Orton, RJ., Sturm, OE., Gormand, A., Kolch, W. and Gilbert, DR. (2008) 'Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway'. IET Systems Biology, 2 (4). pp. 173 - 183. ISSN: 1751-8849

Liu, X., Jiang, J., Ajayi, O., Gu, X., Gilbert, D. and Sinnott, R. (2008) 'BioNessieG - a grid enabled biochemical networks simulation environment', in Solomonides, T., Silverstein, JC., Saltz, J., Legré, Y., Kratz, M., Foster, I., Breton, V. and Beck, JR. et al. (eds.) Studies in Health Technology and Informatics. IOS PRESS. , 138. pp. 147 - 157. ISBN 13: 978-1-58603-874-8.

Reyes, JA. and Gilbert, D. (2008) 'Combining one-class classification models based on diverse biological data for prediction of protein-protein interactions', in Bairoch, A., Cohen-Boulakia, S. and Froidevaux, C. (eds.) Data Integration in the Life Sciences. Springer Berlin Heidelberg. , 5109/2008. pp. 177 - 191. ISBN 13: 9783540698272.

Oehm, S., Gilbert, D., Tauch, A., Stoye, J. and Goesmann, A. (2008) 'Comparative Pathway Analyzer - A web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms'. Nucleic Acids Research, 36 (suppl_2). pp. W433 - W437. ISSN: 0305-1048

Jourdan, F., Breitling, R., Barrett, MP. and Gilbert, D. (2008) 'MetaNetter: inference and visualization of high-resolution metabolomic networks'. Bioinformatics, 24 (1). pp. 143 - 145. ISSN: 1367-4803

Nebel, J-C., Herzyk, P. and Gilbert, DR. (2007) 'Automatic generation of 3D motifs for classification of protein binding sites'. BMC Bioinformatics, 8 (1). pp. 321. ISSN: 1471-2105

Gu, X., Gilbert, D., Higham, D. and Houslay, M. (2007) 'Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation)'. BMC Systems Biology, 1 (Supplement 1). ISSN: 1752-0509

Al-Shahib, A., Breitling, R. and Gilbert, DR. (2007) 'Predicting protein function by machine learning on amino acid sequences – a critical evaluation'. BMC Genomics, 8 (1). pp. 78 - 78. ISSN: 1471-2164

Park, SH., Gilbert, D. and Ryu, KH. (2007) 'Fast structural similarity search based on topology string matching'.5th Asia-Pacific Bioinformatics Conference (APBC2007). Hong Kong, Peoples Republic of China. 15 - 17 January. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO.. pp. 341 - 351. ISSN: 1751-6404

Al-Shahib, A., Gilbert, D. and Breitling, R. (2007) 'Discriminating microbial species using protein sequence properties and machine learning'. Springer Berlin Heidelberg. pp. 890 - 897. ISSN: 0302-9743

Viksna, J. and Gilbert, D. (2007) 'Assessment of the probabilities for evolutionary structural changes in protein folds'. Bioinformatics, 23 (7). pp. 832 - 841. ISSN: 1367-4803

Gilbert, D., Heiner, M. and Lehrack, S. (2007) 'A unifying framework for modelling and analysing biochemical pathways using Petri nets', in Calder, M. and Gilmore, S. (eds.) Computational Methods in Systems Biology. Springer Berlin Heidelberg. , 4695/2007. pp. 200 - 216. ISBN 13: 9783540751397.

Viksna, J. and Gilbert, DR. (2007) 'Assessment of the probabilities for evolutionary structural changes in protein folds.'. Bioinform., 23. pp. 832 - 841.

Reyes, JA. and Gilbert, D. (2007) 'Prediction of protein-protein interactions using one-class classification methods and integrating diverse data'. Journal of Integrative Bioinformatics, 4 (3). pp. 77. ISSN: 1613-4516

Gilbert, D. and Heiner, M. (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. 26 - 30 June. ATPN. pp. 181 - 200.

Morrison, JL., Breitling, R., Higham, DJ. and Gilbert, DR. (2006) 'A lock-and-key model for protein-protein interactions.'. Bioinformatics, 22 (16). pp. 2012 - 2019. ISSN: 1367-4803

Gilbert, D. and Heiner, M. (2006) 'From Petri nets to differential equations - An integrative approach for biochemical network analysis', in Donatelli, S. and Thiagarajan, PS. (eds.) Petri Nets and Other Models of Concurrency - ICATPN 2006. Springer Berlin Heidelberg. , 4024/2006. pp. 181 - 200. ISBN 10: 3-540-34699-6. ISBN 13: 9783540346999.

Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R. (2006) 'Analysis of signalling pathways using continuous time Markov chains', in Priami, C. and Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. Springer Berlin Heidelberg. , 4220/2006. pp. 44 - 67. ISBN 10: 3-540-45779-8. ISBN 13: 9783540457794.

Gilbert, D., Fuß, H., Gu, X., Orton, R., Robinson, S., Vyshemirsky, V., Kurth, MJ., Downes, CS. and Dubitzky, W. et al. (2006) 'Computational methodologies for modelling, analysis and simulation of signalling networks'. Briefings in Bioinformatics, 7 (4). pp. 339 - 353. ISSN: 1467-5463

Morrison, JL., Breitling, R., Higham, DJ. and Gilbert, DR. (2005) 'GeneRank: Using search engine technology for the analysis of microarray experiments'. BMC Bioinformatics, 6 (1). pp. 233. ISSN: 1471-2105

Park, SH., Ryu, KHO. and Gilbert, D. (2005) 'Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations'. International Journal of Neural Systems, 15 (4). pp. 287 - 296. ISSN: 0129-0657

Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R. (2005) 'Analysis of signalling pathways using the prism model checker'.3rd International Computational Methods in Systems Biology (CMSB 2005). University of Edinburgh. 3 - 5 April. University of Edinburgh. pp. 179 - 190.

Kolch, W., Calder, M. and Gilbert, D. (2005) 'When kinases meet mathematics: the systems biology of MAPK signalling'. FEBS Letters, 579 (8). pp. 1891 - 1895. ISSN: 0014-5793

Al-Shahib, A., Breitling, R. and Gilbert, D. (2005) 'FrankSum: new feature selection method for protein function prediction'. International Journal of Neural Systems, 15 (4). pp. 259 - 275. ISSN: 0129-0657

Orton, RJ., Sturm, OE., Vyshemirsky, V., Calder, M., Gilbert, DR. and Kolch, W. (2005) 'Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway'. Biochemical Journal, 392 (2). pp. 249 - 261. ISSN: 0264-6021

Al-Shahib, A., Breitling, R. and Gilbert, D. (2005) 'Feature selection and the class imbalance problem in predicting protein function from sequence'. Applied Bioinformatics, 4 (3). pp. 195 - 203. ISSN: 1175-5636

Torrance, GM., Gilbert, DR., Michalopoulos, I. and Westhead, DR. (2005) 'Protein structure topological comparison, discovery and matching service.'. Bioinformatics, 21 (10). pp. 2537 - 2538. ISSN: 1367-4803

Viksna, J., Gilbert, D. and Torrance, G. (2004) 'Domain discovery method for topological profile searches in protein structures'.International Conference on Genome Informatics( GIW 2004). Yokohoma. 14 - 17 December. Universal Academy Press. pp. 72 - 81. ISSN: 0919-9454

Thornton, JM., Gilbert, DR. and Brooksbank, C. (2004) 'ISMB/ECCB 2004 Organization'. Oxford University Press (OUP). pp. i3 - i5. ISSN: 1367-4803

Michalopoulos, I., Torrance, GM., Gilbert, DR. and Westhead, DR. (2004) 'TOPS: An enhanced database of protein structural topology'. Nucleic Acids Research, 32 (DATABASE ISS.). pp. 251D - 254. ISSN: 0305-1048

Nasir, L., Gault, E., Campbell, S., Veeramalai, M., Gilbert, D., McFarlane, R., Munro, A. and Argyle, DJ. et al. (2004) 'Isolation and expression of the reverse transcriptase component of the Canis familiaris telomerase ribonucleoprotein (dogTERT)'. Gene, 336 (1). pp. 105 - 113. ISSN: 0378-1119

Al-Shahib, A., He, C., Tan, AC., Girolami, M. and Gilbert, D. (2004) 'An assessment of feature relevance in predicting protein function from sequence', in Yang, ZR., Everson, R. and Yin, H. (eds.) Intelligent Data Engineering and Automated Learning – IDEAL 2004. Springer Berlin Heidelberg. , 3177/2004. pp. 52 - 57. ISBN 10: 3-540-22881-0. ISBN 13: 9783540228813.

Ren, T., Veeramalai, M., Tan, AC. and Gilbert, D. (2004) 'MSAT: a multiple sequence alignment tool based on TOPS'. Applied Bioinformatics, 3 (2-3). pp. 149 - 158. ISSN: 1175-5636

Tan, A., Gilbert, D. and Deville, Y. (2003) 'Multi-class protein fold classification using a new ensemble machine learning approach.'.14th International Conference on Genome Informatics (GIW 2003). Yokohama, Japan. 14 - 17 December. GIW. pp. 206 - 217.

