REDIRECTING ....................

Julian Gough

FROM JANUARY

University of Bristol,
Department of Computer Science,
Merchant Venturers Building,
Woodland Road,
Bristol,
BS8 1UB,
UK


Reader in Computer Science
University of Bristol
gough@supfam.org
Public Key  (encryption)

Background

I did my undergraduate degree in joint hon.s Mathematics and Physics at the University of Bristol. Following that I gained my Phd from Cambridge University working with Cyrus Chothia in the "Theoretical and computational biology group". I then served as a research associate for the MRC Laboratory of Molecular Biology, before becoming a PMMB fellow at Stanford University working with Michael Levitt in "Computational and Structural Biology".

I am now a RIKEN Scientist with the GER group at the GSC and an Associate Professor at Tokyo Medical and Dental University.


Research

Bioinformatics

Although most of my research could fall under the umbrella of 'bioinformatics', the most informatics-specific part of the work is the SUPERFAMILY database which I created and continue to develop. Although the database provides several public services and resources, it was primarily created to answer scientific questions. It is thus central to both the methods developement and the biologically-driven directions in my research. Currently (May 2004) the software and data is licensed to over 400 institutions and the web-site is visited from about 250 different domains every day. The SUPERFAMILY papers already have over 100 citations between them.

Genome Analysis

I am intimately involved in the FANTOM mouse projects past and present.
One of the things provided by the SUPERFAMILY database is the most complete structural domain annotation of all genomes. This is driven by a desire to better understand evolution (see below), but a more obvious and immediate application is genome annotation. The structural assignments are used by most of the eukaryote genome projects and some of the smaller bacterial projects.

Protein Structure

I began my PhD thesis by working on protein structure analysis. I would say that my perspective is profoundly structural; much of my work is in some way related to the SCOP database, and I continue to interact with the authors. I submitted two automatic servers to the CASP5 structure prediction competition and take part in the ongoing LiveBench and Eva projects. In fact I have contributed my own SCOP-based assessment of the CAFASP3 and LiveBench templates.

Hidden Markov Models

Hidden Markov models (HMMs) are the underlying machinery which is used to produce most of the data which forms the basis of everything which is built upon it. Not only do I use HMMs extensively but I am interested in the development of new techniques and methods. I have written a chapter for a book on HMMs, and am intimately involved with Martin Madera's new work on HMM profile-profile comparison.

Gene Ontology

On the more functional side of things, I am developing a Gene Ontology (GO) classification for structural domains. This is ongoing work but the current working version is available here.

Evolution

Evolution is central to all aspects of biology. The ultimate purpose of all of my current and past work is to try to improve our understanding of the evolutionary processes at work at the level of proteins. Everything else revolves around forming the necessary tools to answer the questions.


