [Acrobat] pp 463-477 Springer [More Details].

Bioinformatique et contraintes JFPLC2000:
Gilbert,D. Neuvièmes Journées Francophones de Programmation Logique et Programmation par Contraintes, (invited tutorial) [HTML] pp 11 [More Details].

Une technique déclarative pour filtrer des motifs topologiques de protéinesJFPLC2000
Gilbert,D. Westhead,D. Thornton,J. Yvon,K. Computational Biology (Olivier Gascule and Marie-France Sagot, Eds pp 165-185 Academic Press [More Details].

Representing and analysing molecular and cellular function in the computer
van Helden,J. Naim,A. Mancuso,R. Eldridge,M. Wernisch,L. Gilbert,D. Wodak,S.J. Journal of Biological Chemistry [PubMed] pp v.381,no. 9-10: 921-35 [More Details].

1999

Motif-based searching in TOPS protein topology databases
Gilbert,D. Westhead,D. Nagano,N. Thornton,J. Bioinformatics, 15:4. [PubMed] pp 317-326 [More Details].

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

The development of interactive algorithms for a mathematical environment,
Letichevsky,A.A. Kapitonva,J.V. Volkov,V.A. Chugayenko,A. Chomenko,V. Gilbert,D. Proceedings of CALCULEMUS 99, Electronic Notes in Theoretical Computer Science, http://www.elsevier.nl/locate/entcs. An extended version will be published in the Journal of Symbolic Computation. Academic Press [More Details].

1998

Approaches to the automatic discovery of patterns in biosequences
Brazma,A. Jonassen,I. Eidhammer,I.
Gilbert,D. Journal of Computational Biology. 5:2 An earlier version is available as a Bergen Reports in Informatics no 113. [PubMed] pp 277-303. [More Details].

A general theory of action languages A general theory of action languages
Letichevsky,A.A. Gilbert,D. Cybernetics and System Analysis, 1 pp 16-37 [More Details].

Agents and environments
Letichevsky,A.A. Gilbert,D. In Proc. Conf. Ukrprog'98. Cybernetics Center, National Academy of Sciences of Ukraine, Kiev, Ukraine pp 225-232 Academic Press [More Details].

1996

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

Timetabling in Constraint Logic Programming
Kambi,M. Gilbert,D. Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan [More Details].

Transient Analysis and Synthesis of Linear Circuits using Constraint Logic Programming
Shankar,A. Gilbert,D. Jampel,M. Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan [More Details].

Economic Modelling using Constraint Logic Programming
Donovon,N. Gilbert,D. Proceedings of INAP-96: Symposium and Exhibition on Industrial Applications of Prolog, Tokyo, Japan [More Details].

A Process Algebra for Synchronous Concurrent Constraint Programming
Brim,L. Gilbert,D. Jacquet,J-M. Kretinsky,M. Proceedings of ALP96:Fifth International Conference on Algebraic and Logic Programming, Michael Hanus and Mario Rodríguez-Artalejo (Editors), Springer LNCS volume 1139, Aachen, Germany pp 165-178 Springer [More Details].

Transformations between HCLP and PCSP
Jampel,M. Jacquet,J-M. Gilbert,D. Hunt,S. Proceedings of CP96: Second International Conference on Principles and Practice of Constraint Programming, Eugene C. Freuder (Ed), Cambridge, Massachusetts, USA Academic Press [More Details].

Transient Analysis of Linear Circuits using Constraint Logic Programming
Shankar,A. Gilbert,D. Jampel,M. Proceedings of PACT96: Practical Application of Constraint Technology, The Practical Applications Company Ltd pp 221-247 Academic Press [More Details].

1995

Curriculum development in Informatics in Lithuania
Gilbert,D. Innovations in Teaching of Computing 2: Imporving the Quality of Teaching and Learning. Editor M Smith pp ch.5 43-50 [More Details].

1994

Transforming specifications of observable behaviour into programs
Gilbert,D. Hogger,C. Zlatuska,J. Springer Verlag [More Details].

1993

Deriving logic programs from observations
Gilbert,D. Hogger,C. Constructing Logic Programs, Editor Jean-Marie Jacquet pp 113-126 Wiley [More Details].

1992

Logic for representing and implementing knowledge about system behaviour
Gilbert,D. Hogger,C. 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), Prague pp 42-49 Springer Verlag [More Details].

1990

Specification and Implementation of Concurrent Systems using PARLOG
Gilbert,D. Workshop on Specification and Verification of Concurrent Systems, organised by BCS-FACS, 6-8 July, 1988 Stirling, Scotland. Published by Springer Verlag 1990. Academic Press [More Details].

Specifying Concurrent Systems using Logic
Gilbert,D. FORTE89- Formal Description Techniques 1989, Formal Description Techniques II, Editor S.T. Vuong, North-Holland 1990. pp 245-260 [More Details].

1989

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

1987

PARLOG: a tutorial introduction
Gilbert,D. Current trends in Parallel Processing and Supercomputing, Belgian Institute for Automatic Control [More Details].

Executable LOTOS: Using PARLOG to Implement an EDT
Gilbert,D. Protocol Specification, Testing and Verification VII. Editors, H.Rudin, C.H.West, North Holland pp 281-295 [More Details].

1984

Multicultural Mathematics
Gilbert,D. Education in a Multicultural Society, Editor, M.Straker-Wells, Bell and Hyman pp 97-104 [More Details].