Mathematical Biology and Medicine

Permanent Lecturer in Applied Mathematics EPSRC AstraZeneca Scholarship
CASE PhD Studentship in Computational Biology at the University of York and GSK

Forthcoming seminars: Wed 12 noon in MALL, School of Maths

  • 23 May 2012 Chris Greenman (University of East Anglia)
    Resolving Cancer Genomes with Next Generating Sequencing
    Cancer arises from selective growth advantage imparted by mutations in cancer genes. This talk will present some applications of next generation sequencing to better understand these processes of mutation and selection. In particular, sequences of breakage-fusion-bridge cycles can lead to amplicons in cancer genomes. These rearrangements have some nice mathematical properties that are quite similar to paper folding sequences which can be utilised to describe genomes arising from these processes. The aims of the international cancer genome consortium is to sequence thousands of these genomes with a view toward finding new cancer genes. Some of the approaches to detect these genes from a panel of samples will be discussed, along with translational approaches correlating the genetic status of genomes with drug response.

Forthcoming programs, conferences and workshops

Recent Publications & Preprints

Recent programs, conferences and workshops

Recent Mathematical Biology and Medicine seminars

  • 9 May 2012 Marcus Tindall (University of Reading)
    Understanding cholesterol regulation: An evolving story
    Cholesterol is vital for cell integrity and survival. However, in the face of a growing obesity epidemic cholesterol often attracts bad press. In this talk I will discuss recent mathematical models we have developed of cholesterol regulation at both the genetic and cellular levels and how we are developing this models to understand cholesterol regulation in the context of problems ranging from diet to crop protection. I will outline current efforts to integrate the two models and the overall long term strategy of our work.
  • 25 April 2012 Reidun Twarock (University of York)
    Viruses and Geometry - Where Symmetry meets Function
    Viruses display symmetry for reasons of genetic economy: By packaging their genomic material into protein containers (capsids) that are organised with icosahedral symmetry, they maximize container volume while minimizing the portion of the genomic sequence needed to code for the capsid. From a mathematical point of view, this implies that techniques from group, graph and tiling theory can be used to predict virus architecture. We show here that via an affine extension of the icosahedral group and associated tilings new information regarding structural constraints on virus architecture can be obtained, that reveals a previously unrecognised structural correlation between different viral components. We discuss the implications of such structural features for function, i.e. for how viruses form and infect their hosts. In particular, we show that the assembly of single-stranded RNA viruses follows a set of local rules that can be understood in terms of the interactions between genomic RNA and capsid protein. We moreover present a new mathematical approach for the prediction of the structural transitions of viral capsids important for infection.
  • 11 April 2012: Sandro Azaele (University of Leeds)
    A spatially explicit model for linking ecological patterns Until recently, ecological communities have been studied through a collection of empirical patterns whose underlying interconnections are yet unclear. For instance, we know that species are usually clumped in space, but how does this rebound on the richness of species of a region? Over the last few decades, ecologists have come to realize that the explicit introduction of spatial structure can greatly improve our understanding of populations and communities. However, whether a unifying theory is able to explain simultaneously several empirical patterns remains a matter of debate. In this seminar we introduce a minimal spatially explicit framework based on the assumption that species are non-interacting within a trophic level. In a simple fashion it encapsulates four basic processes: dispersal, immigration/emigration, birth/death and demographic stochasticity. We show how this model produces and theoretically interlinks several realistic biodiversity patterns, and benchmark it against empirical data. The approach also explains why species' richness as a function of area is characterized by three different regimes.
  • 21 March 2012 Andrew Teschendorff (University College London)
    Overcoming statistical challenges arising in epigenome-wide cancer studies
    Abstract: Large-scale epigenome-wide profiling promises to improve our understanding of complex genetic diseases like cancer and to identify the much needed cancer risk and early detection markers. However, a common difficulty encountered in large-scale high-throughput studies is the presence of confounding factors, which may significantly skew estimates of statistical significance and cause unreliable feature selection. Confounders are also frequently unknown or only known with error, posing an additional challenge. I will motivate and describe an Independent Surrogate Variable Analysis (ISVA) framework, based on a blind source separation technique, which can help overcome these difficulties. It will be shown how ISVA improves inference in the context of quantitative molecular data such as DNA methylation and gene expression. Time allowing, I will discuss some of the more specific statistical challenges we encounter in cancer DNA methylation studies and will present a novel adaptive index prediction algorithm for the diagnosis and risk prediction of precursor cancer lesions.
  • 30 November 2011 Alison Etheridge (Oxford)
    Modelling evolution in a spatial continuum
  • 23 November 2011 Stephen Webb (Glasgow)
    Computational modelling of cell migration and chemotaxis
  • 16 November 2011 Carlo Berzuini (Cambridge)
    Causal inference in genetic epidemiology: looking into mechanism
  • 19 October 2011 Thomas Fink (Cambridge)
    The relation between robustness, adaptability, and fitness
  • 18 May 2011 Jon Pitchford (York)
    Evolving stochastic strategies: analytical, statistical and computational approaches
  • Darren Wilkinson (Newcastle) 8 December 2010
    Modelling and learning for noisy cellular decisions: motility of Bacillus subtilis
  • David Westhead (Leeds) 1 December 2010
    Metabolic networks, horizontal gene transfer and evolution
  • Wally Gilks 24 November 2010
    (Statistical Genomics Group, Rothamsted Research and Department of Statistics, University of Leeds)
  • Jorge Carneiro (Instituto Gulbenkian) 10 November 2010
    Multiscale modelling of regulatory T cells and immunological tolerance
  • Christian Yates (Oxford) 27 October 2010
    United by noise: Randomness helps swarms stay together

Seminar list with abstracts