Douglas B Kell

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. pmc Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing
    Steve O'Hagan
    School of Chemistry, The University of Manchester, Manchester, UK
    PLoS ONE 7:e48862. 2012
  2. pmc Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing
    Ben G Small
    Doctoral Training Centre, Integrative Systems Biology Molecules to Life, Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
    Nat Chem Biol 7:902-8. 2011
  3. pmc Automated tracking of gene expression in individual cells and cell compartments
    Hailin Shen
    School of Chemistry, The University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    J R Soc Interface 3:787-94. 2006
  4. pmc Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery
    Douglas B Kell
    School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK Electronic address
    Drug Discov Today 19:171-82. 2014
  5. ncbi request reprint Serum ferritin is an important inflammatory disease marker, as it is mainly a leakage product from damaged cells
    Douglas B Kell
    School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK
    Metallomics 6:748-73. 2014
  6. doi request reprint The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so
    Douglas B Kell
    School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
    Drug Discov Today 18:218-39. 2013
  7. pmc The genetic control of growth rate: a systems biology study in yeast
    Pinar Pir
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Syst Biol 6:4. 2012
  8. pmc Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
    Philos Trans R Soc Lond B Biol Sci 367:1589-97. 2012
  9. pmc Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments?
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, Lancs, UK
    Bioessays 34:236-44. 2012
  10. pmc Interactions among oscillatory pathways in NF-kappa B signaling
    Yunjiao Wang
    Mathematical Biosciences Institute, The Ohio State University, Jennings Hall, Columbus, Ohio 43210, USA
    BMC Syst Biol 5:23. 2011

Detail Information

Publications98

  1. pmc Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing
    Steve O'Hagan
    School of Chemistry, The University of Manchester, Manchester, UK
    PLoS ONE 7:e48862. 2012
    ..The non-proprietary code that we have used is made freely available (via Supplementary information)...
  2. pmc Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing
    Ben G Small
    Doctoral Training Centre, Integrative Systems Biology Molecules to Life, Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
    Nat Chem Biol 7:902-8. 2011
    ..Evolutionary searches provide a powerful and general approach to the discovery of new combinations of pharmacological agents with therapeutic indices potentially greater than those of single drugs...
  3. pmc Automated tracking of gene expression in individual cells and cell compartments
    Hailin Shen
    School of Chemistry, The University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    J R Soc Interface 3:787-94. 2006
    ..This will lead to substantial benefits for time-lapse-based high-content screening...
  4. pmc Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery
    Douglas B Kell
    School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK Electronic address
    Drug Discov Today 19:171-82. 2014
    ..However, even these qualitative network models are not yet complete. As our understanding improves so do we recognise more clearly the need for a systems (poly)pharmacology. ..
  5. ncbi request reprint Serum ferritin is an important inflammatory disease marker, as it is mainly a leakage product from damaged cells
    Douglas B Kell
    School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK
    Metallomics 6:748-73. 2014
    ..This leads to suggestions for how one might exploit the corollaries of the recognition that serum ferritin levels mainly represent a consequence of cell stress and damage. ..
  6. doi request reprint The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so
    Douglas B Kell
    School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
    Drug Discov Today 18:218-39. 2013
    ..This needs to be acquired in cells that contain the relevant proteins, and we highlight an experimental system for simultaneous genome-wide assessment of carrier-mediated uptake in a eukaryotic cell (yeast)...
  7. pmc The genetic control of growth rate: a systems biology study in yeast
    Pinar Pir
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Syst Biol 6:4. 2012
    ..It has not been determined whether the set of HFC genes is the same at all growth rates or whether it is the same in conditions of nutrient limitation or excess...
  8. pmc Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK
    Philos Trans R Soc Lond B Biol Sci 367:1589-97. 2012
    ..These bring additional benefits related to improvements in soil structure and in the usage of other nutrients and water...
  9. pmc Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments?
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, Lancs, UK
    Bioessays 34:236-44. 2012
    ..This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes...
  10. pmc Interactions among oscillatory pathways in NF-kappa B signaling
    Yunjiao Wang
    Mathematical Biosciences Institute, The Ohio State University, Jennings Hall, Columbus, Ohio 43210, USA
    BMC Syst Biol 5:23. 2011
    ..Many authors have suggested that this core oscillator should couple to other oscillatory pathways...
  11. ncbi request reprint The virtual human: towards a global systems biology of multiscale, distributed biochemical network models
    Douglas B Kell
    School of Chemistry and The Manchester Centre for Integrative Systems Biology, The Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
    IUBMB Life 59:689-95. 2007
    ..This kind of architecture permits the distributed yet integrated goal of an evolving 'digital human' model to be realized...
  12. ncbi request reprint Systems biology, metabolic modelling and metabolomics in drug discovery and development
    Douglas B Kell
    School of Chemistry, Faraday Building, The University of Manchester PO Box 88, Manchester, M60 1QD, UK
    Drug Discov Today 11:1085-92. 2006
    ....
  13. ncbi request reprint The markup is the model: reasoning about systems biology models in the Semantic Web era
    Douglas B Kell
    School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    J Theor Biol 252:538-43. 2008
    ..Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization...
  14. ncbi request reprint Metabolic footprinting and systems biology: the medium is the message
    Douglas B Kell
    School of Chemistry, University of Manchester, Faraday Building, PO Box 88, Sackville Street, Manchester M60 1QD, UK
    Nat Rev Microbiol 3:557-65. 2005
    ..Here, we review the principles, experimental approaches and scientific outcomes that have been obtained with this useful and convenient strategy...
  15. ncbi request reprint Metabolomics, machine learning and modelling: towards an understanding of the language of cells
    D B Kell
    School of Chemistry, The University of Manchester, Faraday Building, Sackville Street, P O Box 88, Manchester M60 1QD, UK
    Biochem Soc Trans 33:520-4. 2005
    ..The language of cells is much richer than we had supposed, and we are now well placed to decode it...
  16. ncbi request reprint Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest
    Douglas B Kell
    School of Chemistry, Faraday Building, The University of Manchester, UK
    FEBS J 273:873-94. 2006
    ..These include fields such as chemical genomics, synthetic biology, distributed computational environments for biological data and modelling, single cell diagnostics/bionanotechnology, and computational linguistics/text mining...
  17. ncbi request reprint Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only
    Douglas B Kell
    School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
    Drug Discov Today 16:704-14. 2011
    ..The recognition that drugs necessarily require carriers for uptake into cells provides many opportunities for improving the effectiveness of the drug discovery process...
  18. pmc Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
    Ann Bot 108:407-18. 2011
    ....
  19. pmc Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples
    Douglas B Kell
    School of Chemistry and The Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK
    Arch Toxicol 84:825-89. 2010
    ..A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions...
  20. pmc Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases
    Douglas B Kell
    School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
    BMC Med Genomics 2:2. 2009
    ..Understanding these requires an integrative, systems-level approach that may lead to novel therapeutic targets...
  21. pmc A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
    Kieran Smallbone
    Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK
    FEBS Lett 587:2832-41. 2013
    ..This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought. ..
  22. pmc Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast
    Karin Lanthaler
    School of Chemistry, University of Manchester, Manchester, UK
    BMC Biol 9:70. 2011
    ..The recent recognition that drug uptake is mostly carrier-mediated raises the question of which drugs use which carriers...
  23. pmc Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    BMC Bioinformatics 9:S5. 2008
    ..However, it is time-consuming and non trivial to construct these resources manually...
  24. pmc Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach
    Kathleen M Carroll
    Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
    Mol Cell Proteomics 10:M111.007633. 2011
    ..In addition, the same proteins were quantified by intensity-based label-free analysis, and both sets of data were compared with other quantification methods...
  25. pmc MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
    Irena Spasic
    School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
    BMC Bioinformatics 7:281. 2006
    ..The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions...
  26. pmc Calling International Rescue: knowledge lost in literature and data landslide!
    Teresa K Attwood
    School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Biochem J 424:317-33. 2009
    ..We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers.....
  27. ncbi request reprint Metabolomics by numbers: acquiring and understanding global metabolite data
    Royston Goodacre
    Department of Chemistry, UMIST, P O Box 88, Sackville Street, Manchester M60 1QD, UK
    Trends Biotechnol 22:245-52. 2004
  28. ncbi request reprint Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo
    Bayu Jayawardhana
    Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK
    Bioinformatics 24:1191-7. 2008
    ..In this regard, the ability to identify target and off-target effects of a specific compound or gene therapy is both a major challenge and critical in drug discovery...
  29. pmc Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data
    Peter Li
    Manchester Centre for Integrative Systems Biology and School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 9:334. 2008
    ..Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools...
