Our
people
Professor David Westhead
Title
Professor of BioinformaticsPhone
0113 34(33116)Address
Institute of Molecular and Cellular BiologyFaculty of Biological Sciences,Garstang Building,University of LeedsBHRC Role
Director, Bioinformatics Technology Group
Research Interests
Bioinformatics, systems biology, high-throughput data analysis, molecular networks, regulatory networks, machine learning, metabolic networks, single nucleotide polymorphisms, protein interactions, prediction methods, evolution of networks.
About
First degree (class I) in Natural Sciences (Physics and Theoretical Physics), University of Cambridge, 1988. D.Phil (Theoretical Solid State Physics), University of Oxford, 1992. Industrial Scientist Positions with ICI (1992-1993) and Proteus (1993-1996). European Bioinformatics Institute (1996-1998). University of Leeds, Lecturer (1998-2002), Senior Lecturer (2002-2006), Professor (2006-). BBSRC Research Development Fellow (2005-2008).
The Westhead group pursues a programme of bioinformatics research spanning fundamental work on methods development to applied studies, the latter in collaboration with experimental groups generating or working with large genomic datasets. Fundamental methods development has focused on machine learning and statistical methods, including decision trees (Bioinformatics 2003 19:2199-2209; Human Mutation 2009 30:485-492) to predict the functional consequences of mutations; hidden Markov models (Nucl. Acids Res. 2005 33:1399-1409) for genome sequence and metabolic network analysis; and, Bayesian networks (BNs) (Nature Biotech 200624:51-53; J Mol. Biol. 2006 362:365-386; BMC Systems Biology 2009 3:85; Plant J. 2010 61:713-721) for the prediction of gene function and transcriptional networks. Much of the work with experimental groups has been focused on transcriptional regulation, including studies of plant GATA transcription factors (Plant J. 2007 143: 941-958) and the mammalian REST factor (Nucl. Acids Res. 2006 34:3862-3877),using microarrays and genome sequence data. More recently, we have been involved extensively in the analysis of data from high-throughput ‘new generation’ sequencing methods, including analysing small RNAs in plants (RNA 2009 15:1012-1020).
Collaboration
Current collaborations with the Bonifer and Tooze groups at LIMM involve extensive analysis of ChIP-chip and microarray expression data (Nucl. Acids Res. 2010, 38(16) 5336-5350), and Chip-seq data, in haemopoietic cells in the context of cellular differentiation and leukaemia. We are developing novel methods to analyse single strand break data derived by sequencing with the Bonifer group and collaborating with several groups in the analysis of RNA-seq data. In the area of metabolic network analysis we collaborate with Dr. G. A. McConkey on the malaria parasite and drug target discovery.
Grants Awarded
Current grants are listed below
Bonifer C and Westhead DR. Establishment of new generation sequencing technology aimed at investigating epigenetic alterations in pre-leukaemic and leukaemic cells of individual patients. Candlelighters Foundation. August 2008-July 2010. £150k.
Bonifer C and Westhead DR. The role of the transcription factor Sp1 in embryonic macrophage development. MRC ref. G0901579:93427. £513k. July 2010 – 2013.
Bonifer C, Gottgens B, Lacaud G, Kouskoff V, Westhead DR. Establishment of the haemopoietic transcriptional programme: from systems approaches to molecular mechanisms. BBSRC: BB/I001220/1 April 2011-2016 (approx £4.5M).
Related Links
Astbury Centre for Structural Molecular Biology
Bioinformatics at Leeds
