Now recruiting: Research Associate/Fellow in Antimicrobial Resistance Modelling

We are now recruiting the mathematical modelling post-doc for the EVAL-FARMS project. This post will work with me, Theo Kypraios in Maths, and the EVAL-FARMS team more generally, developing mathematical models for risk of emergence of AMR pathogens in agricultural waste, using all the exciting data that are being generated by the empirical researchers on the grant. Details of the advert, as well as links to it, are:

Research Associate/Fellow in Antimicrobial Resistance Modelling

Agricultural & Environmental Sciences

Location:  Sutton Bonington
Salary:  £26,052 to £38,183 per annum, depending on skills and experience (minimum £29301 with relevant PhD). Salary progression beyond this scale is subject to performance
Closing Date:  Wednesday 28 June 2017
Reference:  SCI158617

We are seeking an excellent researcher in modelling of antimicrobial resistance. The successful applicant will use mathematical and statistical models to make predictions on risk of emergence of antimicrobial resistant pathogens in a farm slurry system and slurry amended soil. The post is funded by NERC-led EVAL-FARMS project (Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries). Thus the role holder will work closely with an interdisciplinary team, including experimental researchers in microbiology and analytical chemistry, and social researchers in science and technology studies, in order to develop meaningful, data driven risk models that could inform policy and practise. The work will involve deterministic and stochastic models, Bayesian statistics, data analysis and presentation.

Applicants must have, or be very close to completing, a PhD in mathematical, computer or statistical models applied to a relevant area in the biological or environmental sciences. Research experience in applying such models in antimicrobial resistance, metagenomics, analytical chemistry and/or water quality would be desirable. Applicants must be able to demonstrate skills in Bayesian approaches, including relevant computational techniques such as MCMC, development and analysis of deterministic and stochastic models, programming in a relevant language (e.g. R, Python or Matlab) and a broader appreciation of science. Applicants must also be able to demonstrate research ambition through timely publication of research, coupled with commitment to the research project as part of their on-going career development. Excellent oral and written English language skills are essential.

The post is a joint appointment between the Schools of Biosciences and Mathematical Sciences. The post holder will normally work on the Sutton Bonington Campus, and will also have meetings on the University Park Campus with staff in the School of Mathematics and other collaborating schools.

Fixed term for 2 years from 1st September 2017

Applications can be made through the University of Nottingham web site. I am happy to receive informal enquiries.

Research Associate/Fellow in Science and Technology Studies (STS)

We are now advertising the next postdoctoral job for the EVAL-FARMS project. This is a part time role (3 days/week) for three years.

Research Associate/Fellow in Science and Technology Studies (STS)

Sociology & Social Policy

Location:  Sutton Bonington
Salary:  £26,052 to £38,183 per annum, pro rata depending on skills and experience (minimum £29301 with relevant PhD). Salary progression beyond this scale is subject to performance
Closing Date:  Friday 02 December 2016
Reference:  SOC323516

We are seeking an excellent researcher in Science and Technology Studies.

The post-holder will conduct qualitative ethnographic work and interviews on social and cultural aspects of knowledge on antimicrobial resistance in laboratory and farm settings, with the University of Nottingham, UK as the main focus.

Applicants must have a PhD (or be near to completion)  in science and technology studies (STS), human geography or related field, including postgraduate training in social science research methods, or have equivalent relevant knowledge, skills and experience. You must be able to engage with a wide range of stakeholders, including scientists and farmers, as you would be part of a highly multidisciplinary team. Excellent oral and written English language skills are essential. Applicants must be highly motivated, ambitious and have a proven track record of timely research publications (from PhD or beyond).

The post is funded by the NERC EVAL-FARMS project (Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries), and will be jointly supervised by the School of Sociology and Social Policy (Institute for Science and Society/ISS) and the School of Geography.

The Associate/Fellow will be primarily located in the School of Biosciences and expect to be physically present on the Sutton Bonington campus, where the scientific work in EVAL-FARMS will be carried out. The fellow will spend roughly a third of their time on University Park where the Schools of Sociology and Social Policy, and of Geography are located.


Informal enquiries may be addressed to Sujatha Raman tel: 0115 846 7039 or email Please note that applications sent directly to this email address will not be accepted.

Research Fellowships at University of Nottingham – be in touch

The University of Nottingham has advertised for its internally funded Research Fellowships (all applicants) and Anne McLaren Fellowships (women only). If you are interested in a fellowship in computational biology, biostatistics or related area, please be in touch. These are three year fellowships that could lead to a permanent academic post.

The competition is highly competitive – I know this as I have once sat on our School panel – so it is only worth applying if you have an excellent doctoral and post-doctoral track record: you will need excellent first-author papers in top journals to be succesful. You would also need the support of the school, so it is very important to be in touch if you are interested.

So, if you think you could be interested, please be in touch, and include links/pdfs of your two best first author papers.





PhD opportunity: Tunable zinc responsive bacterial promoters for controlled gene expression


Tunable zinc responsive bacterial promoters for controlled gene expression

Supervisory Team: Dr Jon Hobman (School of Biosciences), Dr Phil Hill (School of Biosciences), Dr Dov Stekel (School of Biosciences).

