PhD student in Bioinformatics (Gene regulatory network inference)

Stockholm University

Application deadline

August 16, 2020

Project description

Your studies in Bioinformatics will be in the project: “Gene regulatory network inference”.

The goal of the project is to develop and apply methods for inference of accurate and predictive gene regulatory networks (GRNs). The Sonnhammer group has extensive experience in GRN inference and has developed several algorithms to improve the reliability of the GRNs inferred from perturbations. The toolkit includes the GeneSpider package for GRN and data generation, which is used for GRN inference benchmarking with controlled network and data properties. The NestBoot GRN inference algorithm was devised to control the false discovery rate of network links.

The project aims to improve existing methods to make them faster and even more reliable. They will be applied to perturbation data from ENCODE and in-house data. The inferred GRNs will be analyzed for predictiveness and how well they replicate known links. The project involves programming, data analysis, benchmarking, and application of the developed methods to experimental data generated by the group.

The successful candidate must be highly motivated and have an M.Sc. in bioinformatics or related field, and knowledge of molecular biology. Alternatively, an M.Sc. in molecular biology or related field and at least 1 year of documented practical experience in bioinformatics research and programming. Demonstrable familiarity with sequence and molecular data analysis techniques is essential. Computer programming with Matlab, Python, R, (Perl, C++, Java), UNIX skills, and knowledge of biological database systems are necessary merits.

Qualification requirements

In order to meet the general entry requirements, the applicant must have completed a second-cycle degree, 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 program the applicant must have passed courses within the first and second cycles of at least 120 credits in Biochemistry/Life Science, including at least 15 credits Biochemistry at the second cycle level and a Degree Project (thesis) also in Biochemistry of 30 credits.

The qualification requirements must be met by the deadline for applications.


The selection among 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 are available at: and regulations.

Application deadline

16 August 2020.


For more information, please contact the project leader, Professor Erik Sonnhammer,

General information about the PhD programs can be given by the Director of Doctoral Studies, Pia Ädelroth, or the Head of the Department, Lena Mäler,


Last updated: 2020-08-03

Content Responsible: David Gotthold(