Faculty of Biological Sciences

Prof David Westhead

MA, Cambridge; DPhil, Oxford; PhD - 1992
Professor of Bioinformatics
School 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.

Contact:  Garstang 10.127a | +44(0) 113 34 33116 | email address for  

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

Research Interests

Bioinformatics: the use of computational methods to advance biological understanding

The group is interested in prediction methods for biological problems based on machine learning and statistical methods. Recently we have worked on predicting protein structure, protein-protein interaction sites, gene function and the functional effects of single nucleotide polymorphisms. Another major interest is functional genomics and systems biology, where we have been concerned with predicting molecular networks (particularly metabolism in parasites for drug target applications) using genome sequence data, and the use of large genomic data sets (DNA microarrays, proteomics etc) in gene function and gene network prediction.  More recently we have worked extensively with new generation sequencing data in the context of genetic regulatory network prediction.

 

Faculty Research and Innovation


Studentship information

Undergraduate project topics:

  • The evolution of blood (up to 4 students)
  • Host-parasite interactions as drug targets?
  • Cancer as an inhomogeneous disease

Postgraduate studentship areas:

  • Genetic regulatory network discovery from new generation sequencing data
  • Malaria systems biology
  • Machine learning from high-throughput biomolecular data

See also:

Admin roles

External Examiner (taught course): London (Birkbeck)
Faculty Research & Innovation Committee
FBS Equality and Diversity Committee
FBS Exective Committee
FBS Faculty Board
FBS Health and Safety Committee
FBS Strategy Group
FBS Student Recruitment Committee
Head of School
Wellcome Trust Module Manager

Modules managed

BIOL5274M - High-throughput technologies

Modules taught

BIOC1301 - Intro Inte Biochem Mol Process
BIOC1302 - Intro Biochem Practical Skills
BIOC1303 - Intro Biochem Problem Solving
BIOC2301 - Interm Integrated Biochemistry
BIOC2303 - Intermediate Biochem: Skills
BIOC3160 - Lab/Lit/Comp Research Project
BIOC3303 - Advanced Biochem: Skills
BIOL3306 - Biol Sciences Research Project
BIOL5274M - High-throughput technologies
BIOL5292M - Bioscience MSc Research Proj
BIOL5294M - MSc Bioscience Res Project Pro
BIOW5906X - Theory, computation and bioinformatics
BLGY2201 - Introduction to Bioinformatics

Centre membership: The Astbury Centre for Structural Molecular Biology

Group Leader Prof David Westhead  (Professor of Bioinformatics)

Bioinformatics: the use of computational methods to advance biological understanding 


Dr Salam Assi  (Visiting Research Fellow)

Dr Alastair Droop  (Visiting Research Fellow)


Postgraduates

Josie Hayes  
Nicole Kerrison  
Shola Richards  
Chulin Sha  
Nisar Shar  
Girish Tampi  
Francis Isidore Totanes  
Fatin Zainul Abidin  

Stead LF; Thygesen H; Westhead DR; Rabbitts P Using common variants to indicate cancer genes. Int J Cancer -, 2014
DOI:10.1002/ijc.28951
View abstract

Gilmour J; Assi SA; Jaegle U; Kulu D; van de Werken H; Clarke D; Westhead DR; Philipsen S; Bonifer C A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification. Development 141 2391-2401, 2014
DOI:10.1242/dev.106054
View abstract

Care MA; Cocco M; Laye JP; Barnes N; Huang Y; Wang M; Barrans S; Du M; Jack A; Westhead DR; Doody GM; Tooze RM SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity. Nucleic Acids Res 42 7591-7610, 2014
DOI:10.1093/nar/gku451
View abstract

Care MA; Barrans S; Worrillow L; Jack A; Westhead DR; Tooze RM A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma. PLoS One 8 e55895-, 2013
DOI:10.1371/journal.pone.0055895
View abstract

Ptasinska A; Assi SA; Mannari D; James SR; Williamson D; Dunne J; Hoogenkamp M; Wu M; Care M; McNeill H; Cauchy P; Cullen M; Tooze RM; Tenen DG; Young BD; Cockerill PN; Westhead DR; Heidenreich O; Bonifer C Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding. Leukemia 26 1829-1841, 2012
DOI:10.1038/leu.2012.49
View abstract

