PhD student in Bioinformatics

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

Your studies in Bioinformatics will be in the project: "AI-driven Multiscale Modelling of Membrane Protein Complexes".

Cell membranes are highly organized assemblies of proteins and lipids whose structure and composition change during disease, drug exposure, and cellular stress, but current structural biology and AI methods largely treat membrane proteins one at a time and rarely capture how proteins, lipids, and glycans jointly shape membrane organization.

In this project, the PhD student(s) will develop deep-learning-based methods to build multiscale structural models of cell membranes, starting from erythrocyte and mitochondrial membranes. Building on our group’s work on AlphaFold-based prediction of protein complexes [1], the project will extend these approaches to (1) predict the structure and interactions of membrane protein complexes embedded in a lipid environment, (2) integrate experimental constraints from proteomics, glycoproteomics, structural mass spectrometry, and lipidomics generated by collaborating experimental groups into the modelling pipeline, (3) scale the predictions from individual protein complexes to the organisation of entire membranes, building on our work on assembling large complexes with AlphaFold and Monte Carlo tree search [2], and (4) compare membrane organization across cell types and conditions - drawing on our proteome-scale map of the human protein interaction network [3] - to identify conserved and disease- or drug-specific remodeling patterns. The project may also connect to work on AI-based prediction of drug transport across membranes, building on our studies of the structural evolution of membrane transporters [4].

The PhD student(s) will work at the interface of structural bioinformatics, machine learning, and membrane biology, in close collaboration with experimental groups in membrane biology and structural biology.

The Elofsson group is located at SciLifeLab, Stockholm University. Elofsson has worked on protein structure prediction, protein evolution and in particular membrane proteins for more than two decades, using machine learning and other computational techniques. Among the group’s most important contributions are methods for assessing the quality of protein models, as well as recent work on predicting protein-protein interactions and building large protein complexes. The group currently comprises seven PhD students, three postdocs, and five senior researchers, and collaborates closely with computational and experimental groups at SciLifeLab and internationally. Arne Elofsson is currently the co-director of CEMERAI . For more information see https://bioinfo.se/ .

Representative recent publications relevant to this project are listed below. [1] Bryant, P, Pozzati, G. & Elofsson, A. “Improved prediction of protein-protein interactions using AlphaFold2”. Nat Commun, 2022 Mar 10;13(1):1265 [2] Bryant P, Pozzati G, Zhu W, Shenoy A, Kundrotas P, Elofsson A. “Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search”. Nat Commun. 2022 Oct 12;13(1):6028 [3] Burke, D.F., Bryant, P., Barrio-Hernandez, I., … Elofsson, A. “Towards a structurally resolved human protein interaction network”. Nat Struct Mol Biol 2023, 30(2):216-225 [4] Sudha, G., Bassot, C., Lamb, J., Shu, N., Huang, Y. & Elofsson, A. “The evolutionary history of topological variations in the CPA/AT transporters”. PLoS Comput Biol 2021, 17(9):e1009278

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 .