Professor 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 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 any 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:
Hickman G. & Hodgman C. (2009) Inference of gene regulatory networks using boolean-network inference methods. Journal of Bioinformatics and Computational Biology. (in press)
Balkwill G.D, Derecka K, Garner T.P, Hodgman C, Flint A.P.F. & Serle M. (2009) Repression of Translation of Human Estrogen Receptor α by G-Quadruplex Formation. Biochemistry. (in press)
Hodgman C, Westhead D, French A. (2009) Instant Notes in Bioinformatics.
ISBN-10: 0415394945, ISBN-13: 978-0415394949. Taylor & Francis. 2nd edition.
Levitsky V.G, Ignatieva E.V, Ananko E.A, Aman E, Turnaev I.I, Kolchanov N.A. & Hodgman T.C. (2008) Genetic algorithm and optimized weight matrix application for peroxisome proliferator response elements recognition: Prerequisites of accuracy growth for wide genome research.
Intell Data Anal. 12(5): 513-526.
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.
Levitsky V.G, Ignatieva E.V, Ananko E.A, Turnaev I.I, Merkulova T.I, Kolchanov N.A. & Hodgman T.C. (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.
Hodgman C (Guest Editor, 2007) Integrative biology - the way forward. Briefings in Bioinformatics 8(4): 208-209.
Levitsky V.G, Ignatieva E.V, Ananko E.A, Turnaev I.I, Merkulova T.I, Kolchanov N.A, Hodgman T.C. (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 N.A, Merkulova T.I, Ignatieva E.V, Ananko E.A, Oshchepkov D.Y, Levitsky V.G, Vasiliev G.V, Klimova N.V, Merkulov V.M, 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.
Hodgman T.C. (2004) Editorial: The informatics of post-translational modification and its implications for systems biology. Briefings in Bioinformatics 5(2): 104-106.
Thomson R, Hodgman C, Yang Z.R. & Doyle A. (2003) Characterizing proteolytic cleavage site activity using bio-basis function neural networks.
Bioinformatics. 19(14): 1741-1747.
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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