PhD student in Bioinformatics, Inference of protein function from domain architecture and orthology

Published: 2018-10-17


Project description
Your studies in Bioinformatics will be in the project: Inference of protein function from domain architecture and orthology. Project Leader: Professor Erik Sonnhammer, erik.sonnhammer@scilifelab.se.

The function of a protein is very challenging to establish experimentally. A faster route is to predict the function based on the amino acid sequence. This project will employ several approaches that use sequence features to this end. The main goal is to develop computational tools for studying domain architecture evolution and its relation to function and orthology.

The project includes both development of new algorithms and methods, as well as applications such as tools and workbenches to enable public access for database queries of Pfam, InParanoid, and Hieranoid. The methods include hidden Markov models, clustering methods, various statistical analyses, and own developed algorithms. The project involves programming, data analysis, benchmarking, as well as application of the developed methods to genes of particular interest in order to discover new protein functions.

The successful candidate should 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. Familiarity with sequence analysis techniques is essential, as well as a high level of motivation. Computer programming (e.g. Perl, Python, R, 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, 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, Professor Erik Sonnhammer, erik.sonnhammer@scilifelab.se.
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.