Joining us

University of Edinburgh students

Honours and Master's projects will normally be offered and allocated through your program's centralised organisation. The projects we offer will vary from year to year, but may include Honours projects across the Biological Sciences (with priority to Ecology, Zoology, and Evolutionary Biology programs), MSc in Computational and Applied Mathematics, MRes Infectious Diseases, and others. If you are particularly interested in joining our group for your project, you are welcome to contact Helen Alexander in advance to discuss a project proposal.

External students

We have limited capacity to offer projects to students from other universities. However, you are welcome to contact Helen Alexander to ask about possibilities for summer projects, Master's thesis rotations, etc. Please briefly explain what topic(s) you are interested in studying, outline your relevant skills, and attach your CV. Further practical information for short-term visiting research students is available from the School of Biological Sciences.

Current opportunities

Applications now open! We are looking to recruit a PhD student to start in October 2025. The proposed project is described below. Other projects within our general research interests may be possible in discussion with the supervisor (Helen Alexander), with priority given to mathematical modelling projects this year.

Project title: Modelling stochastic emergence of antibiotic resistance in bacterial populations

Project description:

Bacterial evolution of antibiotic resistance within patients can compromise the efficacy of antibiotic treatment and represents a serious threat to public health. However, outcomes vary among patients and even in controlled lab populations of bacteria. This suggests that the emergence of antibiotic resistance is subject to stochastic effects within the bacterial population, in both the occurrence of mutations and their chances of establishment (i.e. survival and growth to large numbers).

The emergence of resistance occurs in a complex environment that changes over time. Abiotic factors, such as nutrient availability and antibiotic dose, impact cell division and death rates. Some antibiotics induce stress responses that increase mutation rates. Importantly, bacteria also feed back on their own environment, e.g. by consuming nutrients, secreting metabolites, and degrading antibiotics. This implies that the environment faced by nascent resistant lineages is strongly shaped by the surrounding bacterial population. 

Experiments from our lab show that the presence of sensitive bacteria can either increase or reduce the probability that a resistant cell establishes a surviving lineage under different conditions. The interacting factors driving these effects are presently unclear.

To address this knowledge gap, this PhD project aims to:

• Develop mathematical models describing bacterial population dynamics under antibiotic treatment, incorporating bacterial interactions with environmental factors. We anticipate using ordinary differential equations, stochastic birth-death processes, and stochastic simulations.
• Implement computational frameworks to solve model equations and calculate the probability that resistance emerges under different environmental conditions and timings of appearance.
• Compare model predictions to experimental data generated in our lab: specifically, the estimated establishment probability of resistant cells (ref.1).
• Use the model to explore optimal antibiotic dosing patterns that reduce the probability of resistance emerging (cf. ref.2).

References:

1. Alexander & MacLean, PNAS 2020 (doi:10.1073/pnas.1919672117)
2. Czuppon et al, PLoS Comp Biol 2023 (doi:10.1371/journal.pcbi.1011364)

What we are looking for: The ideal candidate for this interdisciplinary PhD will have strong mathematical/computational skills, e.g. a degree in Mathematics, Physics, or another discipline with substantial mathematical training and experience with coding. Extensive biological knowledge is not required at the outset, but the candidate should be motivated to learn, to answer biological research questions, and to interact with both theoretical and experimental researchers.

What you can expect: The PhD candidate would join our interdisciplinary research group based in the Institute of Ecology and Evolution, with strong connections to the cross-School mathematical biology community at the University of Edinburgh. The anticipated secondary supervisor is Dr. Michael Nicholson (School of Mathematics). The PhD will offer the opportunity to develop skills in mathematical modelling, computational methods (including reproducible coding), data analysis, and broader professional skills such as communicating with diverse academic teams.

Funding and how to apply:

• Step 1: Check your eligibility and find out more about the application process.
• Step 2: You are strongly encouraged (and for certain funding routes required) to contact Helen Alexander by email as early as possible to express your interest and clarify any questions you may have. In your initial email, please briefly explain what interests you about this project and describe your relevant skills/qualifications, attaching a CV. It is useful to mention your relevant university-level coursework and grades, but please do not send reference letters at this stage.
• Step 3: Apply for a PhD at the University of Edinburgh via the EUCLID online system, in advance of any funding application deadlines.
• Step 4: Apply for funding, which will cover university fees and provide a stipend. Different funding routes have different requirements and offer different training opportunities and support, so please read details carefully. You can apply for multiple funding routes provided you meet their eligibility criteria.
  • NERC E5 doctoral training programme (UK and international students): application deadline 6 January 2025 (12:00 GMT)
    • General information
    • Advertised project
  • Darwin Trust scholarships (international students only): download application pack by 3 January 2025, submit application by 15 January 2025
    • General information
    • Advertised project
  • one further option likely to be announced soon, stay tuned!

General information

PhD projects will normally be advertised around October to November, with application deadlines ranging from late November to early January, to begin studies the following October. Some funding programmes may recruit on a later timescale. If you have your own research ideas, within the scope of our research interests, please get in touch as early as possible to discuss potential projects.

PhD scholarships (covering a stipend and tuition fees) are available on a competitive basis for both UK and international students. In most cases, funding is for 4 years. We commonly recruit through the following programs:

• EastBio doctoral training program
• NERC E4 doctoral training program
• Darwin Trust Scholarship
• Wellcome Trust PhD programme in Hosts, Pathogens, and Global Health
• EPSRC doctoral training program

If you are considering an external scholarship (e.g. from your home country), please get in touch as early as possible to discuss feasibility.

If you are interested in applying, you are strongly encouraged to get in touch as early as possible (email Helen) to discuss funding options and the application process. When contacting me, please summarise your academic background, attach your CV, and explain which project(s) interest you. You will have the best chances of a quick, positive response if you send a *specific* email showing that you have already done some background reading and explaining why you are interested in doing a PhD in our group.

Further information on postgraduate research in the School of Biological Sciences

PhD funding opportunities and how to apply

Open positions

There are currently no funded positions available.

Fellowship applications

We welcome candidates interested in applying for externally funded postdoctoral fellowships to be hosted in our group. If you want to develop your own project, broadly within the scope of our research interests, you are welcome to contact Helen Alexander to discuss the possibilities. 

Important notes: Many fellowships have only one application round per year, and the process from application to starting a position can take up to a year. Please check eligibility requirements when identifying potential fellowship(s). Institute-level support will generally be required for applications, so please get in touch early to discuss.

Potential funding sources include:

• BBSRC Discovery Fellowship
• Human Frontier Science Program Postdoctoral Fellowships
• Royal Commission for the Exhibition of 1851 Research Fellowships
• Royal Society Newton International Fellowships
• Schmidt Science Fellows
• Wellcome Early Career Award
• University of Edinburgh Cross-Disciplinary Fellowships (XDF)
• You can also try searching the funding database at ECR Central or looking for fellowships offered by your home country.