  30. pmc Information management for high content live cell imaging
    Daniel Jameson
    Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 10:226. 2009
    ..There is therefore a requirement for an information management solution that facilitates the indexing of experimental metadata and results of high content live cell imaging experiments...
  31. pmc Improving metabolic flux predictions using absolute gene expression data
    DAVE LEE
    Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
    BMC Syst Biol 6:73. 2012
    ..Moreover, for the purposes of biotechnological applications, it is normally the flux to a specific metabolite or product that is of interest rather than the rate of production of biomass per se...
  32. pmc Further developments towards a genome-scale metabolic model of yeast
    Paul D Dobson
    School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
    BMC Syst Biol 4:145. 2010
    ....
  33. ncbi request reprint Automated manipulation of systems biology models using libSBML within Taverna workflows
    Peter Li
    School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, UK
    Bioinformatics 24:287-9. 2008
    ..The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model...
  34. ncbi request reprint Detection and identification of novel metabolomic biomarkers in preeclampsia
    Louise C Kenny
    Maternal and Fetal Health Research Centre, University of Manchester, St Mary s Hospital, Manchester, United Kingdom
    Reprod Sci 15:591-7. 2008
    ..The identity of these metabolites provides new insights into the pathology of this condition and raises the possibility of the development of a predictive test...
  35. doi request reprint In silico modelling of directed evolution: Implications for experimental design and stepwise evolution
    David C Wedge
    Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    J Theor Biol 257:131-41. 2009
    ..Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes...
  36. doi request reprint Enzyme kinetics informatics: from instrument to browser
    Neil Swainston
    Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK
    FEBS J 277:3769-79. 2010
    ..The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques...
  37. pmc Analysis of a complete DNA-protein affinity landscape
    William Rowe
    Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    J R Soc Interface 7:397-408. 2010
    ..These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides...
  38. ncbi request reprint Predictive models for population performance on real biological fitness landscapes
    William Rowe
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, UK
    Bioinformatics 26:2145-52. 2010
    ..Here, we use the method for the first time to simulate a biological fitness landscape based on experimental evaluation...
  39. doi request reprint Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry
    Warwick B Dunn
    Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    Nat Protoc 6:1060-83. 2011
    ..Methods for quality control-based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described...
  40. ncbi request reprint A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    Chris F Taylor
    School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nat Biotechnol 21:247-54. 2003
    ..These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository...
  41. ncbi request reprint Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum
    Eva Zelena
    Bioanalytical Sciences Group, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK
    Anal Chem 81:1357-64. 2009
    ..This method allows the acquisition of data and subsequent comparison of data collected across many months or years...
  42. ncbi request reprint Optimal construction of a fast and accurate polarisable water potential based on multipole moments trained by machine learning
    Chris M Handley
    Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, UK
    Phys Chem Chem Phys 11:6365-76. 2009
    ..Compared to the Kriging results, combinations are found that are no less accurate (at the 90th energy error percentile), yet are 58% faster for the dimer, and 26% faster for the pentamer...
  43. ncbi request reprint Multiobjective optimization in bioinformatics and computational biology
    Julia Handl
    School of Chemistry, The University of Manchester, Manchester, UK
    IEEE/ACM Trans Comput Biol Bioinform 4:279-92. 2007
    ....
  44. doi request reprint Analysis of aptamer sequence activity relationships
    Mark Platt
    Manchester Interdisciplinary Biocentre, The University of Manchester, UK
    Integr Biol (Camb) 1:116-22. 2009
    ....
  45. ncbi request reprint A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols
    Warwick B Dunn
    Bioanalytical Sciences Group, School of Chemistry, Manchester Interdiscplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    Int J Epidemiol 37:i23-30. 2008
    ....
  46. doi request reprint KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester, UK
    Bioinformatics 25:1404-11. 2009
    ..It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given the size of genome-scale models...
  47. pmc Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets
    Marie Brown
    School of Biomedicine, The University of Manchester, Manchester M13 9PT, UK
    Bioinformatics 27:1108-12. 2011
    ..One of the limiting factors is that of chemically identifying metabolites from mass spectrometric signals present in complex datasets...
  48. pmc Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
    Christopher G Knight
    Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
    Nucleic Acids Res 37:e6. 2009
    ..We demonstrate an extension to the approach by incorporating prior knowledge into CLADE, resulting in some of the tightest binding sequences...
