Professor David Westhead

BA, Cambridge; DPhil, Oxford; MA
Professor of Bioinformatics
Institute of Molecular and Cellular Biology

Background: Post doctoral work at Zeneca plc, Proteus Molecular Design Ltd. and European Bioinformatics Institute with Professor Janet Thornton FRS. Appointed Lecturer in Bioinformatics 1998.

Office: Garstang 10.127a
Phone: +44(0) 113 34 33116
Email: email address for Professor David Westhead 

Centre membership: The Astbury Centre for Structural Molecular Biology

Lab: Leader of the Westhead_DR group

You can read more about Professor Westhead's interests here:
www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=DRW
www.bioinformatics.leeds.ac.uk/

Publications

List Professor Westhead's Publications


BALSAMIC. A protein surface colour coded by local shape index, a key quantity used in the matching algorithms

TOPS. The figure shows the folding topology of an immunoglobulin light chain. The peptide chain follows the connecting lines between triangular symbols starting at the amino terminus (N) and ending at the carboxy terminus (C). The variable domain is N1-C2 and the constant domain is N2-C3. The triangles represent b strands: upward pointing triangles represent strands oriented out of the plane of the page and downward pointing triangles oriented into the plane

Research Interests

Bioinformatics: the use of computational methods to advance biological understanding

Bioinformatics has become increasingly important in recent years as experimental methods have advanced and begun to produce enormous quantities of data. Automated methods of DNA sequencing are now able to sequence large quantities of DNA very quickly, and sequencing projects now aim to sequence whole genomes. The database of known protein three-dimensional structures now contains more than 18000 entries. New methods for examining gene expression and the protein content of cells and tissues now starting to provide large quantities of data. But, data is just data. Research in this group is concerned with the development of computational methods whose aim is to make the best possible use of these databases in our efforts to advance biological knowledge and understanding.

 

Current Projects

Several current projects are given below:

  1. Protein functional site and surface matching for prediction of function from 3D structure. This project uses novel methods from computer vision research and graph theory to compare protein functional sites structures. An illustration of a protein surface for comparison is shown above.
  2. TOPS Protein folding topology database. This project is building a database of efficient, abstract descriptors of protein folds (see figure below) for use in fast database searching and machine learning. The ultimate aim is the creation of new methods to predict protein fold and function from sequence.
  3. Amyloid fibril formation. We have built a database of mutations associated with amyloid fibril formation and disease and research is now focusing on the prediction of structural properties influencing this process.
  4. Single nucleotide polymorphisms. We are developing novel machine learning based methods (using decision trees and support vector machines) to predict the functional/phentotypic consequences of SNPs.
  5. Microarray data analysis. Microarray based gene expression data is is now flooding in from local collaborating groups. We are working to build repositories for this data and to extract new biological knowledge from it. Particular projects involved the plant Arabidopsis thaliana and human data associated with cancer.
  6. Metabolic reconstruction. In collaboration with Dr G. McConkey we are developing new ways to reconstruct metabolic networks from genome sequence data and applying this to the malaria parasite. This work will lead ultimately to the discovery of new targets for therapeutic intervention.
 

Studentship information

Principal interests:

  • Bioinformatics: the use of computational methods to advance biological understanding

Undergraduate project topics:

  • Bioinformatics of amyloid fibril formation
    Keywords: Bioinformatics, databases, medical applications
    (Computer/Literature)
  • In silico sequence analysis
    Keywords: Bioinformatics, sequence analysis
    (Computer)
  • DNA microarray data analysis
    Keywords: Bioinformatics, microarrays, gene expression, functional genomic
    (Literature)

Postgraduate studentship areas:

  • Bioinformatics from Genome Sequence to Structure, Function and Expression

See also: