Statistical Bioinformatics and Stochastic Systems Biology

The group has broad interests covering statistical bioinformatics and stochastic systems biology:

  • stochastic and deterministic modelling of complex biological processes, particularly those related to ageing (CISBAN, BASIS)
  • Bayesian inference for kinetic rate constants in stochastic/deterministic models using partially observed experimental data, particularly using simulators and emulators (CaliBayes)
  • data integration in bioinformatics using Bayesian inference (ComparaGRID, ONDEX)
  • phylogenetics, particularly the origin of the eukaryotes (EUKORIGINMIT)

The group has close links with mathematical/statistical modelers within the Institute for Ageing and Health, the Institute of Human Genetics, the Institute of Cell and Molecular Biosciences and the research group in Biology, Neurosciences and Computing within Computing Science, as well as other academic and industrial bioinformatics researchers in the region. The group also contributes to the teaching and project supervision on the MSc in Bioinformatics and Computational Systems Biology.

Current grants, fellowships and studentships

  • EUKORIGINMIT — Eukaryotic genomic origins, parasites, and the essential nature of mitochondria (PI: Prof Martin Embley; CI: Prof Richard Boys, Dr Tom Nye and others), funded by European Research Council (2011–2015)
  • The Yeast Telomere Cap (PI: Prof David Lydall; CI: Prof Darren Wilkinson), funded by Wellcome Trust (2011–2014)
  • Probability and kinetics of inclusion formation — Nina Wilkinson, supervised by Prof Doug Gray, Prof Richard Boys and Dr Colin Gillespie, BBSRC DTG funded PhD student (2010–2014)
  • Modelling gene tree heterogeneity in phylogenetic inference — Rute Vieira, supervised by Prof Richard Boys and Dr Tom Nye, Portugese FCT funded PhD student (2010–14)
  • Bayesian inference for high throughput yeast robotic genetic experiments — Jonathan Heydari, supervised by Prof Darren Wilkinson and Prof David Lydall, BBSRC DTG funded PhD student (2010–2013)
  • Bayesian inference for stochastic models in systems biology — Holly Ainsworth, supervised by Prof Richard Boys and Dr Colin Gillespie, EPSRC funded PhD student (2009–12)
  • ONDEX — Data integration and visualisation (Newcastle PI: Prof Anil Wipat, CI: Dr Phillip Lord, Prof David Lydall, Prof Darren Wilkinson), funded by BBSRC (2008–11)

Recent grants, fellowships and studentships

  • Integrative modelling of stochasticity, noise, heterogeneity and measurement error in the study of model biological systems — BBSRC Research Development Fellowship held by Prof Darren Wilkinson (2008–11)
  • CISBAN — Centre for Integrated Systems Biology of Ageing and Nutrition (PI: Prof Tom Kirkwood, Prof David Lydall, Prof Thomas von Zglinicki, Prof Anil Wipat; CI: Prof Darren Wilkinson, Prof Richard Boys and others), a BBSRC funded Centre for Integrative Systems Biology (2005–11)
  • Moment closure and parameter estimation in stochastic biological models — Peter Milner, supervised by Prof Darren Wilkinson and Dr Colin Gillespie, funded by EPSRC. PhD awarded 2011.
  • Variational Bayesian inference for comparison of VAR(1) models — Adrian Houghton, supervised by Prof Darren Wilkinson, funded by EPSRC. PhD awarded 2009.
  • CaliBayes — Integration of GRID-based post-genomic data resources through Bayesian calibration of biological simulators (PI: Prof Darren Wilkinson; CI: Prof Tom Kirkwood, Prof Richard Boys), funded by BBSRC.
  • ComparaGRID — Enabling technologies for comparative genomics (Newcastle PI: Prof Anil Wipat; CI: Prof Darren Wilkinson, Prof Richard Boys), funded by BBSRC.
  • BASIS — Biology of Ageing e-Science Integration and Simulation system (PI: Prof Tom Kirkwood; CI: Prof Darren Wilkinson, Prof Richard Boys), funded by BBSRC/MRC/DTI.
  • Hidden Markov models for DNA sequence segmentation — Newcastle University Fellowship held by Dr Daniel Henderson
  • GeneNets — Bayesian inference for stochastic kinetic genetic networks (PI: Prof Richard Boys; CI: Prof Darren Wilkinson, Prof Tom Kirkwood), funded by BBSRC.

Publications

For information on publications, please see the personal webpage of each member of the group.