School of Mathematics, Statistics and Physics

Statistical Bioinformatics & Stochastic System

Statistical Bioinformatics and Stochastic Systems Biology

Overview

We have a broad range of interests covering statistical bioinformatics and stochastic systems biology and work closely with other Institutes and research groups across the University.

This group has a broad range of interests, covering statistical bioinformatics and stochastic systems biology:

  • stochastic and deterministic modelling of complex biological processes, particularly those related to ageing (CISBANBASIS)
  • 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:

The group also contributes to the teaching and project supervision on the MSc in Bioinformatics.

Grants and Fellowships

Details of the grants and fellowships awarded to members of the Statistical Bioinformatics and Stochastic Systems Biology research group.

Current:

NUFEB: Newcastle University Frontiers in Engineering Biology
CI: Prof Darren Wilkinson, funded by EPSRC.

Functional dissection of the genetic interaction network that affects growth of cells with telomere defects: implications for health and disease
CI: Prof Darren Wilkinson, funded by MRC.

Quantitative Fitness Analysis to understand the Schizosaccharomyces pombe telomere cap
CI: Prof Darren Wilkinson, funded by Cancer Research UK.

Algorithms for inference in stochastic kinetic models
Jamie Owen, PhD student, supervised by Prof Darren Wilkinson and Dr Colin Gillespie

 

Past:

Bayesian inference for stochastic differential mixed-effects models
Gavin Whittaker, PhD student (2011-15), supervised by Dr Andrew Golightly and Prof Richard Boys

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, BBSRC DTG funded PhD student (2010–2014), supervised by Prof Doug Gray, Prof Richard Boys and Dr Colin Gillespie

Modelling gene tree heterogeneity in phylogenetic inference
Rute Vieira, Portuguese FCT funded PhD student (2010–14), supervised by Prof Richard Boys and Dr Tom Nye

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).

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.

Staff

The following members of staff from the School of Mathematics and Statistics are members of the Statistical Bioinformatics and Stochastic Systems Biology research group.

Dr Peter Avery
Senior Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 7317

Dr Malcolm Farrow
Senior Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 7308

Dr Colin Gillespie
Senior Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 7248

Dr Andrew Golightly
Senior Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 7312

Dr Daniel Henderson
Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 7246

Dr Tom Nye
Senior Lecturer in Statistics

Email:
Telephone: +44 (0) 191 208 5369

Professor Darren Wilkinson
Professor of Stochastic Modelling

Email:
Telephone: +44 (0) 191 208 7320