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Manchester Centre for Integrative Systems Biology

Publications


Dada J.O. and Mendes P. (2009) Design and Architecture of Web Services for Simulation of Biochemical Systems. DILS 2009, LNBI 5647, pp. 182-195.

E Murabito, E Simeonidis, K Smallbone, J Swinton (2009) Capturing the essence of a metabolic network: A flux balance analysis approach. J. Theor. Biol. (in press)

Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, Begley P, Carroll K, Broadhurst D, Tseng A, Swainston N, Spasic I, Goodacre R, Kell DB. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst (2009) 134(7):1322-32. Epub 2009 Apr 9.

Swainston N, Mendes P. (2009) libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics (2009) Jun 26. [Epub ahead of print]

I. Spasić, E. Simeonidis, H. Messiha, N. Paton and D. Kell (2009) KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics, 25 (11), 1404-1411.

K Smallbone, E Simeonidis (2009) Flux balance analysis: A geometric perspective. J. Theor. Biol. 258 (2), 311-315.

H. Yang, I. Spasic, J. Keane and G. Nenadic (2009) A text mining approach to the prediction of a disease status from clinical discharge summaries. Journal of the American Medical Informatics Association, in press

H. Yang, I. Spasic, J. Keane and G. Nenadic (2008) Combining lexical profiling, rules and machine learning for disease prediction from hospital discharge summaries, in Proceedings of 2nd i2b2 Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data, Washington DC, USA

M Bilalić, K Smallbone, P McLeod, F Gobet. Why are (the best) women so good at chess? Participation rates and gender differences in intellectual domains. Proc. R. Soc. B (2009) 276: 1161-1165

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Blüthgen N, Li P, Pettifer S, Simeonidis E, Smallbone K, Spasi? I, Weichart D, Broomhead DS, Westerhoff HV, Mendes P, Kell DB, et al. A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnology (2008) 26: 1155-1160.

Swainston N. The KineticsWizard: a Data Capture Tool for the Submission of Enzyme Kinetics Data. Proceedings of 3rd International ESCEC Symposium on Experimental Standard Conditions on Enzyme Characterizations, Rüdesheim-am-Rhein, Germany, 23-26 September 2007.

Smallbone, K., Gatenby, R.A., Maini, P.K. (2008) Mathematical modelling of tumour acidity. J. Theor. Biol. 255: 106-112.

Kelly C.J., Smallbone, K., Brady, J.M. (2008) Tumour glycolysis: The many faces of HIF. J. Theor. Biol. 254: 508-513.

Li P., Oinn T., Soiland S. and Kell D.B. (2008) Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics 24: 287-289.

Dunn, W.B. (2008) Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes, Phys. Biol. 5 011001

Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, et al. Development of a Robust and Repeatable UPLC-MS Method for the Long-Term Metabolomic Study of Human Serum. Analytical Chemistry 2009;81(4):1357-1364

Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, et al. Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites. Analytical Chemistry 2008;80(8):2939-2948.

MacKenzie DA, Defernez M, Dunn WB, Brown M, Fuller LJ, de Herrera S, et al. Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics. Yeast 2008;25(7):501-512.

Kenny LC, Broadhurst D, Brown M, Dunn WB, Redman CWG, Kill DB, et al. Detection and identification of novel metabolomic biomarkers in preeclampsia. Reproductive Sciences 2008;15(6):591-597.

Heazell AEP, Brown M, Dunn WB, Worton SA, Crocker IP, Baker PN, et al. Analysis of the metabolic footprint and tissue metabolome of placental villous explants cultured at different oxygen tensions reveals novel redox biomarkers. Placenta 2008;29(8):691-698.

Dunn WB, Broadhurst D, Ellis DI, Brown M, Halsall A, O'Hagan S, et al. A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols. International Journal of Epidemiology 2008;37:23-30.

Dunn WB, Broadhurst D, Brown M, Baker PN, Redman CWG, Kenny LC, et al. Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 2008;871(2):288-298.

Pope GA, MacKenzie DA, Defemez M, Aroso M, Fuller LJ, Mellon FA, et al. Metabolic footprinting as a tool for discriminating between brewing yeasts. Yeast 2007;24(8):667-679.

