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

Project title: Perturbation-based Multi-omics Inference of Gene Regulatory Networks .

The goal of this project is to advance gene regulatory network (GRN) inference from multi-omics data by developing novel AI techniques that exploit the knowledge of gene perturbations (experimental design). It has previously been shown that using the perturbation design greatly boosts the quality of GRN inference on bulk data. The aim is to leverage this principle and develop new technology to unleash perturbation-based GRN inference for single-cell and spatial multi-omics data, to boost GRN quality and add the cell type and tissue heterogeneity dimensions to causal regulatory analysis. A deep learning framework will be developed with a specialized architecture to efficiently connect data with specific gene perturbations. A system for inferring the perturbation design based on gene expression and chromatin accessibility data will also be developed. The framework will be addapted and applied to spatial data to connect the GRN models to specific tissue phenotypes and to gain a better understanding of e.g. cancer development.

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.

Extensive experience with Python, Matlab, and R, and good UNIX knowledge are essential skills, as well as familiarity with biological omics data analysis techniques. Experience with PyTorch or TensorFlow is highly meriting.

Admission Regulations for Doctoral Studies at Stockholm University.

About the employment

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 Erik Sonnhammer, erik.sonnhammer@scilifelab.se.

General information about the PhD programs can be given by the Professor and 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.