Barrans SL; Crouch S; Care MA; Worrillow L; Smith A; Patmore R; Westhead DR; Tooze R; Roman E; Jack AS Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome. Br J Haematol 159 441-453, 2012
DOI:10.1111/bjh.12045
View abstract

Lichtinger M; Ingram R; Hannah R; Müller D; Clarke D; Assi SA; Lie-A-Ling M; Noailles L; Vijayabaskar MS; Wu M; Tenen DG; Westhead DR; Kouskoff V; Lacaud G; Göttgens B; Bonifer C RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis. EMBO J 31 4318-4333, 2012
DOI:10.1038/emboj.2012.275
View abstract

Cocco M; Stephenson S; Care MA; Newton D; Barnes NA; Davison A; Rawstron A; Westhead DR; Doody GM; Tooze RM In Vitro Generation of Long-lived Human Plasma Cells JOURNAL OF IMMUNOLOGY 189 5773-5785, 2012
DOI:10.4049/jimmunol.1103720

Leddin M; Perrod C; Hoogenkamp M; Ghani S; Assi S; Heinz S; Wilson NK; Follows G; Schonheit J; Vockentanz L; Mosammam AM; Chen W; Tenen DG; Westhead DR; Gottgens B; Bonifer C; Rosenbauer F Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells BLOOD 117 2827-2838, 2011
DOI:10.1182/blood-2010-08-302976

Stead LF; Wood IC; Westhead DR KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels BIOINFORMATICS 27 2181-2186, 2011
DOI:10.1093/bioinformatics/btr365

Bradford JR; Needham CJ; Tedder P; Care MA; Bulpitt AJ; Westhead DR GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data PLANT J 61 713-721, 2010
DOI:10.1111/j.1365-313X.2009.04097.x

Doody GM; Care MA; Burgoyne NJ; Bradford JR; Bota M; Bonifer C; Westhead DR; Tooze RM An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression NUCLEIC ACIDS RES 38 5336-5350, 2010
DOI:10.1093/nar/gkq268

Stead LF; Wood IC; Westhead DR KvDB; Mining and Mapping Sequence Variants in Voltage-Gated Potassium Channels HUM MUTAT 31 908-917, 2010
DOI:10.1002/humu.21295

Tedder PMR; Bradford JR; McConkey GA; Bulpitt AJ; Westhead DR PlasmoPredict: a gene function prediction website for Plasmodium falciparum TRENDS PARASITOL 26 107-110, 2010
DOI:10.1016/j.pt.2009.12.004

Forth T; McConkey GA; Westhead DR MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format BIOINFORMATICS 26 2352-2353, 2010
DOI:10.1093/bioinformatics/btq425

Tedder PMR; Bradford JR; Needham CJ; McConkey GA; Bulpitt AJ; Westhead DR Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum BIOINFORMATICS 26 2431-2437, 2010
DOI:10.1093/bioinformatics/btq450

Yu JT; Guo MZ; Needham CJ; Huang YC; Cai L; Westhead DR Simple sequence-based kernels do not predict protein-protein interactions BIOINFORMATICS 26 2610-2614, 2010
DOI:10.1093/bioinformatics/btq483

Whitaker JW; McConkey GA; Westhead DR The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes GENOME BIOL 10 -, 2009
DOI:10.1186/gb-2009-10-4-r36

Whitaker JW; Westhead DR; McConkey GA Alio intuitu: the automated reconstruction of the metabolic networks of parasites TRENDS PARASITOL 25 396-397, 2009
DOI:10.1016/j.pt.2009.06.001

Whitaker JW; McConkey GA; Westhead DR Prediction of horizontal gene transfers in eukaryotes: approaches and challenges (vol 37, pg 792, 2009) BIOCHEM SOC T 37 1145-1145, 2009

Care MA; Bradford JR; Needham CJ; Bulpitt AJ; Westhead DR Combining the Interactome and Deleterious SNP Predictions to Improve Disease Gene Identification HUM MUTAT 30 485-492, 2009
DOI:10.1002/humu.20917

Webb EC; Westhead DR The transcriptional regulation of protein complexes; a cross-species perspective GENOMICS 94 369-376, 2009
DOI:10.1016/j.ygeno.2009.08.003