  49. ncbi request reprint Computational cluster validation in post-genomic data analysis
    Julia Handl
    School of Chemistry, University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 21:3201-12. 2005
    ..Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics...
  50. pmc A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
    Makoto Miwa
    The National Centre for Text Mining and School of Computer Science and School of Chemistry and the Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
    Bioinformatics 29:i44-52. 2013
    ..These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge...
  51. ncbi request reprint Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures
    Daniela Delneri
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    Nat Genet 40:113-7. 2008
    ..This chromosome determines a yeast's mating type, and the concentration of haploinsufficient genes there may be a mechanism to prevent its loss...
  52. pmc Systematic integration of experimental data and models in systems biology
    Peter Li
    School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
    BMC Bioinformatics 11:582. 2010
    ..Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources...
  53. pmc Visualising biological data: a semantic approach to tool and database integration
    Steve Pettifer
    School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
    BMC Bioinformatics 10:S19. 2009
    ....
  54. ncbi request reprint Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system
    Warwick B Dunn
    Manchester Centre for Integrative Systems Biology, School of Chemistry, The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
    J Chromatogr B Analyt Technol Biomed Life Sci 871:288-98. 2008
    ..The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum...
  55. pmc Information-theoretic sensitivity analysis: a general method for credit assignment in complex networks
    Niklas Lüdtke
    School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    J R Soc Interface 5:223-35. 2008
    ..Unlike variance-based approaches, our novel methodology can easily accommodate correlated inputs...
  56. doi request reprint 'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug libraries
    Paul D Dobson
    School of Chemistry and The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
    Drug Discov Today 14:31-40. 2009
    ....
  57. ncbi request reprint Development and performance of a gas chromatography-time-of-flight mass spectrometry analysis for large-scale nontargeted metabolomic studies of human serum
    Paul Begley
    Bioanalytical Sciences Group, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK
    Anal Chem 81:7038-46. 2009
    ..This methodology allows the continuous acquisition and application of data acquired over many months in long-term metabolomic studies, including the HUSERMET project (http://www.husermet.org/)...
  58. ncbi request reprint Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?
    Paul D Dobson
    School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    Nat Rev Drug Discov 7:205-20. 2008
    ....
  59. pmc maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
    David Hancock
    School of Computer Science, The University of Manchester, Kilburn Building, Oxford Road, Manchester, UK
    BMC Bioinformatics 6:264. 2005
    ..maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool...
  60. pmc Extracting semantically enriched events from biomedical literature
    Makoto Miwa
    The National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
    BMC Bioinformatics 13:108. 2012
    ..The automatic recognition of such information can permit the training of systems allowing finer-grained searching of events according to the meta-knowledge that is associated with them...
  61. pmc Predicting the points of interaction of small molecules in the NF-κB pathway
    Yogendra Patel
    Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    BMC Syst Biol 5:32. 2011
    ..Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway...
  62. ncbi request reprint Implications of the dominant role of transporters in drug uptake by cells
    Paul D Dobson
    School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M17DN, UK
    Curr Top Med Chem 9:163-81. 2009
    ..Finally, the central importance of computational modelling of transporter substrate preferences by structure-activity relationships is discussed...
  63. ncbi request reprint Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: influence of instrumental settings and implications for proteomics
    Seetharaman Vaidyanathan
    Department of Chemistry, Faraday Building, Sackville Street, UMIST, P O Box 88, Manchester M60 1QD, UK
    Anal Chem 76:5024-32. 2004
    ....
  64. ncbi request reprint Closed-loop, multiobjective optimization of analytical instrumentation: gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations
    Steve O'Hagan
    School of Chemistry, University of Manchester, Faraday Building, Sackville Street, P O Box 88, Manchester M60 1QD, U K
    Anal Chem 77:290-303. 2005
    ..The evolutionary closed-loop machine learning strategy we describe is generic to any type of analytical optimization...
  65. ncbi request reprint Proximate parameter tuning for biochemical networks with uncertain kinetic parameters
    Stephen J Wilkinson
    School of Chemistry, Princess St, Manchester, UK
    Mol Biosyst 4:74-97. 2008
    ....
