PhD opportunities at the University of Nottingham

The University of Nottingham and the Rothamsted Research Institute are now advertising for 42 fully funded four-year PhD places in their Doctoral Training Partnership. For applicants with a maths, physics or computing background interested in mathematical / computational biology, there are opportunities in all three themes to become involved in world-leading bioscience research. There are three projects on which I would be a second / third supervisor.

  1. Bayesian Inference for Dynamical Systems: From Parameter Estimation to Experimental Design with Theodore Kypraios (maths) as main supervisor. This project will be entirely mathematical / computational.
  2. The role of a novel zinc uptake system (C1265-7) in uropathogenic E. coli, with Jon Hobman as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.
  3. Tunable zinc responsive bacterial promoters for controlled gene expression in E. coli, with Phil Hill as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.

For more information, please visit the advert site on

New Publication: Adaptation for Protein Synthesis Efficiency in a Naturally Occurring Self-Regulating Operon

Dorota’s second paper has just been published in PLoS ONE as:

Herman, D., Thomas, C.M. and Stekel, D.J. 2012. Adaptation for Protein Synthesis Efficiency in a Naturally Occurring Self-Regulating Operon. PLoS ONE 7(11): e49678.

We are particularly pleased with this work, and had some very nice comments from the reviewers. The quotes (from two different reviewers) here are reproduced with permission from PLoS ONE:

“the kinds of questions the authors address appear to be the most rewarding uses of computational/mathematical uses in biology”

“I found this paper important because it investigates a system with biological plausible parameters, thus, revealing whether the results of previous purely theoretical studies are biologically plausible.”

We are hoping for that sort of reception more generally in the community!

The abstract of the paper is:

The korAB operon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed investigation of the role of the regulatory mechanism using a biologically grounded mechanistic multi-scale stochastic model that includes plasmid gene regulation and replication in the context of host growth and cell division. We use the model to compare four hypotheses for the action of the regulatory mechanism: increased robustness to extrinsic factors, decreased protein fluctuations, faster response-time of the operon and reduced host burden through improved efficiency of protein production. We find that the strongest impact of all elements of the regulatory architecture is on improving the efficiency of protein synthesis by reduction in the number of mRNA molecules needed to be produced, leading to a greater than ten-fold reduction in host energy required to express these plasmid proteins. A smaller but still significant role is seen for speeding response times, but this is not materially improved by the cooperativity. The self-regulating mechanisms have the least impact on protein fluctuations and robustness. While reduction of host burden is evident in a plasmid context, negative self-regulation is a widely seen motif for chromosomal genes. We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis.

Birmingham-Nottingham Strategic Collaboration Fund awarded

We are delighted that the Universities of Birmingham and Nottingham have awarded a Strategic Collaboration Fund award to Josh Rappoportand myself. The project is titled “Experimental analysis and modeling of occludin trafficking during epithelial polarization and wound healing”. We will be looking at the modelling end, developing an ODE model and fitting to data from Josh’s lab using Monte Carlo techniques. The funding awarded is £20,000 and we will be looking for a short-term post-doctoral research fellow for a two month period to carry out the work – to start at some point in 2013 (further details to be posted).

We are very much looking forward to collaborating with Josh and others on this project.

ADAC Bioinformatics Posts on-line

Data Analyst in Bioinformatics (two posts, fixed-term)

Applications are invited for the above posts specialising in Advanced Data Analysis, with a particular emphasis on bioinformatics. The successful candidates will carry out multi-disciplinary data analysis as part of the newly formed Advanced Data Analysis Centre (ADAC: at the University of Nottingham.

The persons appointed will be aligned with the bioinformatics research group housed at the school of veterinary medicine and science ( and will be associated with other researchers in the Advanced Data Analysis Centre.

Candidates must hold a PhD (or equivalent) in a relevant subject; experience of multi-disciplinary data analysis and a proven ability to apply a wide range of bioinformatics, statistical and computational data analysis approaches in order to analyse a variety of biological/biomedical data. It is desirable that candidates have the ability to both apply existing techniques and develop new techniques in languages such as ‘R’, ‘PERL’ or ‘Python’, have experience of data generated by high throughput techniques such as DNA sequencing or proteomics, and have an interest in broadening multi-disciplinary collaboration across academic disciplines.

Informal enquiries may be addressed to Dr Richard Emes, tel: +44 (0)115 951 6583 or  Please note that applications sent directly to this email address will not be accepted.  Further information about the School of Veterinary Medicine and Science is available at:

The link to the job on the University of Nottingham vacancies site is here.

Launch of University of Nottingham’s Advanced Data Analysis Centre – ADAC

Today the University of Nottingham launches the Advanced Data Analysis Centre – ADAC. This represents an investment of £492,000 of University funding over a five year period. ADAC will support University of Nottingham’s research and discovery by assisting in research grant applications and by analysis of large and complex data sets. The centre will employ seven data analysts over a 5 year period who will be based in the Vet School in the Sutton Bonington Campus and in the School of Computer Science in the Jubilee Campus. ADAC has three directors: Richard Emes, who is Director of Bioinformatics; Jon Garibaldi, who is director of Informatics; and myself.

We are currently recruiting the first post – a research officer in advanced data analysis and database systems – to be based in Computer Science. Two bioinformatics vacancies to be based in the Vet School will be advertised shortly.