University of Dundee

Professor Geoff Barton

Protein and nucleic acid sequence analysis and function prediction
Position: 
Professor of Bioinformatics
Address: 
College of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 385860, int ext 85860
Email: 

Research

The completion in June 2000 of the first draft of the 3 Billion bases of DNA in the Human Genome was the most public demonstration that molecular biology had become a data intensive science. In today's “post-genome era” the DNA sequence of Human and other organisms is only the tip of an iceberg of data that includes information on gene expression (transcriptomics), protein expression (proteomics) and protein structure (structural genomics). These experimental techniques produce prodigious amounts of data that can only be organised, compared, understood and exploited to further scientific understanding and to cure disease by the development and application of advanced computational methods.

Bioinformatics is the research field that seeks to find computational ways of understanding biological systems. The subject is very broad and ranges from research in statistics and computer science, through software engineering and database development, to applications in specific biological systems. The possible biological applications are equally broad, from the study of populations through molecular structure and interactions, to simulations of metabolic and signalling processes. 

Our work draws on and contributes to computer science, software engineering and statistics on one side and many aspects of modern biological research on the other.  We publish our work both in conventional journals and as software packages and on-line resources accessible from our website: www.compbio.dundee.ac.uk.  Many of our techniques and databases are widely used by the biological research community, these include JPred, a service for protein secondary structure prediction that performs up to 100,000 predictions a month for scientists worldwide and Jalview, a protein sequence analysis workbench that is installed on at least 55,000 computers in over 100 countries and is started more than 250,000 times per year.  Our core research interests have long centered on the analysis and prediction of protein structure and function, but in recent years we have turned our attention to the problems of interpreting large and diverse biological datasets as well as the analysis of small RNAs.  We now collaborate extensively with “wet lab” scientists and clinicians across a broad range of biological domains from plants through model organisms (e.g. Dictyostelium, chicken, Drosophila and mouse) to individual humans and human disease.  Our group focuses in particular on the design of experiments and the interpretation of large datasets from proteomics and deep RNA/DNA sequencing to address questions in basic science and their clinical applications.

Addressing the specific biological problems important to each biological research area suggest gaps in our understanding of how proteins or other biological molecules function and so prompts us to perform new general studies. In turn these lead to the development of new and improved predictors that we can apply to the specific systems of interest to our wet-lab colleagues.

A more comprehensive description of our work can be found on the group web site www.compbio.dundee.ac.uk  together with links to our web-accessible software, databases and downloads.   For a complete publication list see our page on Google Scholar.

