Congratulations to Sankalp Arya: International Research Collaboration Award

Congratulations to Sankalp who has received a £2300 International Research Collaboration Award from the University of Nottingham. Sankalp will spend two months (September and October) in Barth Smets’s laboratory at the Technical University of Denmark. This is a really fantastic opportunity for Sankalp to work in one of the leading environmental microbiology groups in the world. His work will focus on developing the iDynomics platform for individual based modelling of microbial interactions to model antimicrobial resistance. Well done Sankalp! And I look forward to visiting Barth’s lab too as part of the project.


Modelling the Spread of Antimicrobial Resistance in the Environment in China

We are delighted to have been awarded a small grant of £25k from an internal distribution of EPSRC Global Challenge Research Fund (GCRF) to the University of Nottingham. We will be working with Professor Yong-guan Zhu from the Chinese Academy of Sciences, Xiamen, to build statistical models for the spread of AMR genes and organisms in the Chinese environment. The money will find a talented post-doc, Laurence Shaw, to join our lab for 6 months from later this year. Young-guan and colleagues have carried out extensive and impressive AMR surveillance work so this is a very exciting opportunity. We are very much looking forward to working with Yong-guan and Laurence on this project.

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.

Welcome to Mike Stout

This week Mike Stout started work in our group as a research fellow on the BBSRC funded project to develop systems for high throughput analysis of cell growth data from BIOLOG phenotype arrays; a lay summary of this project can be found here.

Prior to this, Mike was a PDRA at the the Centre for Plant Integrative Biology, University of Nottingham, working with Professor Charlie Hodgman on developing repositories for multi-scale systems biology models and imaging data, and tools for systems biology simulation visualization. Mike’s PhD, also at the University of Nottingham, was on predicting geometric and topological properties of proteins using a range of machine learning systems, in particular Learning Classifier System. He has a background in both Biology and Computer Science and before his PhD headed the Electronic Journals Group at Oxford University Press, managing transnational projects to develop journal content online.

Mike’s research interests include Complex Systems Science, Evolutionary Computation, Functional Programming, Information Visualization and High Performance Computation using, for example, GPUs.

Mike’s experience and expertise will be particularly valuable for the group and we look forward to working with him.

Research grant award from the BBSRC

On Friday we heard good news from the BBSRC that our research grant application for the analysis of Biolog data has been successful. This is a joint bid with Katherine Smart, Jon Hobman, Helen West and Theodore Kypraios. The relevant quote from the BBSRC is:

Dear Dr Stekel,

I am please to inform you that application BB/J01558X/1 – ‘High throughput analysis of cell growth data from phenotype arrays’ submitted to the BBSRC 2011 Responsive Mode Grant Round 3 (RM3) has been successful.  We are currently in the process of preparing the grants for announcement. 

There will be a postdoctoral position associated with this grant which will be advertised in due course according to usual University of Nottingham procedures.

Lay Summary for the Research Grant

Fifty people died as a result of the recent E. coli outbreak in Germany. Four thousand people were infected. With a growing global human population, how do we ensure that we all have access to safe food? Fossil fuels will run out, and the recent Fukushima disaster highlighted the risks of nuclear energy. How do we provide sustainable sources of fuel to meet our energy and transport needs in the context of a population that is not just growing, but also developing?

These are major challenges, and a key strategy for overcoming them is the study of microbes. In the case of E. coli the disease is caused by harmful bacteria, and we need to understand how harmful bacteria survive in farms, soil, food production, storage and preparation facilities, as well as in animal and human hosts. In the case of fuels, microbes provide an opportunity for a new generation of biofuels. Biofuels are carbon neutral technologies, but conventional biofuels need similar materials or land that could otherwise be used for food. We are now seeking to develop biofuels from plant matter that cannot be used for food and is currently wasted. To do this, we need to find new strains of yeast that can convert this plant matter into fuel.

In recent years, new technologies have been developed that enable us to read the full genome sequence of a microbe in just a day. This is indeed remarkable, but the genome sequence is a set of instructions in a language that we can only begin to understand. What really matters is how a microbe behaves in different environments: on what foods does it thrive, on what foods does it starve? What potential toxins can it survive and what toxins kill it? These questions are essential for understanding how we can combat harmful food-borne bacteria, or develop new bioenergy producing agents. And if we can link these answers to the genome sequence, we have a powerful way of decoding the language of the genes.

This proposal is focussed on a technology, called Biolog Phenotype Microarrays, that precisely measure how well microbes thrive in thousands of conditions, including different food sources and potential toxins. The arrays generate time courses that plot each condition at a regular point in time, with several hundred measurements of cell activity during the course of an experiment. Each time course encodes a wealth of information: how long does it take before the microbes start to become active? How quickly do they grow? Are they able to use more than one food source, and if so, is one better than the other? How much do they grow? Remarkably, there are no analysis methods available that allow users of Biolog arrays to obtain this information from the Biolog output: instead, users typically use a single datum, such as the end-point, or total growth, and discard most of the valuable information.

The aim of this proposal is to bridge this gap. To do so, we intend to build mathematical models that describe cell activity in Biolog arrays; these need to reflect the details of the technology, as well as the complexity of the conditions in which the cells are grown. We propose to develop automated ways of working out which model best fits any given set of data, and identify the key parameters describing microbial behaviour. Automation is essential, because a single experiment can generate 2000 microbial time courses. The methods have to be accessible to the wider scientific community, not just mathematicians, so we need to develop user-friendly interfaces to the methods we develop, and provide training for Biolog users in these methods.

Finally, in our established research programmes, we have generated vast quantities of Biolog data on survival of harmful E. coli strains, microbial soil contamination and the development of new yeast strains for producing biofuel from non-food plant material. We will directly address the food safety and bioenergy challenges by applying our methods to these data.

EPSRC Research Development Fund – Monte Carlo estimation of parameters for large data biological data sets using graphical processing units.

Together with Theodore Kypraios we have been awarded £8699 from the EPSRC Research Development Fund for the project:

Monte Carlo estimation of parameters for large data biological data sets using graphical processing units.

This award will start with immediate effect and will support Dorota Herman for a period of three  months to carry out this work. Thanks also to Matthias Gerstgrasser who was involved in initiating this project and who will work together with Dorota in this area.

We look forward to welcoming Dorota back to Nottingham for a short period!



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.