Biomedical Informatics, Systems and Synthetic Biology
This research theme is concerned with the management, analysis and interpretation of a variety of biological and medical data to reveal hidden secrets in the health/disease process. Research topics include bioinformatics, systems biology, synthetic biology, and clinical decision support systems.
Selected Publications
- Oehm, S., Gilbert, D., Tauch, A., Stoye, J. and Goesmann, A., Comparative Pathway Analyzer - CPA - A Web Server for Comparative Analysis, Clustering and Visualization of Metabolic Networks in Multiple Organisms, Nucleic Acids Research, in press.
- Park, S.H., Reyes, J.A., Gilbert, D., Kim, J.W. and Kim, S., Prediction of Protein-Protein Interaction Types Using Association Rule Based Classification, BMC Bioinformatics, in press.
- Z Wang, X Liu, Y Liu, J Liang and V Vinciotti "An Extended Kalman Filtering Approach to Modelling Nonlinear Dynamic Gene Regulatory Networks via Short Gene Expression Time Series", IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
- Breitling, R., Gilbert, D., Heiner, M. and Orton, R., A Structured Approach for the Engineering of Biochemical Network Models, Illustrated for Signalling Pathways, Briefings in Bioinformatics 9 (5) : 404-421 (2008)
- Z Wang, F Yang, D Ho, S Swift, A Tucker and X Liu (2008), "Stochastic Dynamic Modelling of Short Gene Expression Data", IEEE Transactions on Nanobioscience, 7:44-55.
- Jourdan, F., Breitling, R., Barrett, M. and Gilbert, D., MetaNetter: Inference and Visualization of High-resolution Metabolomic Networks, Bioinformatics 24 (1) : 143-145, (2008)
- Orton, R., Sturm, O., Gormand, A., Kolch, W. and Gilbert, D., Computational Modelling Reveals Feedback Redundancy Within the EGFR/ERK Signalling Pathway, IET Systems Biology 2 (4) : 173-184, (2008)
- Veeramalai, M. and Gilbert, D., A Novel Method for Comparing Topological Models of Protein Structures Enhanced with Ligand Information, Bioinformatics 24 (23) : 2698-2708, (2008)
- Al-Shahib, A., Breitling, R. and Gilbert, D., Predicting Protein Function by Machine Learning on Amino Acid Sequences - A Critical Evaluation, BMC Genomics 8 : 78, (2007)
- M Hirsch, S Swift and X Liu "Optimal Search Space for Clustering Gene Expression Data via Consensus", Journal of Computational Biology, 14(10):1327-1341, (2007)
- Nebel, J.-C., Herzyk, P. and Gilbert, D., Automatic Generation of 3D Motifs for Classification of Protein Binding Sites, BMC Bioinformatics 8 : 321, (2007)
- Viksna, J. and Gilbert, D., Assessment of the Probabilities for Evolutionary Structural Changes in Protein Folds, Bioinformatics 23 (7) : 832-841, (2007)
- V Vinciotti, X Liu, R Turk, E de Meijer and P t Hoen, "Exploiting the Full Power of Temporal Gene Expression Profiling through a New Statistical Test: Application to the Analysis of Muscular Dystrophy Data", BMC Bioinformatics, 7:183, (2006).
- S Khalid, K Fraser, M Khan, P Wang, X Liu and S Li, "Analysing Microarray Data using the Multi-functional Immune Ontologiser", Journal of Integrative Bioinformatics, 3(2):25, (2006). http://journal.imbio.de/index.php?paper_id=25
- V Vinciotti, A Tucker, P Kellam and X Liu, "The Robust Selection of Predictive Genes via a Simple Classifier", Applied Bioinformatics, 5:1-12, (2006).
- R Khanin, V Vinciotti and E Wit, " Reconstructing repressor protein levels from expression of gene targets in E.Coli", PNAS 103(49):18592-6, 2006.
- N Strouthidis, V Vinciotti, A Tucker, S Gardiner, D Crabb, and D F Garway-Heath, "Structure and Function in Glaucoma: The Relationship Between a Functional Visual Field Map and an Anatomical Retinal Map", Investigative Opthalmology and Visual Science, in press.
- V Vinciotti, R Khanin, D DAlimonte, X Liu, N Cattini, G Bucca, O de Jesus, J Rasaiyaah, C Smith, P Kellam and E Wit, " An Experimental Evaluation of Loop versus Reference Design for Two-Channel Microarrays", Bioinformatics, 21:492-501, (2005).
- (2005) Morrison, J., Breitling, R., Higham, D. and Gilbert, D., GeneRank: Using Search Engine Technology for the Analysis of Microarray Experiments, BMC Bioinformatics 6 : 233
- (2005) Orton, R., Sturm, O., Vyshemirsky, V., Calder, M., Gilbert, D. and Kolch, W., Computational Modelling of the Tyrosine Receptor Kinase Activated MAPK Pathway, Biochemical Journal 392 : 249-261
- (2005) Torrance, G.M., Gilbert, D.R., Michalopoulos, I. and Westhead, D.R., Protein Structure Topological Comparison, Discovery and Matching Service, Bioinformatics 21 (10) : 2537-2538
- A Tucker, V Vinciotti, X Liu and D Garway-Heath, "A Spatio-Temporal Bayesian Network Classifier for Understanding Visual Field Deterioration", Artificial Intelligence in Medicine, 34:163-177, (2005).
- S Swift, A Tucker, V Vinciotti, N Martin, C Orengo, X Liu and P Kellam, " Consensus Clustering and Functional Interpretation of Gene Expression Data ", Genome Biology, 5:R94, (2004).
- K Fraser, P O'Neill, Z Wang and X Liu, "Copasetic Analysis: A Framework for the Blind Analysis of Microarray Imagery", Systems Biology, 1:190-196, (2004).
- (2004) Michalopoulos, I., Torrance, G.M., Gilbert, D.R. and Westhead, D.R., TOPS: An Enhanced Database of Protein Structural Topology, Nucleic Acids Research 32 : D251-D254
- H Critchlow, A Payne, and D Griffin, "Genes and Proteins Involved in the Control of Meiosis", Cytogenetic and Genome Research 105:4-10, (2004).
- P O'Neill, G Magoulas, and X Liu, "Improved Processing of Microarray Data using Image Reconstruction", IEEE Transactions on Nanobioscience, 2(4), 176-183, (2003)
- Deville, Y., Gilbert, D., van Helden, J. and Wodak, S., An Overview of Data Models for the Analysis of Biochemical Pathways, Briefings in Bioinformatics 4 (3) : 246-259
- S Swift and X Liu, "Predicting Glaucomatous Visual Field Deterioration Through Short Multivariate Time Series Modelling", Artificial Intelligence in Medicine
