One year Scholarship for Masters by Research

School of Biosciences, University of Nottingham

One Year Masters by Research into Mathematical / Computational Analysis of Phenotype Responses of Brewers’ Yeast

Applicants are invited for a one year MRes co-sponsored by the University of Nottingham and an industrial partner into mathematical / computational analysis of phenotype responses of brewers’ yeast. The project will be under the supervision of Dr Dov Stekel and Professor Katherine Smart and will be part of the MRes in Brewing programme. It will be located in the attractive Sutton Bonington campus, and the researcher will be part of dynamic research communities in both brewing and mathematical/computational biology. The studentship would particularly suit someone with a strong mathematical or computing background with an interest in becoming engaged at the interface with high impact biological research.

Specifically, the research will include: (i) constructing mathematical models using ordinary differential equations for fitting data from Biolog™ phenotype arrays; these models may include complex lag phases, diauxie and other biological phenomena. (ii) Development of an inference scheme to identify model parameters and enable robust automated model choice; this will include use of Markov Chain Monte Carlo techniques. And (iii) application of these methods to data derived from Biolog™ phenotype arrays applied to brewers’ yeast in collaborative projects aimed at improving beer fermentation.

Applicants must hold or be about to complete a first degree in a relevant quantitative subject, for example mathematics, statistics, computer science or bioinformatics, with a minimum grade of 2.1 or equivalent. They should be familiar with ordinary differential equations and knowledge of probability or statistics would be helpful. Applicants must also be able to evidence aptitude for computer programming in a suitable high level language (e.g. C++ or Java) and/or a statistical programming language (e.g. R). This Masters project will require the person appointed to be highly motivated to become engaged in biological research, to work independently and as part of a multi-disciplinary team, and be willing to learn. Excellent English language written and oral skills are also essential (minimum level for overseas students IELTS 6.0 with no less than 5.0 in each element or TOEFL score of 550, 212 for computer based tests, with at least 4 in the Test of Written English. For this scholarship, preference will be given to candidates with scores well above the minimum requirements).

We are able to offer a full scholarship to a UK or EU student that would cover all fees and include a stipend of £13,590 for the year. Candidates from outside the EU will need to find funds for the additional fees costs.

Candidates should send a detailed CV, including university grades and predicted grades, together with the names and contact details of two referees, to dov.stekel [AT] by 13th May.

BBSRC Lux Grant Launch

This weeks sees the launch of our BBSRC Lux grant.

We are delighted to have recruited two experienced and talented PostDocs to work on the project.

Neil Doherty will work with Phil Hill and Dave Scott on the experimental elements of the work. Neil has a BSc in Biochemistry from the University of Warwick and a PhD in molecular microbiology also from the University of Warwick. He has since been carrying out postdoctoral research at the University of Nottingham in a number of molecular microbiology research groups, where he has carried out a wide range of experimental work in Staphylococcus aureus, Helicobacter pylori, Streptococcus pneumoniae and Escherichia coli.

Mudassar Iqbal will work with me on the modelling and inference elements of the work. Mudassar has a MSc in physics from the University of the Punjab, an MRes in modelling and simulation of complex realities from the ICTP/SISSA, Trieste, and a PhD in bioinformatics at the University of Kent. He was since carrying out postdoctoral research at the Warwick Systems Biology Centre. Mudassar’s experience includes development of algorithms for analysis of codon usage bias, protein-protein interactions and inference in transcriptomics.

We welcome both Neil and Mudassar to Nottingham and look forward to several years of interdisciplinary research.


Invitation to speak at IUMS 2011 Congress

Today I received an invitation to give a presentation at the International Union of Microbiological Societies Congress 2011 which will take place in Sapporo on the island of Hokkaido, Japan. I will be speaking in part of the ‘Bioinformatics for Microbiology’ symposium. The meeting will be from 6th-10th September.

I’m very much looking forward to the visit. The conference is nearly 400 miles from the stricken Fukushima plant so should be entirely safe – but will obviously take advice nearer the time. The conference organizers have linked to a very interesting talk on the nuclear reactor melt-down that includes helpful calculations of risk:

I am particularly keen to show support to Japanese science at this difficult time for Japan.