Professor of Integrative Bioinformatics
Research interests
- Bioinformatics
- Data integration
- Systems and synthetic biology
- Molecular biology of Bacillus subtilis
My group researches data integration in bioinformatics at various levels from the local integration of 'omics' datasets to form integrated functional networks, through to the integration of remote heterogeneous databases. We apply these data integration strategies to problems in Systems and Synthetic Biology.
The biological applications of our research are quite diverse ranging from microbiology and metagenomics, through to the mechanisms of human genetic disease and ageing. Traditionally we have a strong interest and background in microbial genomics and functional genomics particularly for Gram-positive microorganisms such as Bacillus and relatives.
We are applying our combined expertise in bioinformatics, data integration, evolutionary computation and microbial genomics to the problem of designing microbial systems, in the area of Synthetic Biology. Please see our project pages for more details.
We are also investigating approaches to facilitate an integrative and systems approach to biology, with a particular emphasis on ageing and nutrition, as part of the BBSRC/EPSRC funded Newcastle Centre for the Integrative and Systems Biology of Ageing and Nutrition (CISBAN).
Our research in e-Science, Grid and cloud computing technology allows us to tackle problems in biological data analysis, simulation, and integration. We are interested in how the biological sciences can, in turn, drive developments in computing science. In particular, we are developing Cloud computing technology for data integration, computational modelling and comparative genomics, with an emphasis on the analysis of metagenomic datasets.
Our group maintains wet-lab facilities in collaboration with the Institute for Cell and Molecular Biosciences to allow the implementation of our computational designs of biological systems, with a particular focus on synthetic biology applied to B. subtilis. One current focus of our research is on the development of synthetic quorum peptide mediated communication systems.
Opportunities to work in our group arise frequently. We recruit both computational and wet-lab researchers. Please visit the positions available link for details or send a CV to anil.wipat[theusualsymbol]ncl.ac.uk.
We gratefully acknowledge funding from a variety of sources, including the BBSRC, EPSRC, NERC and the Wellcome Trust.
Recent publications
Stadler L, Hoffmann T, Tomlinson D, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner S, Knowles M, Davis J, Ko Ferrigno P. (2011). Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and Applications of the SQT variant PEDS (in press).
Alcaraz N, Kucuk H, Weile J, Wipat A, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int. Math. (in press).
Weile, J., Pocock, M. Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E., Wilkinson, D., Lydall, D., Hallinan, J. S. & Wipat, A. (2011). Customisable views on semantically integrated networks for systems biology. Bioinformatics 27(9): 1299 - 1306.
Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T. & Wipat, A. (2011). Model annotation for synthetic biology: Automated model to sequence conversion. Bioinformatics. 2011 Apr 1;27(7):973-9.
Addinall SG, Holstein EM, Lawless C, Yu M, Chapman K, Banks AP, Ngo HP, Maringele L, Taschuk M, Young A, Ciesiolka A, Lister AL, Wipat A, Wilkinson DJ, Lydall D. (2011). Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects. PLoS Genet. 2011 Apr;7(4):e1001362. Epub 2011 Apr 7.
Contact Me
Physical: School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne, NE7 4RU.
Email: Anil.Wipat@newcastle.ac.uk
