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Research Interests
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Research Interests
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.
We are 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).
We also research and develop e-Science and Grid technology to tackle problems in biological data analysis, simulation, and integration, and are interested in how the biological sciences can, in turn, drive developments in computing science. In particular, we are developing Grid technology for data integration, computational modelling and comparative genomics.
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.
More recently, 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. You can see some of the preliminary results in the work of our iGEM team 2008 and iGEM team 2009.
I have now re-established dedicated wet-lab facilities in collaboration with the Institute for Cell and Molecular Biosciences to allow the implementation of our computational designs, with a particular focus on synthetic biology applied to B. subtilis.
Much of the group's research is supervised jointly by Prof. Wipat and Dr. Jen Hallinan.
Funded Projects (past and present)
| APTAMEMS-ID | Detecting infectious organisms using a concerted approach using genomics, bioinformatics, molecular engineering and nano-enabled bio-MEMS technologies | Keith Flanagan | EPSRC | 2009-2011 |
| CISBAN | Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN) | In Computing Science: Cedric Simillion, Morgan Taschuk and Allyson Lister. See here for a complete staff list | BBSRC/EPSRC | 2005-2010 |
| ONDEX | A Data integration platform for Systems Biology | In Computing Science: Matthew Pocock, Jochen Wielle |
BBSRC | 2008-2011 |
| ComparaGrid | ComparaGrid aims to research and develope a GRID-based system to capture the details and semantics of relationships between genomic data both within and across species, facilitating complex ad-hoc queries to integrate and compare information across data sources and facilitate data integration for comparative genomics | At Newcastle: Matthew Pocock, The Newcastle Statistical Bioinformatics Research Group | BBSRC | 2005-2008 |
| Microbase | We are developing a generic system for scheduling compute and data intensive tasks in bioinformatics using Grid technology. The technology has been applied to the development of a comparative genomic system for bacterial genomes. | Keith Flanagan, Matthew Pocock, Pete Lee and Paul Watson | BBSRC |
2003 - 2007 |
| myGrid | Producing personalised research environments for the e-Scientist, Molecular Biologist & Bioinformatician using the Grid |
EPSRC |
2002-2007 | |
| Microbial Metagenomics |
Investigating the metagenome of marine microbial communities | NERC | 2005-2007 | |
| DIMP | Distributed data integration for microbial phenotypic inference | Tracy Craddock and Non-Linear Dynamics | EPSRC (CASE) | 2003-2006 |
| Modelling the adipocyte proteome in diseased states |
Nick Morris, Frank Gibson and Non-Linear Dynamics | BBSRC (CASE) | 2003-2006 | |
| SARGE and Petri Nets | Simulated Annealing to Realise GEnetic networks. Modelling regulatory pathways using Petri nets |
Olly shaw and Jason Steggles | BBSRC | 2002-2005 |
Anil Wipat is a member of the Computing Science Data Intensive Systems group, the North East Regional e-Science Centre, the Digital Research Institute, the Institute for Ageing and Health and the Institute for Cell and Molecular Biosciences