Needham CJ; Manfield IW; Bulpitt AJ; Gilmartin PM; Westhead DR From gene expression to gene regulatory networks in Arabidopsis thaliana BMC SYST BIOL 3 -, 2009
DOI:10.1186/1752-0509-3-85

Tedder P; Zubko E; Westhead DR; Meyer P Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA RNA 15 1012-1020, 2009
DOI:10.1261/rna.1517209

Whitaker JW; Letunic I; McConkey GA; Westhead DR metaTIGER: a metabolic evolution resource NUCLEIC ACIDS RES 37 D531-D538, 2009
DOI:10.1093/nar/gkn826

Gaskell EA; Smith JE; Pinney JW; Westhead DR; McConkey GA A Unique Dual Activity Amino Acid Hydroxylase in Toxoplasma gondii PLOS ONE 4 -, 2009
DOI:10.1371/journal.pone.0004801

Whitaker JW; McConkey GA; Westhead DR Prediction of horizontal gene transfers in eukaryotes: approaches and challenges BIOCHEMICAL SOCIETY TRANSACTIONS 37 792-795, 2009
DOI:10.1042/BST0370792

Wambua L; Mcconkey G; Westhead DR Discovery of Novel Drug Targets Against Pathogenic Protozoa: The Promise of Metabolic Reconstruction INFECT GENET EVOL 9 375-375, 2009

Adamo A; Pinney JW; Kunova A; Westhead DR; Meyer P Heat Stress Enhances the Accumulation of Polyadenylated Mitochondrial Transcripts in Arabidopsis thaliana PLOS ONE 3 -, 2008
DOI:10.1371/journal.pone.0002889

Westhead DR; Manfield IW; Needham CJ Bioinformatic approaches to biological systems., 2008

Liu B; Westhead DR; Boyett MR; Warwicker J Modelling the pH-dependent properties of Kv1 potassium channels. J Mol Biol 368 328-335, 2007
DOI:10.1016/j.jmb.2007.02.041
View abstract

Needham CJ; Bradford JR; Bulpitt AJ; Westhead DR A primer on learning in Bayesian networks for Computational Biology PLoS Computational Biology 3:e129 1409-1416, 2007

Care MA; Needham CJ; Bulpitt AJ; Westhead DR Deleterious SNP prediction: be mindful of your training data! BIOINFORMATICS 23 664-672, 2007
DOI:10.1093/bioinformatics/btl649

Pinney JW; Papp B; Hyland C; Warnbua L; Westhead DR; McConkey GA Metabolic reconstruction and analysis for parasite genomes TRENDS PARASITOL 23 548-554, 2007
DOI:10.1016/j.pt.2007.08.013

Manfield IW; Devlin PF; Jen CH; Westhead DR; Gilmartin PM Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family PLANT PHYSIOL 143 941-958, 2007
DOI:10.1104/pp.106.090761

Garrow AG; Westhead DR A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins PROTEINS 69 8-18, 2007
DOI:10.1002/prot.21439

Mardia KV; Nyirongo VB; Green PJ; Gold ND; Westhead DR Bayesian refinement of protein functional site matching BMC BIOINFORMATICS 8 -, 2007
DOI:10.1186/1471-2105-8-257

Johnson R; Gamblin RJ; Ooi L; Bruce AW; Donaldson IJ; Westhead DR; Wood IC; Jackson RM; Buckley NJ Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication NUCLEIC ACIDS RES 34 3862-3877, 2006
DOI:10.1093/nar/gkl525

Manfield IW; Jen CH; Pinney JW; Michalopoulos I; Bradford JR; Gilmartin PM; Westhead DR Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis NUCLEIC ACIDS RES 34 W504-W509, 2006
DOI:10.1093/nar/gkl204

Hyland C; Pinney JW; McConkey GA; Westhead DR metaSHARK: a WWW platform for interactive exploration of metabolic networks NUCLEIC ACIDS RES 34 W725-W728, 2006
DOI:10.1093/nar/gkl196

Needham CJ; Bradford JR; Bulpitt AJ; Westhead DR Inference in Bayesian networks NAT BIOTECHNOL 24 51-53, 2006

