PhD student in…

PhD student in Molecular Evolution
Are you interested in working with molecular data, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a PhD position at Uppsala University.

The Department of Cell and Molecular Biology is divided into seven research programs, each focusing on different areas within cell and molecular biology: computational biology and bioinformatics, microbiology and immunology, molecular biology, molecular biophysics, molecular evolution, molecular systems biology, and structural biology. The scientific foundation of what we do lies in biology, but our research overlaps with other fields such as medicine, computer science, mathematics, chemistry, engineering, and physics. The department has over 200 employees, including around 60 doctoral students. Please read more about our work at https://icm.uu.se.

Project Description
This PhD position will be entirely computational, focusing on the large-scale bioinformatic analysis of proteome data from a wide range of existing species. The research will focus on understanding mutational robustness. Mutational robustness is the capacity of individuals within populations to express similar phenotypes despite the existence of underlying genetic variation. The project will uncover how mutational robustness relates to phenotypic diversity, and whether mutational robustness promotes evolvability. The project could also expand in scope to the consideration of DNA data. Further specific projects will be developed collaboratively with the successful candidate, depending on their project findings and research interests.

Duties
At the start of the project, the successful candidate will create a protein dataset collaboratively with other group members, collecting amino acid sequence data from across multiple fully sequenced genomes. The student will conduct a variety of measures of protein phenotypic diversity, in the form of variation in protein structure and function, using simple measures such as overall hydrophobicity, in addition to modern protein structural prediction techniques. 

The student will then be responsible for estimating measures of mutational robustness. These measures could include the relative proportion of amino acid changing mutations per codon, and the proportion of changes that result in a radical versus conservative amino acid change, i.e., what proportion of mutations will lead to an exchange between dissimilar amino acids as opposed to similar amino acids. 

To investigate the relationship between phenotypic diversity and mutational robustness, the student will conduct a variety of statistical analyses. Further projects could include assessing whether adaptive substitution rates relate to degree of mutational robustness, and whether levels of genetic diversity relate to levels of phenotypic diversity. 

Requirements

To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in a field of biology, or
• have 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
• have acquired substantially equivalent knowledge in some other way.

Candidates must be able to express themselves fluently in spoken and written English. The applicant should have a strong grasp of key concepts in evolutionary biology. The applicant should also have an interest in learning, or previous experience in, computer programming, particularly using languages such as Python. The ideal candidate is driven and a creative thinker, with a passion for discovery. We are looking for a person with excellent communication skills who will thrive in a collaborative environment but is also able to work on their own initiative. We’re excited to support you in developing your skills and following your scientific interests.

Additional qualifications
Prior experience in computational biology, bioinformatics or generally in computer programming is desirable. Experience working in population genetics and evolutionary biology/genomics or proteomics is also desirable. Experience with statistical analyses will be considered advantageous.

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 2025-05-05 or as agreed. Placement: Uppsala 

For further information about the position, please contact: Jennifer James, jennifer.james@icm.uu.se.

Please submit your application by April 4th 2025, UFV-PA 2025/674.

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