PhD: Understanding Rodent Virus Transmission in Heterogeneous Landscapes

PhD at Yale University in collaboration with partners in the US (Cary Institute, Smithsonian), UK (RVC, Glasgow, Oxford), Uganda (Vector Control Division) and Kenya (International Livestock Research Institute). We particularly encourage East African students to apply.
PhD: Understanding Rodent Virus Transmission in Heterogeneous Landscapes

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We are seeking a highly motivated PhD Student to join our interdisciplinary team investigating wildlife reservoirs of zoonotic viruses. The overarching research project is entitled 'Integrating metaviromics with epidemiological dynamics: understanding rodent virus transmission in the Anthropocene.'

The project is funded through the NSF/NIH/BBSRC US-UK Ecology and Evolution of Infectious Disease (EEID) Programme and involves partners from the US (Cary Institute of Ecosystem Studies, Smithsonian’s Global Health Program), UK (Royal Veterinary College, Glasgow, Oxford), Uganda (Vector Control Division) and Kenya (International Livestock Research Institute - ILRI).

The objective of the PhD project is to quantify how landscape features shape rodent virus transmission dynamics along a gradient of land conversion in eastern Uganda. The successful candidate will lead field and lab studies to quantify Mastomys natalensis (MN) virus transmission dynamics across a gradient of land use defined by tree canopy cover. Rodent populations will be monitored across six sites using capture-mark-recapture methods combined with target-enriched sequencing to characterize RNA viruses. Multiplex characterization of viral species will enable species-level analyses and virus community comparisons between sites. The outcomes of this aim will help inform the necessary scales of intervention strategies, either by focusing on rodent control at a specific site, land use type, or the entire region.

The successful applicant will be enrolled onto a fully funded 5-year PhD program at Yale School of Public Health, where their faculty sponsor will be Prof Serap Aksoy. Their supervisory panel will also include Dr James Hassell, other Yale faculty and broader members of the project team.

What we are looking for:
• A strong interest at the intersection between ecology, epidemiology and sequencing technologies
• Candidates are expected to be interested in working at the boundaries of several research domains
• Bachelor’s or Master’s degree in computational biology, bioinformatics, ecology, evolutionary biology, veterinary medicine or a related discipline
• Knowledge and experience in the analysis of biological high-throughput data
• Knowledge of statistical methods in the context of biological systems
• Experience with programming (Python, C++, R)
• Well-developed collaborative skills

We offer:
• The successful candidate will be integrated into a dynamic, international team with strong expertise in all capacities. They will receive mentorship and training through a world class PhD program at Yale School of Public Health.
• The will receive a full scholarship to cover 5 years PhD fees, stipend, and health insurance.
• The student will participate in field work in eastern Uganda.
• Training on target-enrichment sequencing and laboratory support at ILRI in Nairobi, Kenya, supported by highly experienced lab technicians at ILRI and a Glasgow postdoc.
• We offer an international and multi-disciplinary environment with strong expertise in theoretical and applied research.

We particularly encourage East African students to apply.

How to Apply:
Interested applicants should submit 1) a cover letter describing your background and what motivates you to apply to this PhD position, 2) your CV, and 3) the names and contact information of two people who can be contacted for letters of references, to Dr. James Hassell ( with Dr Barbara Han (, Dr Jayna Raghwani (, Dr Christina Faust ( and Prof Serap Akosy ( in copy by 15th October 2023. Only shortlisted candidates will be contacted. Review of applications will begin immediately and will continue until the position is filled.

Further information:
Dr James Hassell,

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