PhD student in Bioinformatics

The Department of Biochemistry and Biophysics 
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

Your studies in Bioinformatics will be in the project: "Using Deep Learning to Understand Protein Structure Evolution”.

We have studied domain evolution and observed that structural change is roughly linear with sequence change. However, larger structural changes might also occur within a domain during evolution, particularly within transporters3.  Further, domains can be combined to create multi-domain proteins. Most domain architectures arise from adding or removing a single domain at the N- or C-terminal regions, while certain repeat-domain families undergo more internal duplications. We also demonstrated that eukaryotic proteins harbour substantially more disordered and linker regions, which expand more rapidly than globular domains. Most phylogenetic studies of proteins, including ours, have primarily focused on changes in the amino-acid sequences. Today, accurate structural models from AlphaFold make it possible to integrate structure into large-scale phylogenetic and sequence analyses. Therefore, in this application, we propose revisiting earlier studies, scaling them up, and adding structural information to the analysis. This study will provide a detailed structural understanding of changes within domains, how novel protein architectures emerge, and why certain domains and architectures continue expanding and diversifying in specific lineages. We believe this study will provide fundamental insights into protein structure evolution and how evolutionary mechanisms and selective pressures have shaped proteins. Together, the three aims of this project will reveal how domain changes their structure and how rearrangements shape structural protein diversity across the tree of life.

The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions and evolution for over two decades. He has worked on various techniques using machine learning and other computational techniques. Our most important contributions to this work are the methods he has developed to identify the quality of protein models, Pcons, and various versions of ProQ. The group comprises 5 PhD students, one postdoc, and one senior researcher.

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 deadline for applications.

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.

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.