Publications

  • Wilson, D., Madera, M., Vogel, C., Chothia, C., Gough, J. (2007) The SUPERFAMILY database in 2007: families and functions. Nucl. Acids Res. 35, D308-D313. PDF
  • Gough, J. (2006) Genomic scale sub-family assignment of protein domains. Nucl. Acids Res. 34(13) 3625-3633.PDF
  • Vinogradov, S.N., Hoogewijs, D., Bailly, X., Arredondo-Peter, R., Gough, J., Dewilde, S., Moens, L. and Vanfleteren, J.R. (2006). A phylogenomic profile of globins. BMC Evol Biol. 6:31. PDF
  • Liu, J., Gough, J., Rost, B. (2006). Distinguishing Protein-Coding from Non_coding RNAs through Support Vector Machines. PLoS Genetics 2(4), e29. PDF
  • Maeda, N., Kasukawa, T., Oyama, R., Gough, J., et al. (2006). Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. PLoS Geneteics 2(4), e62. PDF
  • Babu, M. M., Priya, M. L., Selvan, A. T., Madera, M., Gough, J. and Sankaran, K. (2006). A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol. 188(8), 2761-73. PDF
  • Carninci, P., Kasukawa, T., Katayama, S., Gough, J., et al. (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309(5740), 1559-63. PDF
  • Vinogradov, S.N., Hoogewijs, D., Bailly, X., Arrendondo-Peter, R., Guertin, M., Gough, J., Dewilde, S., Moens, L., Vanfleteren, J.R. (2005). Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sci USA 102(32), 11385-9. PDF
  • Gough, J. (2005). Convergent evolution of domain architectures (is rare). Bioinformatics 21(8), 1464-71. PDF
  • Mulder, N.J. et al. (2005) InterPro, progress and status in 2005. Nucl. Acids Res. 33, D201-5. PDF
  • Gough, J. (2004). Hidden Markov models: principles and applications. In Computational Genomics (Grant, R. ed.). Horizon scientific press. PDF
  • Gough, J. and Chothia, C. (2004). The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure 12, 917-25. PDF
  • Vogel, C., Berzuini, C., Bashton, M., Gough, J. and Teichmann, S.A. (2004) Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol. 336, 809-823. PDF
  • Madera, M., Vogel, C,, Kummerfeld, S.K., Chothia, C. and Gough, J. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 2004 Jan 1;32(1):D235-9. PDF
  • Gherardi, E., Youles, M.E., Miguel, R.N., Blundell, T.L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G. and Butler, P.J. Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl. Acad. Sci. U.S.A. 2003 100(21): 12039. PDF
  • Kanapin, A., Batalov, S., Davis, M.J., Gough, J., Grimmond, S., Kawaji, H., Magrane, M., Matsuda, H., Schonbach, C., Teasdale, R.D., and Yuan, Z. Mouse Proteome Analysis. Genome Res. 2003 13: 1335-1344. PDF
  • Kasukawa, T., Furuno, M., Nikaido, I., Bono, H., Hume, D.A., Bult, C., Hill, D.P., Baldarelli, R., Gough, J., Kanapin, A., Matsuda, H., Schriml, L.M., Hayashizaki, Y., Okazaki, Y., and Quackenbush, J.. Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System. Genome Res. 2003 13: 1542-1551. PDF
  • Chothia C, Gough J, Vogel C, Teichmann SA. Evolution of the protein repertoire. Science. 2003 Jun 13;300(5626):1701-3. PDF
  • Okazaki, Y. et al. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-73. PDF
  • Gough, J. (2002). The SUPERFAMILY database in structural genomics. Acta Crystalographica D, 2002 Nov; D58:1897-1900. PDF
  • Madera, M. and Gough, J.(2002). A comparison of hidden Markov model procedures for remote homology detection. Nucl. Acids Res., 2002 Oct 1;30(19):4321-4328. PDF
  • Hua SJ, Guo T, Gough J & Sun ZR. (2002) Proteins with alpha/beta Fold Class Have High Participation in Fusion Events. J. Mol. Biol., 2002 Jul 19;320(4):713-9. PDF
  • Jardine, O., Gough, J., Chothia, C., and Teichmann, T.(2001). Comparison of the Small Molecule Metabolic Pathways of Escherichia coli and Saccharomyces cerevisiae. Genome Res., 2002 Mar 8;12(6):916-29. PDF
  • Gough, J., Chothia, C.(2002).SUPERFAMILY:HMMs representing all proteins of known structure. SCOP sequence searches, alignments, and genome assignments. Nucl. Acids Res., 2002 Jan 1;30(1):268-72. PDF
  • Gough, J., Hughey ,R., Karplus ,K., and Chothia ,C.(2001). Assignment of genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001 Nov 2;313(4):903-19. PDF
  • Teichmann, S.A., Rison, S.C.G., Thornton, J.M., Riley, M., Gough, J. & Chothia, C. (2001) Small Molecule Metabolism: An Enzyme Mosaic. Trends Biotechnol., 2001 Dec;19(12):482-6. PDF
  • Gough, J. (2001). Hidden Markov models and their application to genome analysis in the context of protein structure. PhD thesis, 2001 Nov; Cambridge University. PDF
  • Teichmann, S.A., Rison, S.C.G., Thornton, J.M., Riley, M., Gough, J. & Chothia, C. (2001) The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli. J. Mol. Biol., Aug 24;311(4):693-708. PDF
  • Apic, G., Gough, J., and Teichmann, S.A.(2001). Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 310(2) 311-25. PDF
  • Apic, G., Gough, J., and Teichmann, S.A.(2001). An insight into domain combinations. Bioinformatics Suppl 1 83-89. PDF
  • Gough, J.,Chothia, C.,Karplus, K.,Barrett, C.,and Hughey, R.(2000).Optimal hidden Markov models for all sequences of known structure. In Currents in Computational Molecular Biology(Miyano S.,Shamir R., and Takagi T., eds), Universal Academy Press INC. 124-125. PDF
  • Conferences and meetings

