Thomas Thorne

Summary

Affiliation: Imperial College
Country: UK

Publications

  1. ncbi request reprint Evolution at the system level: the natural history of protein interaction networks
    Michael P H Stumpf
    Division of Molecular Biosciences, Imperial College London, London, UK
    Trends Ecol Evol 22:366-73. 2007
  2. pmc A systems biology analysis of long and short-term memories of osmotic stress adaptation in fungi
    Tao You
    Institute for Complex Systems and Mathematical Biology, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, UK
    BMC Res Notes 5:258. 2012
  3. doi request reprint Graphical modelling of molecular networks underlying sporadic inclusion body myositis
    Thomas Thorne
    Centre for Bioinformatics and Systems Biology, Imperial College London, London, UK
    Mol Biosyst 9:1736-42. 2013
  4. pmc Inference of temporally varying Bayesian networks
    Thomas Thorne
    Centre of Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    Bioinformatics 28:3298-305. 2012
  5. pmc Graph spectral analysis of protein interaction network evolution
    Thomas Thorne
    Centre of Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J R Soc Interface 9:2653-66. 2012
  6. pmc Generating confidence intervals on biological networks
    Thomas Thorne
    Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, UK
    BMC Bioinformatics 8:467. 2007
  7. doi request reprint Prediction of putative protein interactions through evolutionary analysis of osmotic stress response in the model yeast Saccharomyces cerevisae
    Thomas W Thorne
    Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW72AZ, United Kingdom
    Fungal Genet Biol 48:504-11. 2011
  8. pmc Estimating the size of the human interactome
    Michael P H Stumpf
    Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 105:6959-64. 2008
  9. doi request reprint Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation
    Juliane Liepe
    Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, UK
    Integr Biol (Camb) 4:335-45. 2012
  10. pmc The effects of incomplete protein interaction data on structural and evolutionary inferences
    Eric de Silva
    Theoretical Genomics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, UK
    BMC Biol 4:39. 2006

Collaborators

Detail Information

Publications11

  1. ncbi request reprint Evolution at the system level: the natural history of protein interaction networks
    Michael P H Stumpf
    Division of Molecular Biosciences, Imperial College London, London, UK
    Trends Ecol Evol 22:366-73. 2007
    ..Currently, such analyses are statistically challenging, but could link present initiatives in systems biology with results and methodologies that have developed in evolutionary biology over the past 60 years...
  2. pmc A systems biology analysis of long and short-term memories of osmotic stress adaptation in fungi
    Tao You
    Institute for Complex Systems and Mathematical Biology, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, UK
    BMC Res Notes 5:258. 2012
    ..Candida albicans also adapts to hyperosmolarity via a HOG signaling network. However, it remains unknown whether Hog1 exerts integral or proportional control over glycerol production in C. albicans...
  3. doi request reprint Graphical modelling of molecular networks underlying sporadic inclusion body myositis
    Thomas Thorne
    Centre for Bioinformatics and Systems Biology, Imperial College London, London, UK
    Mol Biosyst 9:1736-42. 2013
    ....
  4. pmc Inference of temporally varying Bayesian networks
    Thomas Thorne
    Centre of Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    Bioinformatics 28:3298-305. 2012
    ..Although some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data...
  5. pmc Graph spectral analysis of protein interaction network evolution
    Thomas Thorne
    Centre of Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J R Soc Interface 9:2653-66. 2012
    ..We also illustrate how our method can be used to perform multi-model inference of network parameters to estimate properties of the full network from sampled data...
  6. pmc Generating confidence intervals on biological networks
    Thomas Thorne
    Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, UK
    BMC Bioinformatics 8:467. 2007
    ..We show that this can fail to capture important features of network structure, and may result in unrealistic significance levels, when potentially confounding additional information is available...
  7. doi request reprint Prediction of putative protein interactions through evolutionary analysis of osmotic stress response in the model yeast Saccharomyces cerevisae
    Thomas W Thorne
    Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW72AZ, United Kingdom
    Fungal Genet Biol 48:504-11. 2011
    ..We do find that correlated evolution provides some useful information for the prediction of protein-protein interactions, but that these alone are not sufficient to explain detectable patterns of correlated evolution...
  8. pmc Estimating the size of the human interactome
    Michael P H Stumpf
    Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 105:6959-64. 2008
    ..We find that the human interaction network is one order of magnitude bigger than the Drosophila melanogaster interactome and approximately 3 times bigger than in Caenorhabditis elegans...
  9. doi request reprint Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation
    Juliane Liepe
    Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, UK
    Integr Biol (Camb) 4:335-45. 2012
    ..Our approach relies only on the ability to simulate numerically the process under investigation and is therefore also applicable in other in vivo contexts and studies...
  10. pmc The effects of incomplete protein interaction data on structural and evolutionary inferences
    Eric de Silva
    Theoretical Genomics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, UK
    BMC Biol 4:39. 2006
    ..Here we demonstrate the need to consider network sampling properties explicitly and from the outset in any analysis...
  11. pmc Parameter-free model discrimination criterion based on steady-state coplanarity
    Heather A Harrington
    Theoretical Systems Biology, Division of Molecular Biosciences, Imperial College London, London, United Kingdom
    Proc Natl Acad Sci U S A 109:15746-51. 2012
    ....