Current opportunities
Applications now open! We are looking to recruit a PhD student to start October 2026. Competitive funding is available through the Darwin Trust scholarships for international students. You can also find the project description and application instructions here.
Project title: Mathematically modelling the 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). Indeed, evolution of resistance is an exemplar of the general process of ‘evolutionary rescue’ (ref.1), a stochastic event where sufficiently rapid adaptation saves a population from extinction under severe environmental change.
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, death, and 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 (ref.3 & ongoing work) show that the presence of an initially large population 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.
- Derive analytical approximations and/or implement computational frameworks to solve model equations and predict the probability that resistance emerges under different conditions (cf. ref.1,2)
- Compare model predictions to experimental data generated in our lab: specifically, the estimated establishment probability of resistant cells (ref.3).
- Use the model to explore optimal antibiotic dosing patterns that minimise the probability of resistance emerging (cf. ref.2).
Adaptations to this PhD project, within the general topic area and using mathematical modelling, may be possible in discussion with the supervisor.
References:
- Marrec & Bitbol, Genetics 2020 (doi:10.1534/genetics.120.303624)
- Czuppon et al, PLoS Comp Biol 2023 (doi:10.1371/journal.pcbi.1011364)
- Alexander & MacLean, PNAS 2020 (doi:10.1073/pnas.1919672117)
What we're looking for: Candidates should hold at least an undergraduate degree prior to starting the PhD. The ideal candidate for this PhD would 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 (School of Biological Sciences), with strong connections to the cross-School mathematical biology community at the University of Edinburgh. The PhD will offer the opportunity to gain skills in mathematical modelling, computational methods (including reproducible coding), data analysis, and broader professional skills such as communicating with diverse academic teams. You can find more information about studying for a PhD in the School of Biological Sciences here.
Funding and eligibility information: Funding is available on a competitive application basis through the Darwin Trust. Scholarships cover university tuition fees and provide a stipend for 4 years. Scholarships are available to international students who are not already graduates of the University of Edinburgh. Please refer to the Darwin Trust website for full eligibility details.
How to apply:
- Email Helen to discuss your interest in the project. Please aim to contact me by 15 December to have the best chance of a response before the Christmas break.
- Apply to the University of Edinburgh through the online system ('Euclid').
- Apply for a Darwin Trust scholarship using the application form available on their website (deadline: 7 January 2026)
General information
PhD projects will normally be advertised starting around October to November, with application deadlines ranging from late November to early February, 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:
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