Dunn WB, Broadhurst DI, Deepak SM, Buch MH, McDowell G, Spasic I, et al. Serum metabolomics reveals many novel metabolic markers of heart failure, including pseudouridine and 2-oxoglutarate. Metabolomics 2007;3(4):413-426.

Spasić, I., Schober, D., Sansone, S., Rebholz-Schuhmann, D., Kell, D.B. & Paton, N.W. (2008) Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinformatics, 9, Suppl. 5, S5

Oinn, T., Li, P., Kell, D. B., Goble, C., Goderis, A., Greenwood, M., Hull, D., Stevens, R., Turi, D. & Zhao, J. (2007) Taverna / myGrid: Aligning a workflow system with the life sciences community. In Workflows for e-Science: Scientific workflows for Grids (ed. I. J. Taylor, E. Deelman, D. B. Gannon and M. Shields), pp. 300-319, Springer, Guildford.

O'Hagan, S., Dunn, W. B., Broadhurst, D., Williams, R., Ashworth, J. A., Cameron, M., Knowles, J. & Kell, D. B. (2007) Closed-loop, multi-objective optimisation of two-dimensional gas chromatography (GCxGC-tof-MS) for serum metabolomics. Anal. Chem., 79, 464-476.

Siepen, J.A., Swainston, N., Jones, A.R., Hart, S.R., Jones, P., Oliver, S.G., Gaskell, S.J. & Hubbard, S.J. (2007) An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Science, 5, 4.

Castrillo, J.I., Zeef, L.A., Hoyle, D.C., Zhang, N., Hayes, A., Gardner, D.C., Cornell, M.J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W.B., Broadhurst, D., O'Donoghue, K., Hester, S.S., Dunkley, T.P., Hart, S.R., Swainston, N., Li, P., Gaskell, S.J., Paton, N.W., Lilley, K.S., Kell, D.B. & Oliver, S.G. (2007) Growth control of the eukaryote cell: A systems biology study in yeast. J. Biol., 6, 1, 4. [local copy]

Smallbone, K., Simeonidis, E., Broomhead, D.S. & Kell, D.B. (2007) Something from nothing: Bridging the gap between constraint-based and kinetic modelling. FEBS J., 274, 21, 5576-5585.

Lau KW, Jones AR, Swainston N, Siepen JA, Hubbard SJ (2007) Capture and analysis of quantitative proteomic data. Proteomics, 7, 2787-2799

Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, James DeGreef, Nigel Hardy, Henning Hermjakob, Simon J Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K Julian, Jr, Kent Laursen, Stephen G Oliver, Norman W Paton, Susanna-Assunta Sansone, Ugis Sarkans, Christian J Stoeckert, Jr, Chris F Taylor, Patricia L Whetzel, Joseph A White, Paul Spellman & Angel Pizarro (2007) The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology, 25, 10, 1127-1133

Garwood, K., Garwood, C., Hedeler, C., Griffiths, T., Swainston, N., Oliver, S.G. & Paton, N.W. (2006) Model-driven user interfaces for bioinformatics data resources: Regenerating the wheel as an alternative to reinventing it. BMC Bioinformatics, 7, 532.

Yue, H., Brown, M., Knowles, J., Wang, H., Broomhead, D.S. & Kell, D.B. (2006) Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kB signalling pathway. Molecular BioSystems, 2, 640-649.

Pratt, J.M., Simpson, D.M., Doherty, M.K., Rivers, J., Gaskell, S.J. & Beynon, R.J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nature Protocols, 1, 2, 1029-1043.

Broadhurst, D. & Kell, D.B. (2006) Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics, 2, 171-196.

Spasić, I., Dunn, W., Velarde, G., Tseng, A., Jenkins, H., Hardy, N.W., Oliver, S.G. & Kell, D.B. (2006) MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinformatics, 7, 281.

Ananiadou, S., Kell, D. B. & Tsujii, J.-I. (2006) Text Mining and its potential applications in Systems Biology. Trends Biotechnol., 24, 571-579.

Kell, D.B. (2006) Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discovery Today, 11, 1085-1092.