Anslaget vid Stockholms unversitet
2013-10-20
Dnr SU FV-4.2.3-2990-13
Dok nr 1
PhD position in biochemistry towards bioinformatics
at the Department of Biochemistry and Biophysics.
Reference number SU FV-2990-13.
Deadline for application: November 20, 2013.
Project leader: Erik Sonnhammer, Erik.Sonnhammer@scilifelab.se, http://sonnhammer.sbc.su.se
Project title: Inference of protein function from domain architecture and orthology
The research project will be supervised by Professor Erik Sonnhammer
(http://sonnhammer.sbc.su.se/) at the Stockholm Bioinformatics Center (http://www.sbc.su.se/), which
is located at Science for Life Laboratory Stockholm (http://www.scilifelab.se/) and has excellent
contacts with a number of life science and computer science departments at Stockholm University,
KTH, and Karolinska Institutet.
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. A major goal is to understand the functional impact of the combination
of domains in multidomain architectures by analysing the evolutionary history of both individual
protein domains and domain architectures. This will be done by developing computational tools for
studying domain architecture, and by applying orthology analysis to entire proteomes. Another area of
study is “domain versatility”, which indicates a domain's propensity to form functional partnerships
with other domains.
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 at http://Pfam.sbc.su.se/ and
http://InParanoid.sbc.su.se/. 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.
The position is for 4 years of full-time study and will administratively belong to the Department of
Biochemistry and Biophysics, Stockholm University. Applications are made on-line, the latest on
November 20, 2013. For further information about the research project, contact
Erik.Sonnhammer@scilifelab.se
The Department of Biochemistry and Biophysics is mainly located with the other Departments of
Chemistry and Life Sciences in the Arrhenius Laboratories for Natural Sciences, which are situated in
the northern part of the University Campus at Frescati. Presently around 200 people are working at the
Department of which 90 are PhD students engaged in internationally highly recognized research
covering a broad range of subjects. The Department is also deeply involved in teaching, with courses
at all undergraduate levels, including a wide range of Master courses. A close link between the
undergraduate program and the research projects has since long been a tradition and a trademark of
Stockholms universitet
106 91 Stockholm
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the Department. Three centers are linked to the Department: Stockholm Center for Biomembrane
Research, Science for Life Laboratory and Stockholm Bioinformatics Centre.
More than 20 research groups are active at the Department of Biochemistry and Biophysics. The
research projects span across a broad range of topics covering various aspects of structure and
function of biological systems. A majority of these topics are centered on biological membranes,
where many groups working within this area are part of the Center for Biomembrane Research, which
is hosted by the department. Also the Stockholm Bioinformatics Centre and the Science for Life
Laboratory are closely linked to the department. 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 and theory. Some specific
topics that are addressed include membrane protein biogenesis, membrane protein topology &
assembly, mitochondria & chloroplasts, protein structure & function, protein folding & trafficking,
lipid biosynthesis & function, energy conversion, DNA-RNA-PNA interactions, biological nitrogen
fixation, viral membrane glycoproteins, protein structure & disease, bioinformatics, computational
structural biology and development of theoretical tools. The experimental studies are performed in
different organisms and are also combined with the use of a wide range of advanced biochemical and
biophysical techniques. For more information about the department, see www.dbb.su.se.
Requirements
To be accepted as a PhD student, credits corresponding to four years of full-time studies at the
undergraduate level are required, including credits corresponding to at least two years of fulltime
studies in chemistry, life sciences or physics, depending on the program. The credits should include
courses at the advanced level (second cycle) corresponding to one year and of these one semester
should be a degree thesis. In order to facilitate the evaluation of merits and suitability for the PhD
studies the curriculum vitae (CV) should contain information about the extent and focus of the
academic studies. The quantity (as part of an academic year) and the quality mark of courses in
chemistry and physics are of particular interest. The title, number of credits and the length in full-time
months of undergraduate thesis and project work, should be specified.
The selection among applicants will be based on the assessment of their capacity to successfully
complete the PhD program. In practical terms, this means that the study merits will be the main
selection criterion. The local study merits, such as passed advanced courses or project work at the
department, will be given a relatively high weight. Equal opportunity aspects between men and
women will be given a certain weight.
Terms of employment
Economic support is guaranteed during the agreed time in the individual study syllabus (study plan)
for the PhD studies, totally for a maximum of four years. The department may request that the
graduate student takes part in teaching or other departmental work in an activity additional to the
graduate studies for up to 20% of full work time. The PhD positions are open for international
students on equal terms. No tuition fee is charged. Stockholm University strives to be a work place
that is free from discrimination and with equal opportunities for all.
More information
More information about the project can be provided by the project leader. General information about
the application procedure can be provided by Haidi Astlind (haidi@dbb.su.se). General information
about the PhD training program may be requested from the director of graduate studies, Stefan
Nordlund (stefan@dbb.su.se) or from Lena Mäler, Head of Department (prefekt) (lenam@dbb.su.se).
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Union representatives
Anqi Lindblom-Ahlm (Saco-S) and Lisbeth Häggberg (Fackförbundet ST), telephone +46-(0)8162000 (switch board), and Gunnar Stenberg (SEKO), telephone +46-(0)70-316 43 41.
Further information on the web:
The Department of Biochemistry and Biophysics: www.dbb.su.se
Stockholm University: www.su.se/english
Faculty of Science: www.science.su.se/english
The handbook for postgraduate students: www.doktorandhandboken.nu/english
Application
The application should contain a personal letter (a letter of intent explaining why you are interested in
the specific project, why you are interested in studying for a PhD, what you hope to accomplish during
your PhD studies, and what skills you can bring to this project), a curriculum vitae, a list of two persons
who may act as referees (with telephone numbers and e-mail addresses), copies of degree certificates
and transcripts of academic records, and a copy of your undergraduate thesis and articles, if any.
In order to apply for this position, please use the Stockholm University web-based application form
(where it is possible to select language): To the application form for this position.
Welcome with your application no later than November 20, 2013.