Tan, AC., Gilbert, D. and Deville, Y. (2003) 'Integrative machine learning approach for multi-class SCOP protein fold classification'.German Conference on Bioinformatics (GCB 2003). Neuherberg. 12 - 14 October. GCB. pp. 153 - 159.

Jacquet, JM., Brim, L., Gilbert, D. and Křetínský, M. (2003) 'Coordination by means of synchronous and asynchronous communication in concurrent constraint programming'. Electronic Notes in Theoretical Computer Science, 68 (3). pp. 347 - 370. ISSN: 1571-0661

Tan, AC. and Gilbert, D. (2003) 'An empirical comparison of supervised machine learning techniques in bioinformatics'.First Asia Pacific Bioinformatics Conference (APBC 2003). Adelaide, Australia. 4 - 7 February. Australian Computer Society. pp. 219 - 222.

Gilbert, D., Westhead, D. and Viksna, J. (2003) 'Techniques for comparison, pattern matching and pattern discovery: from sequences to protein topology', in Frasconi, P. and Shamir, S. (eds.) Artificial intelligence and heuristic methods in bioinformatics. IOS PRESS. , 183. pp. 128 - 147. ISBN 10: 1-58603-294-1.

Deville, Y., Gilbert, D., van Helden, J. and Wodak, S. (2003) 'An overview of data models for the analysis of biochemical pathways (Abstract only)', in Priami, C. (ed.) Computational Methods in Systems Biology. Springer Berlin Heidelberg. , 2602/2003. pp. 174. ISBN 10: 3-540-00605-2. ISBN 13: 9783540006053.

Williams, A., Gilbert, D. and Westhead, DR. (2003) 'Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing'. Protein Engineering, 16 (12). pp. 913 - 923. ISSN: 0269-2139

Tan, AC., Gilbert, D. and Deville, Y. (2003) 'Multi-class protein fold classification using a new ensemble machine learning approach'. Genome Informatics, 14. pp. 206 - 217. ISSN: 0919-9454

Deville, Y., Gilbert, D., van Helden, J. and Wodak, SJ. (2003) 'An overview of data models for the analysis of biochemical pathways.'. Briefings in bioinformatics, 4 (3). pp. 246 - 259. ISSN: 1467-5463

Viksna, J., Gilbert, DR. and Torrance, GM. (2003) 'Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples.'. German Conference on Bioinformatics. pp. 159 - 165.

Tan, AC. and Gilbert, D. (2003) 'Ensemble machine learning on gene expression data for cancer classification'. Applied Bioinformatics, 2 (3 Suppl). pp. S75 - S83. ISSN: 1175-5636

Brim, L., Kretinsky, M., Jacquet, JM. and Gilbert, D. (2002) 'Modelling multi-agent systems as synchronous concurrent constraint processes'. Computing and Informatics, 21 (6). pp. 565 - 590. ISSN: 1335-9150

Tan, AC., Gilbert, D. and Tuson, A. (2002) 'Characterisation of FAD-family folds using a machine learning approach'.International Conference on Bioinformatics, (INCOB 2002). Bangkok, Thailand. INCOB.

Gilbert, D., Westhead, V., Viksna, J. and Thornton, J. (2001) 'A computer system to perform structure comparison using TOPS representations of protein structure'. Journal of Computers and Chemistry, 26 (1). pp. 23 - 30. ISSN: 0097-8485

Brim, L., Gilbert, D., Jacquet, JM. and Kretinsky, M. (2001) 'Multi-agent systems as concurrent constraint processes'.28th Conference on Current Trends in Theory and Practice of Informatics Piestany (SOFSEM 2001). Slovak Republic. 24 - 1 December. Springer-Verlag. pp. 201 - 210. ISSN: 0302-9743

Viksna, J. and Gilbert, D. (2001) 'Pattern matching and pattern discovery algorithms for protein topologies'.First International Workshop on Algorithms in BioInformatics BRICS. University of Aarhus, Denmark. 28 - 31 August. Springer. pp. 98 - 111. ISSN: 0302-9743

Backofen, R. and Gilbert, D. (2001) 'Bioinformatics and constraints'. Constraints, 6 (2/3). pp. 141 - 156. ISSN: 1383-7133

Eidhammer, I., Jonassen, J., Grindhaug, SH., Gilbert, D. and Ratnayake, M. (2001) 'A constraint based structure description language for Biosequences'. Constraints, 6 (2/3). pp. 173 - 200. ISSN: 1383-7133