Professor Charlie Hodgman


Prof. Charlie Hodgman

Professor Charlie Hodgman has a longstanding reputation for elucidating the structure and function of biomolecular sequences. Orginally this was primarily at the protein sequence level, but more recently it concerns gene regulatory regions and multimolecular complexes.


I have been promoting Integrative Systems Biology since I joined GlaxoWellcome in 1995, paying particular emphasis on the development of informatics approaches to turn what is an otherwise manual-developed "cottage industry" into an industrial process in which representative models can be generated automatically. This will be necessary if bio-systems modelling is to keep pace with the rate of data generation. Owing to my diverse background, I am not wedded to and particular branch of the life sciences and welcome collaborative projects where they are of most benefit, especially with industry.


Specific Projects


    Director of the Centre of Plant Integrative Biology CPIB

    Software pipelines for:
         1. increasing the productivity of biopharmaceutical development.
         2. elucidation of changes in biological function arising from single nucleotide polymorphisms.
         3. in silico cDNA cloning from expressed sequence tags.

    Holistic biological network models of various organisms, including Arabidopsis, Dog, Cow, Haloferax, Tea and Wheat.

    Data acquisition and the development of dynamic models of plant root growth.

    Web services for network construction and feature detection and gene regulatory region analysis.

    Predictive tools to support biopharmaceutical development.


Selected publications:


Hodgman C, Westhead D, French A. December 2009. Instant Notes in Bioinformatics. ISBN-10: 0415394945, ISBN-13: 978-0415394949. Taylor & Francis. 2nd edition.

Gollapudi S+, Marshall A+, Zadik D+, Hodgman C (+ Joint First Authors) 2008. Chapter 16: Graphical Analysis and visualisation tools for protein interaction networks. Biological Data Mining in Protein Interaction Networks, Edited by Xiao-Li Li and See-Kiong Ng.

Hodgman C (Guest Editor). (2007) Integrative biology - the way forward. Briefings in Bioinformatics 8(4): 208-209.

Levitsky VG, Ignatieva EV, Ananko EA, Turnaev II, Merkulova TI, Kolchanov NA, Hodgman TC 2007. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics. 8:481.

Kolchanov NA, Merkulova TI, Ignatieva EV, Ananko EA, Oshchepkov DY, Levitsky VG, Vasiliev GV, Klimova NV, Merkulov VM, Charles Hodgman T 2007. Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Briefings in Bioinformatics 8(4): 266-74.

T.C. Hodgman, Y. Ugartechea-Chirino, G. Tansley and I. Dryden 2006. The implications for Bioinformatics of integration across physical scales. Journal of Integrative Bioinformatics 3(2).

Yang Z.R, Dry J, Thomson R. Hodgman T.C. 2006. A bio-basis function neural network for protein peptide cleavage activity characterisation. Neural Networks. 19(4): 401-407.

Horne A, Hodgman T.C, Spence H.D, Dalby A.R 2004. Constructing an enzyme-centric view of metabolism. Bioinformatics 20(13): 2050-2055.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531.

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