Phd Student position in computational genomics - Hiring in process/Finished, not possible to apply

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM broadly spans the areas of comparative and evolutionary genomics, functional genomics, biochemistry, cell and molecular biology, immunology and microbiology. The research is of fundamental nature, but with relevance and application in health and disease in both animals and humans. More info: Research - Uppsala University.

We are looking for a highly motivated PhD student to be involved in the project “Adaptation Genomics in the Ocean: Predicting Functional Variation in Marine Life with Machine Learning”, led by Andreas Wallberg (main supervisor; funded by Swedish Research Council) and Leif Andersson (co-supervisor; funded by Knut and Alice Wallenberg Foundation). The PhD student needs to have strong interests in evolutionary genomics and will be located at the Biomedical Centre, Uppsala, Sweden.

Project description

Predicting how genetic variation gives rise to adaptive traits is a central challenge in biology. Machine Learning (ML) is now transforming our ability to meet this challenge by enabling rapid, large-scale prediction of gene function and gene editing directly from DNA sequences.

In this four-year PhD project, the candidate will apply advanced ML and genomics methods to understand the genomic basis of ecological adaptation in krill and Atlantic herring, which are marine keystone species. In krill, the candidate will focus on visual adaptation, combining population and comparative genomics with ML models to predict the functional properties of opsin proteins directly from sequences, enabling detection of functionally important mutations across species that inhabit distinct ocean light environments. This allows us to uncover how sensory systems evolve in these species in response to environmental gradients, with implications for their resilience to ocean change. In herring, the candidate will integrate population genomics with state-of-the-art ML tools to functionally annotate and prioritize both coding and regulatory variants that could be important for adaptation in the Baltic Sea and elsewhere. We will assess the impact of missense mutations at scale and train deep learning models on tissue-specific ATAC-seq data from various tissues (e.g., brain, gills, liver, larvae) to predict the regulatory activity of noncoding adaptive variants.

Together, these efforts aim to build a novel and comprehensive ML-driven framework for identifying causal variants underlying local adaptation and environmental sensitivity in non-model species that are foundational to marine ecosystems. Better insight into how species adapt to different environments is critical to help forecast how marine life will respond to climate change and anthropogenic pressures over the next century and support sustainable use of marine resources.

Duties

The main duties of PhD students are to devote themselves to their research studies, which includes participating in research projects and third cycle courses. The project entails mostly bioinformatics and computational analyses. The work duties can also include teaching and other departmental duties (not more than 20 % of full time).

Requirements

To meet the entry requirements for doctoral studies, you must have

• a Master’s (second-cycle) degree in bioinformatics, computer science, biology, population or functional genomics, or similar field, or completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or acquired substantially equivalent knowledge in some other way
• documented training in using Linux/UNIX, programming/scripting (e.g. Python, Bash, Perl) and statistical analyses (e.g. R)
• experience in processing next-generation sequencing data (NGS)
• background understanding of, and interest in, biodiversity and evolution
• proficiency in spoken and written English; 
• strong ability to conceive, execute, and complete research projects independently
• creativity and good group-working skills

More information: Doctoral studies - Uppsala University

The selection is based on the following criteria

Completion of the above qualifications, grades in relevant courses, suitability of the courses to the research program, previous experience in working and performing research in the wider area that relates to the project described above. An integrated assessment of the applicant is generated in order to employ the best possible candidate that can succeed in the doctoral studies and contribute to a positive development of the research program. Emphasis will be given on personal qualities, including analytical capacity, accuracy, flexibility and collaborative skills.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment

The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as agreed. Placement: Uppsala.

For further details, please contact Andreas Wallberg, andreas.wallberg@imbim.uu.se .

Application: Please submit your application using the Uppsala University application portal, by including a CV, a letter describing your research interest and skills, copy of Master’s thesis (or a draft thereof and/or some other self-produced technical or scientific text), publications, and other relevant documents, contact information of two referees (phone number and e-mail address).

Please submit your application by September 10, 2025, UFV-PA 2025/2422.