PhD student in Bioinformatics, Network Inference and Pathway Analysis

Published: 2018-10-17


Project description
Your PhD studies will be in the Biochemistry especially Bioinformatics program, specifically within the project Network Inference and Pathway Analysis at the Stockholm Bioinformatics Center, located at Science for Life Laboratory in Stockholm, Sweden, with excellent contacts to a number of life science and computer science departments at Stockholm University, KTH, and the Karolinska Institute. The research project will be supervised by Professor Erik Sonnhammer, erik.sonhammer@dbb.su.se, http://sonnhammer.org.

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.

Contact
For more information, please contact the Project Leader. General information about the PhD programs can be given by the Director of Doctoral Studies, Pia Ädelroth, pia.adelroth@dbb.su.se, or the Head of the Department, Lena Mäler, lenam@dbb.su.se.

Read more and apply.