Bradford JR; Needham CJ; Bulpitt AJ; Westhead DR Insights into protein-protein interfaces using a Bayesian network prediction method J MOL BIOL 362 365-386, 2006
DOI:10.1016/j.jmb.2006.07.028

Jen CH; Manfield IW; Michalopoulos I; Pinney JW; Willats WGT; Gilmartin PM; Westhead DR The Arabidopsis co-expression tool ((ACT)): a WWW-based tool and database for microarray-based gene expression analysis PLANT J 46 336-348, 2006
DOI:10.1111/j.1365-313X.2006.02681.x

Needham CJ; Bradford JR; Bulpitt AJ; Care MA; Westhead DR Predicting the effect of missense mutations on protein function: analysis with Bayesian networks BMC BIOINFORMATICS 7 -, 2006
DOI:10.1186/1471-2105-7-405

Mardikian S; Gillet VJ; Jackson RM; Westhead DR CINF 68-Studying the effects of individual interaction energies in a variety of protein-ligand complexes ABSTR PAP AM CHEM S 232 -, 2006

Mardikian S; Gillet VJ; Jackson RM; Westhead DR Using multiobjective optimization to study the strengths of different interaction energies in protein-ligand complexes ABSTR PAP AM CHEM S 232 411-411, 2006

Taib M; Pinney JW; Westhead DR; McDowall KJ; Adams DJ Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus ARCH MICROBIOL 184 78-81, 2005
DOI:10.1007/s00203-005-0028-x

Bradford JR; Westhead DR Improved prediction of protein-protein binding sites using a support vector machines approach BIOINFORMATICS 21 1487-1494, 2005
DOI:10.1093/bioinformatics/bti242

Garrow AG; Agnew A; Westhead DR TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins NUCLEIC ACIDS RES 33 W188-W192, 2005
DOI:10.1093/nat/gki384

Jen CH; Michalopoulos I; Westhead DR; Meyer P Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol 6 R51-, 2005
DOI:10.1186/gb-2005-6-6-r51
View abstract

Torrance GM; Gilbert DR; Michalopoulos I; Westhead DR Protein structure topological comparison, discovery, and matching service Bioinformatics 21 2537-2538, 2005
DOI:10.1093/bioinformatics/bti331
View abstract

Pinney JW; Shirley MW; McConkey GA; Westhead DR metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella NUCLEIC ACIDS RES 33 1399-1409, 2005
DOI:10.1093/nar/gki285

Nyirongo V; Mardia KV; Westhead DR EM algorithm, bayesian and distance approaches to matching functional sites In Quantitative Biology, Shape Analysis, and Wavelets , 2005

Sharma-Oates A; Quirke P; Westhead DR TmaDB: a repository for tissue microarray data BMC BIOINFORMATICS 6 -, 2005
DOI:10.1186/1471-2105-6-218

Sadowski MI; Parish JH; Westhead DR Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation BIOSYSTEMS 81 247-254, 2005
DOI:10.1016/j.biosystems.2005.05.001

Garrow AG; Agnew AM; Westhead DR TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins BMC Bioinformatics 6 pp.56-, 2005
DOI:10.1186/1471-2105-6-56
View abstract

Sharma-Oates A; Quirke P; Westhead DR TmaDB: A tissue microarray database Journal of Pathology 204 pp.51-, 2004

Michalopoulos I; Torrance GM; Gilbert DR; Westhead DR TOPS: an enhanced database of protein structural topology NUCLEIC ACIDS RES 32 D251-D254, 2004
DOI:10.1093/nar/gkh060

McConkey GA; Pinney JW; Westhead DR; Plueckhahn K; Fitzpatrick TB; Macheroux P; Kappes B Annotating the Plasmodium genome and the enigma of the shikimate pathway TRENDS PARASITOL 20 60-65, 2004
DOI:10.1016/j.pt.2003.11.001

Gilbert DR; Westhead DR; Viksna J Techniques for comparison, pattern matching and pattern In Artificial Intelligence and Heuristic Methods in Bioinformatics , 2003

Mardia KV; Taylor CC; Westhead DR Structural bioinformatics revisited In Stochastic geometry, biological structure and images , 2003

