e-Science Institute Theme 14 starts today

Today saw the start of Theme 14 – Modelling and Microbiology – at the e-Science Institute in Edinburgh. The theme will run for 12 months and covers the interface between high performance computation and microbiology. We will bring together mathematicians, physicists, computer scientists and microbiologists in a series of focused workshops followed by a larger research conference next summer. The topics covered are:

  • Stochasticisty and microbial infection (this week)
  • Experiments and simulations of evolution
  • Modelling of metabolism

The next two workshops will be held in January and April and the conference at the end of June.

The theme has been funded by the e-Science Institute and is a collaboration between Rosalind Allen, Jamie Wood and myself.

The opening lecture (by Ros) will be webcast and I will post a link when it becomes available.

Two posters at 9th European Conference on Computational Biology

Two PhD students in the lab will be presenting posters at this week’s 9th European Conference on Computational Biology in Ghent, Belgium.

Rafik Salama will be presenting a poster titled Transcription Factor Binding Site Multiple Sequence Alignment on new work developing MSAs specifically optimized for TF binding sites.

Dorota Herman will be presenting a poster titled Combined Monte Carlo and Dynamical Modelling of Gene Regulation Enables Multiple Parameter Estimations and Parameter Estimations. This poster covers our work on deterministic modeling of the transcription regulation of the central control operon of the RK2 plasmid.

Herman, Thomas and Stekel Poster

Both works are currently being prepared for journal publication and we aim to have them published in 2011.

If you get a chance to view the posters, do post comments!

New PhD student starts today

Today we welcome new PhD student Richard Crossland to the group.

Richard has a degree in Biology and Masters in Bioinformatics and Systems Biology from the University of Newcastle and will be working on multiscale mathematical / computational models of metal responses in bacteria, especially E. coli. Richard is co-supervised by Jon Hobman.

News from the BBSRC on our lux research grant

We have heard the following from the BBSRC:

BBSRC RESEARCH GRANT AWARD: BB/I001875/1  Quantification of Promoter
activity using lux Read-outs and Mathematical Models

As you are aware, the above research grant application has been recommended
for funding by Committee C.  I am writing to inform you that the start date
of all grants has been set to 4 April 2011 and no grants can start before
this date. This has been necessary in order to limit grant expenditure
during the 2010/11 financial year.

A small reduction has been made across the direct costs on all grants
awarded in this round.  You will be expected to accommodate this reduction
by achieving efficiency savings during the course of the project.

So, all being well, we expect to start our recruitment process in December/January. If something close to the full amount is awarded, there will be  two positions, one theoretical (with me) and one experimental (with Phil Hill and Dave Scott). If you are interested in working with us, watch this space!

Publication: De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory Mechanisms

Recent paper by Dafyd Jenkins and myself, De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory Mechanisms, has now been published in the Journal of Molecular Evolution, Volume 71, Number 2, p128-140. We have paid for Open Access because we are very pleased with this work. This is the last paper from Dafyd’s PhD so more work in this area now depends on further funding!


Gene regulatory networks exhibit complex, hierarchical features such as global regulation and network motifs. There is much debate about whether the evolutionary origins of such features are the results of adaptation, or the by-products of non-adaptive processes of DNA replication. The lack of availability of gene regulatory networks of ancestor species on evolutionary timescales makes this a particularly difficult problem to resolve. Digital organisms, however, can be used to provide a complete evolutionary record of lineages. We use a biologically realistic evolutionary model that includes gene expression, regulation, metabolism and biosynthesis, to investigate the evolution of complex function in gene regulatory networks. We discover that: (i) network architecture and complexity evolve in response to environmental complexity, (ii) global gene regulation is selected for in complex environments, (iii) complex, inter-connected, hierarchical structures evolve in stages, with energy regulation preceding stress responses, and stress responses preceding growth rate adaptations and (iv) robustness of evolved models to mutations depends on hierarchical level: energy regulation and stress responses tend not to be robust to mutations, whereas growth rate adaptations are more robust and non-lethal when mutated. These results highlight the adaptive and incremental evolution of complex biological networks, and the value and potential of studying realistic in silico evolutionary systems as a way of understanding living systems.