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.

Subject area

Your studies in Bioinformatics will be in the project: "Deep Learning for protein structure prediction”.

Protein structure is essential for understanding their function and developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available and released a database with predicted protein structures. However, proteins do not act alone - they work together with other proteins. Therefore, the next major challenge is using these methods for predicting protein-protein interactions. Our initial studies have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, many proteins cannot be built accurately, nor can we always distinguish interacting from non-interacting protein pairs and building larger complexes accurately is still an unsolved problem. In this project, we are recruiting additional Ph.D. student to leverage recent advances in machine learning to create better deep-learning models to predict protein-protein interactions and to apply these methods to biologically relevant problems.

The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions for more than 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, two postdocs 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 among the eligible candidates will be based on their capacity to benefit from the training. The following criteria will be used to assess this capacity:

• documented knowledge in a relevant field of research
• capacity for analytical and creativ thinking
• initiative
• independence
• ability to collaborate
• written and oral proficiency in both Swedish and English.

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.

You are welcome to apply!