  66. ncbi request reprint Metabolomics and systems biology: making sense of the soup
    Douglas B Kell
    Department of Chemistry, UMIST, Faraday Building, Sackville St, PO Box 88, Manchester M60 1QD, UK
    Curr Opin Microbiol 7:296-307. 2004
    ....
  67. pmc Arcadia: a visualization tool for metabolic pathways
    Alice C Villéger
    School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
    Bioinformatics 26:1470-1. 2010
    ..Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations...
  68. doi request reprint Event extraction for systems biology by text mining the literature
    Sophia Ananiadou
    University of Manchester, Manchester M13 9PL, UK
    Trends Biotechnol 28:381-90. 2010
    ..The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states...
  69. doi request reprint Aptamer evolution for array-based diagnostics
    Mark Platt
    Manchester Interdisciplinary Biocenter, University of Manchester, Manchester M1 7DN, UK
    Anal Biochem 390:203-5. 2009
    ..The best aptameric sequence was void of the set of four guanine repeats typifying thrombin aptamers and, thus, highlights the benefits of evolution performed in an environment closely mimicking the final diagnostic application...
  70. ncbi request reprint Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics
    M Brown
    Bioanalytical Sciences Group, School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, UK M1 7DN
    Analyst 134:1322-32. 2009
    ..To provide definitive identification metabolite-specific mass spectral libraries for UPLC-MS and GC-MS have been constructed for 1,065 commercially available authentic standards. The MMD data are available at http://dbkgroup.org/MMD/...
  71. ncbi request reprint Convergent evolution to an aptamer observed in small populations on DNA microarrays
    W Rowe
    Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
    Phys Biol 7:036007. 2010
    ..Regime specific differences in the evolutions, such as speed of convergence, could also be observed...
  72. pmc Utopia documents: linking scholarly literature with research data
    T K Attwood
    School of Computer Science, Faculty of Life Sciences, University of Manchester, Manchester, UK
    Bioinformatics 26:i568-74. 2010
    ..The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged...
  73. pmc A systematic survey of the response of a model NF-κB signalling pathway to TNFα stimulation
    Yunjiao Wang
    Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
    J Theor Biol 297:137-47. 2012
    ....
  74. pmc Growth control of the eukaryote cell: a systems biology study in yeast
    Juan I Castrillo
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    J Biol 6:4. 2007
    ..Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking...
  75. ncbi request reprint Something from nothing: bridging the gap between constraint-based and kinetic modelling
    Kieran Smallbone
    Manchester Centre for Integrative Systems Biology, The University of Manchester, UK
    FEBS J 274:5576-85. 2007
    ..Moreover, using this particular methodology affords us analytical forms for steady state determination, stability analyses and studies of dynamical behaviour...
  76. ncbi request reprint Closed-loop, multiobjective optimization of two-dimensional gas chromatography/mass spectrometry for serum metabolomics
    Warwick B Dunn
    School of Chemistry, The University of Manchester, Faraday Building, Sackville Street, Manchester M60 1QD, UK
    Anal Chem 79:464-76. 2007
    ..A variety of computational methods served to explain the basis for the improvement. This closed-loop optimization strategy is a generic and powerful approach for the optimization of any analytical instrumentation...
  77. ncbi request reprint Text mining and its potential applications in systems biology
    Sophia Ananiadou
    School of Computer Science, National Centre for Text Mining, The Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
    Trends Biotechnol 24:571-9. 2006
    ..By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models...
  78. pmc Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae
    Thomas Williamson
    Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 3:70. 2009
    ..A stochastic model of the pathway has been reported...
  79. pmc Defrosting the digital library: bibliographic tools for the next generation web
    Duncan Hull
    School of Chemistry, The University of Manchester, Manchester, UK
    PLoS Comput Biol 4:e1000204. 2008
    ....
  80. ncbi request reprint Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway
    Hong Yue
    School of Chemistry, University of Manchester, Sackville St, Manchester, UK
    Mol Biosyst 2:640-9. 2006
    ..The whole analysis scheme we describe provides efficient parameter estimation techniques for complex cell networks...
  81. ncbi request reprint Genotype-phenotype mapping: genes as computer programs
    Douglas B Kell
    Dept of Chemistry, UMIST, Manchester, UK
    Trends Genet 18:555-9. 2002
    ..In this way, the encoding of cellular and higher-order activities by genes is seen as directly analogous to computer programs. This analogy is of utility in biological genetics and in problems of genotype-phenotype mapping...