Krishnan VG; Westhead DR A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 19 2199-2209, 2003
View abstract

Siepen JA; Radford SE; Westhead DR Beta edge strands in protein structure prediction and aggregation. Protein Sci 12 2348-2359, 2003
DOI:10.1110/ps.0306003
View abstract

Williams A; Gilbert DR; Westhead DR Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing. Protein Eng 16 913-923, 2003
DOI:10.1093/protein/gzg116
View abstract

Campbell SJ; Gold ND; Jackson RM; Westhead DR Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol 13 389-395, 2003
View abstract

Mardia KV; Nyirongo V; Westhead DR Protein matching using amino acids information In Stochastic geometry, biological structure and images , 2003

Bradford JR; Westhead DR Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem PROTEIN SCI 12 2099-2103, 2003
DOI:10.1110/ps.0306303

Dalton J; Michalopoulos I; Westhead DR Calculation of helix packing angles in protein structures Bioinformatics 19 1298-1299, 2003
DOI:10.1093/bioinformatics/btg141
View abstract

Pinney JW; Westhead DR; McConkey GA Petri Net representations in systems biology BIOCHEMICAL SOCIETY TRANSACTIONS 31 1513-1515, 2003

Siepen JA; Radford SE; Westhead DR β edge strands in protein structure prediction and aggregation Protein Science 12 2348-2359, 2003
DOI:10.1110/ps.03234503
View abstract

Mardia KV; Westhead DR New major challenges in bioinformatics In Statistics of large datasets - functional and image data, bioinformatics and data mining , 2002

Siepen JA; Westhead DR The fibril one on-line database: Mutations, experimental conditions and trends associated with amyloid fibril formation Protein Science 11 1862-1866, 2002
DOI:10.1110/ps.0204302

Westhead DR; Parish JH; Twyman RM Instant Notes in Bioinformatics, 2002

Williams A; Westhead DR Sequence relationships in the legume lectin fold and other jelly rolls PROTEIN ENG 15 771-774, 2002

Gilbert D; Westhead DR; Viksna J; Thornton J A computer system to perform structure comparison using TOPS representation of protein structure Computers&Chemistry 26 23-30, 2001
DOI:10.1016/S0097-8485(01)00096-1

Pickering SJ; Bulpitt AJ; Efford N; Gold ND; Westhead DR AI-based algorithms for protein surface comparisons COMPUT CHEM 26 79-84, 2001
View abstract

Haider S; Westhead DR; Davies LA; Hopkins PM; Boyett MR; Harrison SM Inhibitory action of halothane on the transient outward K+ channel: Potential sites of interaction with the protein. BIOPHYS J 78 221A-221A, 2000

Gilbert D; Westhead DR; Nagano N; Thornton J Motif-based searching in TOPS protein topology databases Bioinformatics 15 317-326, 1999
View abstract

Westhead DR; Slidel TWF; Flores TPJ; Thornton JM Protein structural topology: Automated analysis and diagrammatic representation Protein Science 8 897-904, 1999

Baxter CA; Murray CW; Clark DE; Westhead DR; Eldridge MD Flexible docking using Tabu search and an empirical estimate of binding affinity Proteins : Structure, Function, and Genetics 33 367-382, 1998
View abstract

Westhead DR; Hatton DC; Thornton JM An atlas of protein topology cartoons available on the World-Wide Web Trends in Biochemical Sciences 23 35-36, 1998

Westhead DR; Thornton JM Protein structure prediction. Curr Opin Biotechnol 9 383-389, 1998
View abstract

Luscombe NM; Milburn D; Jones S; Karmirantzou M; Thornton JM; Laskowski RA; Westhead DR New tools and resources for analysing protein structures and their interactions Acta Crystallographica Section D: Biological Crystallography 54 1132-1138, 1998
DOI:10.1107/S0907444998007318
View abstract

Westhead DR; Clark DE; Murray CW Comparison of heuristic search algorithms for molecular docking Journal of Computer - Aided Molecular Design 11 209-228, 1997

Murray CW; Clark DE; Auton TR; Firth MA; Li J; Sykes RA; Waszkowycz B; Westhead DR; Young SC PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology Journal of Computer-Aided Molecular Design 11 193-207, 1997
View abstract