Publications

  1. MacKenzie, K. F., Clark, K., Naqvi, S., McGuire, V. A., Noehren, G., Kristariyanto, Y., van den Bosch, M., Mudaliar, M., McCarthy, P. C., Pattison, M. J., Pedrioli, P. G., Barton, G. J., Toth, R., Prescott, A., and Arthur, J. S., PGE(2) induces macrophage IL-10 production and a regulatory-like phenotype via a protein kinase A-SIK-CRTC3 pathway. J Immunol, 2013. 190(2): p. 565-77.
  2. Tibarewal, P., Zilidis, G., Spinelli, L., Schurch, N., Maccario, H., Gray, A., Perera, N. M., Davidson, L., Barton, G. J., and Leslie, N. R., PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Sci Signal, 2012. 5(213): p. ra18.
  3. Sherstnev, A., Duc, C., Cole, C., Zacharaki, V., Hornyik, C., Ozsolak, F., Milos, P. M., Barton, G. J., and Simpson, G. G., Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol, 2012. 19(8): p. 845-52.(co-communicating author with G. G. Simpson)
  4. Scott, M. S., Ono, M., Yamada, K., Endo, A., Barton, G. J., and Lamond, A. I., Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res, 2012. 40(8): p. 3676-88.
  5. Pohler, E., Mamai, O., Hirst, J., Zamiri, M., Horn, H., Nomura, T., Irvine, A. D., Moran, B., Wilson, N. J., Smith, F. J., Goh, C. S., Sandilands, A., Cole, C., Barton, G. J., Evans, A. T., Shimizu, H., Akiyama, M., Suehiro, M., Konohana, I., Shboul, M., Teissier, S., Boussofara, L., Denguezli, M., Saad, A., Gribaa, M., Dopping-Hepenstal, P. J., McGrath, J. A., Brown, S. J., Goudie, D. R., Reversade, B., Munro, C. S., and McLean, W. H., Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Nat Genet, 2012.
  6. Muramoto, T., Cannon, D., Gierlinski, M., Corrigan, A., Barton, G. J., and Chubb, J. R., Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A, 2012. 109(19): p. 7350-5.
  7. Miranda-Saavedra, D., Gabaldon, T., Barton, G. J., Langsley, G., and Doerig, C., The kinomes of apicomplexan parasites. Microbes Infect, 2012. 14(10): p. 796-810.
  8. Troshin, P. V., Procter, J. B., and Barton, G. J., Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. Bioinformatics, 2011. 27(14): p. 2001-2.
  9. Troshin, P. V., Postis, V. L., Ashworth, D., Baldwin, S. A., McPherson, M. J., and Barton, G. J., PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities. BMC Res Notes, 2011. 4: p. 48.
  10. Sugden, C., Ross, S., Annesley, S. J., Cole, C., Bloomfield, G., Ivens, A., Skelton, J., Fisher, P. R., Barton, G., and Williams, J. G., A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation. Dev Biol, 2011. 353(2): p. 290-301.
  11. Scott, M. S., Troshin, P. V., and Barton, G. J., NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics, 2011. 12: p. 317.
  12. Scott, M. S., Boisvert, F. M., Lamond, A. I., and Barton, G. J., PNAC: a protein nucleolar association classifier. BMC Genomics, 2011. 12: p. 74.
  13. Overton, I. M., van Niekerk, C. A., and Barton, G. J., XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins, 2011. 79(4): p. 1027-33.
  14. Overton, I. M., Graham, S., Gould, K. A., Hinds, J., Botting, C. H., Shirran, S., Barton, G. J., and Coote, P. J., Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol, 2011. 5: p. 68.
  15. Overton, I. M. and Barton, G. J., Computational approaches to selecting and optimising targets for structural biology. Methods, 2011. 55(1): p. 3-11.
  16. Ono, M., Scott, M. S., Yamada, K., Avolio, F., Barton, G. J., and Lamond, A. I., Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res, 2011. 39(9): p. 3879-91.
  17. Gkikopoulos, T., Singh, V., Tsui, K., Awad, S., Renshaw, M. J., Scholfield, P., Barton, G. J., Nislow, C., Tanaka, T. U., and Owen-Hughes, T., The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J, 2011. 30(10): p. 1919-27.
  18. Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J. L., Barton, G. J., and Owen-Hughes, T., A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science, 2011. 333(6050): p. 1758-60.
  19. Boisvert, F. M., Ahmad, Y., Gierlinski, M., Charriere, F., Lamont, D., Scott, M., Barton, G., and Lamond, A. I., A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol Cell Proteomics, 2011.
  20. van Koningsbruggen, S., Gierlinski, M., Schofield, P., Martin, D., Barton, G. J., Ariyurek, Y., den Dunnen, J. T., and Lamond, A. I., High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell, 2010. 21(21): p. 3735-48.
  21. Scott, M. S., Boisvert, F. M., McDowall, M. D., Lamond, A. I., and Barton, G. J., Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res, 2010. 38(21): p. 7388-99.
  22. Remenyi, J., Hunter, C. J., Cole, C., Ando, H., Impey, S., Monk, C. E., Martin, K. J., Barton, G. J., Hutvagner, G., and Arthur, J. S., Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochem J, 2010. 428(2): p. 281-91.
  23. Procter, J. B., Thompson, J., Letunic, I., Creevey, C., Jossinet, F., and Barton, G. J., Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods, 2010. 7(3 Suppl): p. S16-25.
  24. Ono, M., Yamada, K., Avolio, F., Scott, M. S., van Koningsbruggen, S., Barton, G. J., and Lamond, A. I., Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol Biol Cell, 2010. 21(9): p. 1569-84.
  25. Oke, M., Carter, L. G., Johnson, K. A., Liu, H., McMahon, S. A., Yan, X., Kerou, M., Weikart, N. D., Kadi, N., Sheikh, M. A., Schmelz, S., Dorward, M., Zawadzki, M., Cozens, C., Falconer, H., Powers, H., Overton, I. M., van Niekerk, C. A., Peng, X., Patel, P., Garrett, R. A., Prangishvili, D., Botting, C. H., Coote, P. J., Dryden, D. T., Barton, G. J., Schwarz-Linek, U., Challis, G. L., Taylor, G. L., White, M. F., and Naismith, J. H., The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics, 2010. 11(2): p. 167-80.
  26. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and Barton, G. J., Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics, 2009. 25(9): p. 1189-91.
  27. Scott, M. S., Avolio, F., Ono, M., Lamond, A. I., and Barton, G. J., Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol, 2009. 5(9): p. e1000507.
  28. McDowall, M. D., Scott, M. S., and Barton, G. J., PIPs: human protein-protein interaction prediction database. Nucleic Acids Res, 2009. 37(Database issue): p. D651-6.
  29. Martin, D. M., Miranda-Saavedra, D., and Barton, G. J., Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res, 2009. 37(Database issue): p. D244-50.
  30. Izquierdo, L., Schulz, B. L., Rodrigues, J. A., Guther, M. L., Procter, J. B., Barton, G. J., Aebi, M., and Ferguson, M. A., Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J, 2009. 28(17): p. 2650-61.