  82. ncbi request reprint Synergistic control of oscillations in the NF-kappaB signalling pathway
    A E C Ihekwaba
    School of Chemistry, The University of Manchester, UK
    Syst Biol (Stevenage) 152:153-60. 2005
    ....
  83. ncbi request reprint Explanatory optimization of protein mass spectrometry via genetic search
    Seetharaman Vaidyanathan
    Department of Chemistry, UMIST, P O Box 88, Sackville Street, Manchester M60 1QD, UK
    Anal Chem 75:6679-86. 2003
    ....
  84. ncbi request reprint Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era
    Douglas B Kell
    Department of Chemistry, UMIST, Manchester, UK
    Bioessays 26:99-105. 2004
    ..Many fields are data-rich but hypothesis-poor. Here, computational methods of data analysis, which may be automated, provide the means of generating novel hypotheses, especially in the post-genomic era...
  85. ncbi request reprint Systematic functional analysis of the yeast genome
    S G Oliver
    Department of Biomolecular Sciences, UMIST, Manchester, UK
    Trends Biotechnol 16:373-8. 1998
    ..Systematic and comprehensive approaches to the elucidation of yeast gene function are discussed and the prospects for the functional genomics of eukaryotic organisms evaluated...
  86. ncbi request reprint Monitoring of complex industrial bioprocesses for metabolite concentrations using modern spectroscopies and machine learning: application to gibberellic acid production
    Aoife C McGovern
    Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth, Ceredigion SY23 3DD, Wales, UK
    Biotechnol Bioeng 78:527-38. 2002
    ....
  87. ncbi request reprint Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis
    Leighton Pritchard
    Institute of Biological Sciences, University of Wales, Aberystwyth, UK
    Eur J Biochem 269:3894-904. 2002
    ....
  88. ncbi request reprint Metabolomics and machine learning: explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules
    Douglas B Kell
    Institute of Biological Sciences, University of Wales, Aberystwyth, UK
    Mol Biol Rep 29:237-41. 2002
  89. ncbi request reprint High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
    Jess Allen
    Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth, Aberystwyth SY23 3DD, UK
    Nat Biotechnol 21:692-6. 2003
    ..By using appropriate clustering and machine learning techniques, the latter based on genetic programming, we show that metabolic footprinting is an effective method to classify 'unknown' mutants by genetic defect...
  90. ncbi request reprint Functional genomic hypothesis generation and experimentation by a robot scientist
    Ross D King
    Department of Computer Science, University of Wales, Aberystwyth SY23 3DB, UK
    Nature 427:247-52. 2004
    ....
  91. ncbi request reprint A proposed framework for the description of plant metabolomics experiments and their results
    Helen Jenkins
    Department of Computer Science, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, UK
    Nat Biotechnol 22:1601-6. 2004
    ..armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data...
  92. ncbi request reprint Adoption of the transiently non-culturable state--a bacterial survival strategy?
    Galina V Mukamolova
    Institute of Biological Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3DD, UK
    Adv Microb Physiol 47:65-129. 2003
    ....
  93. ncbi request reprint Metabolomic biomarkers: search, discovery and validation
    Douglas B Kell
    Expert Rev Mol Diagn 7:329-33. 2007
  94. ncbi request reprint Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels
    Andrew M Woodward
    Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth, Ceredigion, UKSY23 3DD
    Analyst 129:542-52. 2004
    ..The method compares favourably with others, since it is computationally rapid, effective and entirely automatic...
  95. pmc Discrimination of modes of action of antifungal substances by use of metabolic footprinting
    Jess Allen
    Department of Biological Sciences, University of Wales, Aberystwyth, UK
    Appl Environ Microbiol 70:6157-65. 2004
    ..Metabolic footprinting thus represents a rapid, convenient, and information-rich method for classifying the modes of action of antifungal substances...
  96. pmc Rapid and quantitative detection of the microbial spoilage of meat by fourier transform infrared spectroscopy and machine learning
    David I Ellis
    Institute of Biological Sciences Department of Computer Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3DD, Wales, United Kingdom
    Appl Environ Microbiol 68:2822-8. 2002
    ..We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels...
  97. ncbi request reprint Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification
    Seetharaman Vaidyanathan
    Institute of Biological Sciences, University of Wales, Aberystwyth, Ceredigion, United Kingdom
    J Am Soc Mass Spectrom 13:118-28. 2002
    ....