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David Gavaghan

Personal photo - David Gavaghan
Professor David Gavaghan
Professor of Computational Biology

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Biography

David Gavaghan received his undergraduate degree in Mathematics from Durham University in 1986. From there he moved to the University of Oxford where he gained an MSc in Numerical Analysis and Mathematical Modelling in 1987 and a D.Phil in the Development of Parallel Numerical Algorithms in 1991. Since then he has been working in the field of Mathematical and Computational Modelling and has established and heads the Computational Biology Group which is based principally within the Department of Computer Science. In 2002 he was awarded substantial funding from the EPSRC to establish the Life Science Interface Doctoral Training Programme. Further programmes in Systems Biology (funded in 2007) and an industrial programme in Systems Approaches to Biomedical Science (funded in 2009) have since been added, and the Doctoral Training Centre is now based in the Rex Richards Building in the heart of the University's South Parks Road Science campus. In October 2004 he was appointed Professor of Computational Biology within the Computing Laboratory (now Department of Computer Science). His research interests are in the mathematical modelling of physiological and biological systems, and in the development of robust approaches to the development of computational science software that will result in fully tested and reliable (open source) codes.  

 

Research Interests

David Gavaghan leads the Computational Biology Group based primarily within the Department of Computer Science at the University of Oxford. His research is interdisciplinary and involves application of mathematical and computational techniques to problems in biomedicine, and in the associated basic sciences. A strong emphasis is placed on solving real-world problems and providing meaningful and practical help to scientific co-workers, and all of the work is therefore conducted in collaboration with internationally leading clinical and experimental groups, both within the UK and overseas.   David's core research revolves around the modelling of physiological and biological systems, and associated measurement techniques. Current application areas include cardiac and cancer modelling, electrochemical measurement techniques, and cell-based approaches in systems biology. The computational complexity of these research problems has resulted in a long-standing interest (starting with his D.Phil research) in the use of state-of-the-art computing facilities, and the development of the necessary computational and software development infrastructure, to support the research scientist. This interest has led to a strong involvement in the UK e-Science programme, through projects such as the EPSRC e-Science Pilot Project in Integrative Biology, and has led on to involvement in large scale EU projects such as the preDiCT project which is developing computational approaches and infrastructures to model the cardiotoxicity of potential new drugs, and most recently a collaborative project with University College London and Microsoft Research in Cambridge which will develop an in silico environment to support systems level modelling in biology and ecology.     

He has also been involved in the Chaste (cancer, heart and soft tissue environment) software development since its inception as part of the Integrative Biology project. Full details are available on the Chaste website. Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. The package is being developed by a team mainly based in the Computational Biology Group at the Department of Computer Science, University of Oxford, and development draws on expertise from software engineering, high performance computing, mathematical modelling and scientific computing.  

Current sources of Funding:

  • EPSRC
  • EU Framework 7
  • BBSRC
  • Industry (Fujitsu, GE Healthcare, Microsoft Research, GSK, AstraZeneca)

D.Phil Funding available

The Doctoral Training Centre has around 40 D.Phil studentships available annually across a range of interdisciplinary areas including Computational Biology (this includes a small number available to international students). Please follow this link for details.


Selected Publications

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Ten simple rules for effective computational research

Osborne J.M. Bernabeu M.O. Bruna M. Calderhead B. Cooper J. Dalchau N. Dunn S−J. Fletcher A.G. Freeman R. Groen D. Knapp B. McInerny G.J. Mirams G.R. Pitt−Francis J. Sengupta B. Wright D.W. Yates C.A. Gavaghan D.J. Emmott S. and C. Deane

In PLoS Computational Biology. Vol. 10. No. 3. Pages e1003506. 2014.

Variability in high−throughput ion channel screening data and consequences for cardiac safety assessment

Ryan C. Elkins‚ Mark R. Davies‚ Stephen J. Brough‚ David J. Gavaghan‚ Yi Cui‚ Najah Abi−Gerges and Gary R. Mirams

In Journal of Pharmacological and Toxicological Methods. Vol. 68. No. 1. Pages 112−122. 2013.

Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge

Kylie A. Beattie‚ Chris Luscombe‚ Geoff Williams‚ Jordi Munoz−Muriedas‚ David J. Gavaghan‚ Yi Cui and Gary R. Mirams

In Journal of Pharmacological and Toxicological Methods. Vol. 68. No. 1. Pages 88−96. 2013.

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