  • (program committee) "ISMB/ECCB" Vienna, Austria, 21-25 Jul 2007
  • (program comittee) "ISMB" Fortaleza, Brazil, 6-10 Aug 2006
  • (speaker) "20th Pasteur Weizmann Symposium: Structural Biology" Paris, France 21-23 Jun 2006
  • (program committee) "ECCB" Madrid, Spain, 28 Sept- 1 Oct 2005
  • (program committee) "ISMB" Michigan, USA, 25-29 Jun 2005
  • (poster) "The 27th annual meeting of the Molecular Biology Society of Japan" Kobe, Japan, 8-11 Dec, 2004
  • (poster/referee) "ISMB/ECCB" Glasgow, Scotland, 31 July- 4 Aug 2004
  • (poster) "RECOMB 2004 Annual Conference on Computational Molecular Biology" San Diego, USA, 27-31 March 2004
  • (participant) "Transcriptome 2003" Tokyo, Japan, 16-19 November 2003
  • (poster) "CASP5: Fifth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction" Assilomar, California, U.S.A. 1-5 Dec, 2002
  • (speaker) "Functional Genomics" Vejle, Denmark 22-23 May, 2002
  • (speaker) "FANTOM2 Cherry Blossom meeting" RIKEN, Japan 1-5 May, 2002
  • (speaker) "Keystone symposium: Structural Genomics: From Gene Sequence to Function", Breckenridge, USA, January 5-11, 2002
  • (speaker) "CCP4 workshop: High-throughput Structure Determination", York, UK 4-5th January 2002
  • (speaker) "LMB graduate symposium", Hinxton Hall, Cambridge, UK, Nov 22 2001
  • (speaker) "FANTOM2 Typhoon meeting (Mouse cDNA collection)" RIKEN, Japan Oct 15-19, 2001
  • (speaker) "Cold Spring Harbor Laboratory/Wellcome Trust Conference: Genome Informatics", Hinxton Hall, Cambridge, UK August 8-12 , 2001
  • (poster) "9th International Conference on Intelligent Systems for Molecular Biology (ISMB)", Copenhagen, Denmark July 21-25, 2001
  • (speaker) "DIMACS Workshop on Protein Strucuture and Structural Genomics: Prediction, Determination, Technology and Algorithms", Rutgers, USA March 8-9, 2001
  • (participant) "From Gene to Structure to Function" Robinson College, Cambridge, UK 20-22 September 2000
  • (poster) "Genes, Proteins & Computers" VI - Chester UK April 26-28 2000
  • (poster) "RECOMB2000 The Fourth Annual International Conference on Computational Molecular Biology" Tokyo, Japan April 8 - 11, 2000
  • (participant) "Bioinformatics '99", Lund, Sweden, April 15-18, 1999

  • Julian Gough
    Last modified: Thu May 27 00:30:24 JST 2004