PhD Students in Bioinformatics

Stockholm University

Sweden

About the Department

The Department of Biochemistry and Biophysics is mainly located with the other Departments of Chemistry and Life Sciences in the Arrhenius Laboratories for Natural Sciences, situated in the northern part of the University Campus at Frescati.

Approximately 270 people, including about 60 PhD students, work at the department and are engaged in internationally recognized research covering a broad range of subjects.

SciLifeLab is a national centre for molecular biosciences with a focus on health and environmental research. The centre combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by:

Karolinska Institutet
KTH Royal Institute of Technology
Stockholm University
Uppsala University

The centre also collaborates with several other universities.

The employment will be placed at the Department of Biochemistry and Biophysics, Stockholm University.

More information about us, please visit: the Department of Biochemistry and Biophysics.

Project Description

Protein domains evolve through sequence divergence, structural modification, duplication, and recombination.

In previous work, we demonstrated that structural divergence often follows sequence divergence in an approximately linear manner. However, substantial structural rearrangements can also occur within conserved domains—particularly in transporter families—and through domain recombination events that generate novel multidomain architectures.

Most domain architectures arise through terminal additions or deletions, whereas repeat-domain families often expand through internal duplications. We have further shown that eukaryotic proteins contain substantially more disordered and linker regions than prokaryotic proteins, and that these regions expand more rapidly than globular domains. Despite these advances, most large-scale phylogenetic analyses—including our own—have relied primarily on amino acid sequence information.

The recent availability of highly accurate structural models from AlphaFold now makes it possible to systematically integrate structural information into evolutionary analyses at the proteome scale.

In this project, we will:

Quantify structural divergence within domains across evolutionary distances using deep learning-based structural embeddings and similarity metrics.
Characterize the emergence of novel domain architectures, identifying structural constraints and evolutionary pathways that shape multidomain proteins.
Investigate lineage-specific expansion patterns, including the role of disorder, linkers, and repeat expansions in driving structural innovation.

We will combine large-scale structural datasets, state-of-the-art deep learning models, and comparative genomics to revisit and substantially extend previous evolutionary analyses.

The project aims to establish a structural framework for understanding how evolutionary mechanisms and selective pressures shape protein architecture across the tree of life.

This work will provide fundamental insights into the principles governing protein structural diversification and the emergence of new folds and architectures.

Research Environment

The Science for Life Laboratory (SciLifeLab) provides a leading environment for data-driven life science research.

The Elofsson Group has worked on protein structure prediction and evolution for more than two decades, contributing foundational methods for assessing model quality, including Pcons and multiple versions of ProQ.

The group currently consists of:

Five PhD students.
One postdoctoral researcher.
One senior researcher.

The group collaborates closely with computational and experimental research groups at SciLifeLab and with international collaborators.

Qualification Requirements

To be admitted to postgraduate education, applicants must satisfy both the general and specific entry requirements.

The qualification requirements must be fulfilled before admission to the PhD programme at the Department of Biochemistry and Biophysics.

General Entry Requirements

Applicants must have:

A second-cycle degree; or
Completed courses equivalent to at least 240 higher education credits, of which 60 credits must be at the second-cycle level; or
Otherwise acquired equivalent knowledge in Sweden or elsewhere.

Specific Entry Requirements

To be admitted to the Biochemistry programme, especially Bioinformatics, applicants must have completed courses totaling at least 90 credits in one of the following areas:

Chemistry
Molecular Biology
Biotechnology

Computer Science
Mathematics
Physics

In addition, applicants must have completed 60 second-cycle credits in:

Life Science
Computer Science
Mathematics
Physics
Bioinformatics

including a 30-credit Degree Project (Master's thesis).

Selection

Selection among eligible applicants will be based on their ability to successfully complete the doctoral programme.

Assessment will consider:

Documented knowledge and skills relevant to the thesis project.
Written and spoken English proficiency.
Analytical ability.
Ability to collaborate.
Creativity.
Initiative.
Independence.

The evaluation will be based on:

Previous academic experience and grades.
Quality of the degree project.
References.
Relevant research experience.
Interviews.
The applicant's written motivation.

Selection follows the Admission Regulations for Doctoral Studies at Stockholm University.

About the Position

The position is a fixed-term doctoral studentship according to Chapter 5 of the Higher Education Ordinance (1993:100).

Employment conditions include:

Full-time doctoral employment.
Maximum employment period corresponding to four years of full-time doctoral education.
Primary focus on doctoral studies.
Teaching, research and administrative duties may be included to a limited extent (maximum 20%).

The initial employment is offered for a maximum of one year, after which it may be renewed for up to two years at a time.

Stockholm University strives to provide a workplace free from discrimination and with equal opportunities for everyone.

Contact

For more information, please contact:

Professor Arne Elofsson
Email: arne.elofsson@dbb.su.se

General information about the PhD programmes can be obtained from:

Andreas Barth
Director of Doctoral Studies
Email: andreas.barth@dbb.su.se

Application

Apply for the PhD student position through Stockholm University's recruitment system.

Attach:

Personal letter.
Curriculum Vitae (CV).
All documents requested in the application form.

It is the applicant's responsibility to ensure that the application is complete according to the instructions in the job advertisement and submitted before the application deadline.

Instructions for applicants are available at:

How to apply for a position

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