Applications are invited for this 4-year PhD project which is part of a University-funded Doctoral Training Programme (DTP) in Synthetic Biology and associated with Nottingham’s new BBSRC/EPSRC Synthetic Biology Research Centre. Students will benefit from a diverse range of training opportunities, including specialist workshops, lectures and seminars, as well as participation in Nottingham’s yearly BBSRC DTP Spring School event.

Zinc is an essential metal, required in ~30% of bacterial proteins, but is toxic at higher intracellular concentrations. Bacteria such as E. coli have evolved sophisticated zinc import and export systems controlled by transcription factors that repress the expression of genes encoding importer proteins (regulator Zur) or activate expression of zinc efflux (regulator ZntR). These regulators and the promoters they control represent a good example of fine tuning of cellular response to external zinc concentrations (1) and different Zur and ZntR regulated promoters have different affinities and transcription levels. The aim of this PhD will be to study the levels of expression from engineered Zur and ZntR regulated promoters in response to zinc, so that a suite of promoters can be used to finely control gene expression in response to zinc levels in growth media. These promoters will be used to control gene expression in engineered bacteria using cheap zinc inducers and zinc chelators, and will allow tuned expression of industrially useful synthetic pathways in E. coli and other Gram-negative bacteria. These tunable promoters could have potential impact in a range of biotechnology/biosynthesis contexts.

The project is available from 1st October 2016 and is open to UK and EU students with a 2(i) degree or above in microbiology, genetics, biochemistry, or a related discipline. The work will be based at the School of Biosciences in Nottingham.

The supervision team for this project is multi-disciplinary, enabling training in a wide-range of subjects and techniques in microbiology, molecular biology, cell engineering, reporter gene systems, mathematical modelling, data analysis, and cell metabolism.

Applicants should submit a covering letter, CV and the names of two academic referees addressed to: Rob Johnston School Administrator

Closing date for applications: 31st July 2016

Informal enquiries to Dr Jon Hobman ( )

(1)       Takahashi et al (2015). Journal of the Royal Society Interface 12: 20150069


EVAL-FARMS: Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries

Today NERC announced that our £1.5M AMR grant has been funded. We are very excited!

First thing to say is that it was a total team effort. I am embarrassed by the fact that only my name is listed on the announcement – it really would have been impossible without the expertise, intelligence, energy, commitment and open spirit of collaboration of my totally awesome colleagues: Jon Hobman, Rachel Gomes, Helen West, Sujatha Raman, Jan Kreft, Stephen Ramsden, Christine Dodd, Chris Thomas, Mike Jones, Andrew Millard, Richard Emes, David Barrett,  Carol Morris, Theodore Kypraios and Chris Hudson. And then the support we received: pump priming  for research from the schools of Biosciences, Pharmacy and Engineering, and for a grant-writing retreat from the University of Nottingham; writing support from Emma Allaway, Chris Satterley, Zoe Wilson and especially Diane Levine; and the enthusiasm of an array of external stakeholders from industry and policy, including NFU, BCVA, Velcourt, Lindhurst Engineering, DEFRA (VMD and APHA), FSA, JHI amd Severn Trent Water.

Project details (summarized from the Case for Support)

Our vision is to establish a strategic research programme in antimicrobial resistance (AMR) in waste from agricultural farm environments. Our aim is to quantify and mitigate the risks of emergence of resistant pathogens and AMR gene reservoirs associated with mixing antimicrobials with waste matter in these environments.

The project is focussed on the University of Nottingham’s (UoN) dairy and arable farm, which is typical of high performance UK dairy production, with ~200 high yielding cows. Slurry is stored in a 3M L slurry tank and subsequently spread on surrounding fields. We hypothesise that conditions in the slurry tank environment drive the evolution and acquisition of antimicrobial resistance, and the slurry acts as a reservoir for AMR that is regularly distributed into the environment

The project consists of six integrated Research Questions:

RQ1: What are the levels and nature of antimicrobial and virulence genes present in the slurry tank, their prevalence, carriage, and bacterial hosts?

RQ2: What are the chemical agents in the tank? What is their persistence?

RQ3: To what extent is resistance maintained after slurry application to soil?

RQ4: How can we elicit culturally embedded ways in which scientists and stakeholders know AMR risks? How can we use narrative and visual methods of engaging across these ways of knowing to develop resources for deliberation on AMR risk management?

RQ5: To what extent can we reduce resistance profiles through changes in slurry tank composition?

RQ6: Can we quantify the risk of emergence of AMR pathogens and what factors are predicted to control this risk best?

The first three posts will be advertised shortly. These will be 24 month post-docs in microbiology (supervised by Jon Hobman and Christine Dodd), pharmaceutical analysis (supervised by Rachel Gomes and David Barrett) and a 36 month 60% post-doc in cultural research (supervised by Sujatha Raman and Carol Morris). In practise, these posts will work across the different Research Questions in the grant, so the postdocs will interact with the full team. Technician posts to follow a little after, and a modelling postdoc will start in January 2018. There will also be three associated PhD studentships (pharmaceutical analysis, social research, mathematical modelling) to start in September 2017.

We have also developed an infographic to help explain how conditions in slurry could lead to emergence and selection for AMR bacteria. Here it is:





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.