at the Department of Biochemistry and BiophysicsClosing date: 21 February 2018.

The Department of Biochemistry and Biophysics is mainly located in the Arrhenius Laboratories, which are situated at the University Campus at Frescati. The Science for Life Laboratory is also closely linked to the department. Presently more than 250 people are working at the department, of which around 100 are PhD students, engaged in internationally highly recognized research. The research projects span across a broad range of topics covering various aspects of structure and function of biological systems. The combination of the highly interdisciplinary expertise and research projects at the department is unique in Sweden and also at an international level. This expertise ranges across cell biology, biochemistry, biophysics, neurochemistry and theory. For more information about the department, see:

Project description
Your studies in Bioinformatics will be in the project: Network Inference and Pathway Analysis. Project leader: Professor Erik Sonnhammer.

The project aims at developing computational methods for integrative modelling of big cancer data sets, using a range of network inference methods. These inferences will result in mechanistic gene regulatory networks, and to better understand the biological basis of these, this position will contribute with pathway analysis using the novel BinoX network crosstalk method as well as classical methods. A further aim is to make pathway analysis available in the project web portal.

The goal is also to develop methods for using prior information in gene regulatory network inference. Previous work has been done on using the FunCoup functional association networks as a prior, but the goal here is to instead use physical regulatory evidence such as ChIP-Seq or ATAC-seq which are likely to be more relevant. As such data is hard to simulate in a sensible way, benchmarking needs to be done on real datasets, using a database such as Yeastract or other compilations of known regulatory links.

The project involves programming, data analysis, benchmarking, and modelling, as well as application of the developed methods to experimental data generated by the project. The successful candidate should 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 practical experience in bioinformatics research. Demonstrable familiarity with network and pathway analysis techniques is essential. Computer programming (ideally R, Matlab, Python, Perl, Java, C, C++), 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, 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).

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 skills 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:

Terms of employment
Only a person who will be or has already been admitted to a third-cycle programme may be appointed to a doctoral studentship.

The term of the initial contract may not exceed one year. The employment may be extended for a maximum of two years at a time. However, the total period of employment may not exceed the equivalent of four years of full-time study.

Doctoral students should primarily devote themselves to their own education, but may engage in teaching, research, and administration corresponding to a maximum of 20 % of a full-time position.

Please note that admission decisions cannot be appealed.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

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

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

Union representatives
Ingrid Lander (Saco-S) and Lisbeth Häggberg (Fackförbundet ST and Lärarförbundet), telephone: +46 8 16 20 00 (operator), (SEKO), and PhD student representative,

Apply for the PhD student position at Stockholm University's recruitment system by clicking the "Apply" button. 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.

Please include the following information with your application

  • Your contact details and personal data
  • Your highest degree
  • Your language skills
  • Contact details for 2–3 references

and, in addition, please include the following documents

  • Cover letter
  • CV – degrees and other completed courses, work experience and a list of degree projects/theses
  • Research proposal (no more than 3 pages) describing: 
    – why you are interested in the field/project described in the advertisement 
    – why and how you wish to complete the project 
    – what makes you suitable for the project in question
  • Degree certificates and grades confirming that you meet the general and specific entry requirements (no more than 6 files)
  • Letters of recommendation (no more than 3 files)
  • Degree projects/theses (no more than 3 files)
  • A computer code you have written (1 file).

The instructions for applicants are available at: Instructions – Applicants.

You are welcome to apply!

Vi är ett av Europas ledande universitet i en av världens mest dynamiska huvudstäder. En relation med Stockholms universitet är meriterande oavsett om du är student, forskare eller intressent. Hos oss ger utbildning och forskning resultat.

Closing date: 21/02/2018