Darren J Wilkinson

Summary

Affiliation: University of Newcastle
Country: UK

Publications

  1. pmc A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation
    Mark T Mc Auley
    Campus for Ageing and Vitality, Newcastle University, Henry Wellcome Biogerontology Building, Newcastle upon Tyne NE4 5PL, United Kingdom
    BMC Syst Biol 6:130. 2012
  2. pmc A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
    Amanda Greenall
    Aging Research Laboratories, Institute for Aging and Health, Newcastle University, Newcastle upon Tyne, UK
    Genome Biol 9:R146. 2008
  3. pmc Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
    Colin S Gillespie
    School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
    BMC Res Notes 3:81. 2010
  4. pmc A mathematical model of aging-related and cortisol induced hippocampal dysfunction
    Mark T McAuley
    Henry Wellcome Building, Biogerontology Building, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, England, NE4 6BE, UK
    BMC Neurosci 10:26. 2009
  5. pmc Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
    Conor Lawless
    Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle Upon Tyne NE45PL, UK
    BMC Bioinformatics 11:287. 2010
  6. doi request reprint Stochastic modelling for quantitative description of heterogeneous biological systems
    Darren J Wilkinson
    School of Mathematics and Statistics and the Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
    Nat Rev Genet 10:122-33. 2009
  7. ncbi request reprint Bayesian methods in bioinformatics and computational systems biology
    Darren J Wilkinson
    School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
    Brief Bioinform 8:109-16. 2007
  8. ncbi request reprint Modelling the actions of chaperones and their role in ageing
    Carole J Proctor
    Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences Gerontology, University of Newcastle, Newcastle upon Tyne NE4 6BE, UK
    Mech Ageing Dev 126:119-31. 2005
  9. ncbi request reprint A mathematical model of ageing in yeast
    Colin S Gillespie
    Henry Wellcome Laboratory for Biogerontology Research, SCMS Gerontology, University of Newcastle, Newcastle General Hospital, Newcastle upon Tyne, NE4 6BE, UK
    J Theor Biol 229:189-96. 2004
  10. ncbi request reprint Bayesian sequential inference for stochastic kinetic biochemical network models
    Andrew Golightly
    School of Mathematics and Statistics, University of Newcastle upon Tyne, NE1 7RU, UK
    J Comput Biol 13:838-51. 2006

Collaborators

Detail Information

Publications14

  1. pmc A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation
    Mark T Mc Auley
    Campus for Ageing and Vitality, Newcastle University, Henry Wellcome Biogerontology Building, Newcastle upon Tyne NE4 5PL, United Kingdom
    BMC Syst Biol 6:130. 2012
    ..The model integrates both current and previously published data relating to molecular biology, physiology, ageing and nutrition in an integrated fashion...
  2. pmc A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
    Amanda Greenall
    Aging Research Laboratories, Institute for Aging and Health, Newcastle University, Newcastle upon Tyne, UK
    Genome Biol 9:R146. 2008
    ..In order to better understand the eukaryotic response to telomere damage, budding yeast strains harboring a temperature sensitive allele of an essential telomere capping gene (cdc13-1) were subjected to a transcriptomic study...
  3. pmc Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
    Colin S Gillespie
    School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
    BMC Res Notes 3:81. 2010
    ..However, proper statistical analysis of time-course data requires the use of more sophisticated tools and complex statistical models...
  4. pmc A mathematical model of aging-related and cortisol induced hippocampal dysfunction
    Mark T McAuley
    Henry Wellcome Building, Biogerontology Building, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, England, NE4 6BE, UK
    BMC Neurosci 10:26. 2009
    ..We further challenged the model with biologically based interventions to ascertain if cortisol associated hippocampal dysfunction could be abrogated...
  5. pmc Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
    Conor Lawless
    Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle Upon Tyne NE45PL, UK
    BMC Bioinformatics 11:287. 2010
    ..g. the logistic growth model). In order to parametrize such a model, a robust image analysis tool capable of capturing a wide range of cell densities from plate photographs is required...
  6. doi request reprint Stochastic modelling for quantitative description of heterogeneous biological systems
    Darren J Wilkinson
    School of Mathematics and Statistics and the Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
    Nat Rev Genet 10:122-33. 2009
    ..Both frameworks are needed to adequately describe observed noise, variability and heterogeneity of biological systems over a range of scales of biological organization...
  7. ncbi request reprint Bayesian methods in bioinformatics and computational systems biology
    Darren J Wilkinson
    School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
    Brief Bioinform 8:109-16. 2007
    ..This review provides an introduction to the growing literature in this area, with particular emphasis on recent developments in Bayesian bioinformatics relevant to computational systems biology...
  8. ncbi request reprint Modelling the actions of chaperones and their role in ageing
    Carole J Proctor
    Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences Gerontology, University of Newcastle, Newcastle upon Tyne NE4 6BE, UK
    Mech Ageing Dev 126:119-31. 2005
    ....
  9. ncbi request reprint A mathematical model of ageing in yeast
    Colin S Gillespie
    Henry Wellcome Laboratory for Biogerontology Research, SCMS Gerontology, University of Newcastle, Newcastle General Hospital, Newcastle upon Tyne, NE4 6BE, UK
    J Theor Biol 229:189-96. 2004
    ....
  10. ncbi request reprint Bayesian sequential inference for stochastic kinetic biochemical network models
    Andrew Golightly
    School of Mathematics and Statistics, University of Newcastle upon Tyne, NE1 7RU, UK
    J Comput Biol 13:838-51. 2006
    ..The methodology is illustrated by applying it to the estimation of parameters in a simple prokaryotic auto-regulatory gene network...
  11. ncbi request reprint Tools for the SBML Community
    Colin S Gillespie
    School of Mathematics and Statistics, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
    Bioinformatics 22:628-9. 2006
    ..The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user...
  12. doi request reprint CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models
    Yuhui Chen
    Institute for Ageing and Health, Centre for Integrated Systems Biology of Ageing and Nutrition at Newcastle, UK
    Brief Bioinform 11:278-89. 2010
    ..In this article, we describe these two systems and demonstrate their integrated use with an example workflow to estimate the parameters of a simple model of Saccharomyces cerevisiae growth on agar plates...
  13. ncbi request reprint The SBML discrete stochastic models test suite
    Thomas W Evans
    Department of Mathematical Sciences, University of Liverpool, Liverpool, L69 7ZL, UK
    Bioinformatics 24:285-6. 2008
    ..Stochastic simulation is a very important tool for mathematical modelling. However, it is difficult to check the correctness of a stochastic simulator, since any two realizations from a single model will typically be different...
  14. ncbi request reprint Towards an e-biology of ageing: integrating theory and data
    Thomas B L Kirkwood
    Institute for Ageing and Heath, University of Newcastle, Newcastle General Hospital, Newcastle upon Tyne NE4 6BE, UK
    Nat Rev Mol Cell Biol 4:243-9. 2003
    ..We describe how a new web-based modelling initiative is seeking to integrate data and hypotheses from diverse biological sources...