PhD student in Bioinformatics

Om tjänsten

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, which are situated in the northern part of the University Campus at Frescati. Some 270 people of which about 60 are PhD students work at the Department, engaged in internationally highly recognised research covering a broad range of subjects.

SciLifeLab (SciLifeLab) is a national center for molecular biosciences with a focus on health and environmental research. The center 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 and Uppsala University. The center also collaborates with several other universities.

The employment will be placed at the Department of biochemistry and biophysics, at 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, and one senior researcher, and collaborates closely with computational and experimental groups at SciLifeLab and internationally.

Qualification requirements

In order to be admitted to postgraduate education, the applicant must have the general and specific entry requirements. The qualification requirements must be met by the time the applicant is admitted to the PhD program at the Department of Biochemistry and Biophysics.

You meet general entry requirements if you have completed a second-cycle degree, or completed courses equivalent to at least 240 higher education credits, of which 60 credits must be in the second cycle, or have otherwise acquired equivalent knowledge in Sweden or elsewhere.

In order to meet the specific entry requirements, for acceptance in the Biochemistry, especially Bioinformatics, program the applicant must have passed courses within the first and second cycles of at least 90 credits in either, a) Chemistry/Molecular Biology/Biotechnology, or b) Computer Science/Mathematics/Physics and at the second cycle level, 60 credits in Life Science, Computer Science Mathematics, Physics or Bioinformatics including a 30 credit Degree Project (thesis).

Selection

The selection amongst the eligible candidates will be based on their capacity to successfully complete the program. Important criteria when assessing this capacity are; documented knowledge and skill in the field of the thesis project, written and oral proficiency in English, the capacity for analytical thinking, the ability to collaborate, as well as creativity, initiative, and independence. The assessment will be based on previous experience and grades, the quality of the degree project, references, relevant experience, interviews and the candidate's written motivation for seeking the position.

Admission Regulations for Doctoral Studies at Stockholm University.

About the post

We offer a fixed-term employment as a doctoral student according to Chapter 5 of the Higher Education Ordinance (1993:100). The period of employment may not be longer than what corresponds to full-time doctoral education for four years. As a doctoral student, you should primarily devote yourself to your own doctoral education, but the employment may include work with education, research and administration to a limited extent (maximum 20 %).

A new employment as a doctoral student is for a maximum of one year, the employment is then renewed for a maximum of two years at a time.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact

For more information, please contact Professor Arne Elofsson, arne.elofsson@dbb.su.se.

General information about the PhD programs can be given by the Director of Doctoral Studies, Andreas Barth, andreas.barth@dbb.su.se.

Application

Apply for the PhD student position at Stockholm University's recruitment system. Attach a personal letter and CV as well as the attachments requested in the application form. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline.

The instructions for applicants are available at: How to apply for a position.

Stockholm University contributes to the development of sustainable democratic society through knowledge, enlightenment and the pursuit of truth.

Extra information

Status

Öppen

Önskad utbildningsnivå

Annan

Ort

Stockholm

Typ av kontrakt

Heltidsjobb (förstajobb)

Löneindikation

60.00SEK per timme

Körkort önskas

Nej

Tillgång till bil önskas

Nej

Personligt brev krävs

Nej