[SocBiN] PhD position in Stockholm

[Arne Elofsson]

*PhD position at the Department of Biochemistry and Biophysics *
*Reference numbers SU FV-0267.15 Deadline for application: February 23,
2015*





*Ref No. SU FV-0267-15 Project title: Prediction and studies of membrane
protein interactions *Project leader: Arne Elofsson, arne at bioinfo.se,
Homepage: http://bioinfo.se/

Membrane proteins are the gateways to the cells and as such they are of
great importance for the development of drugs. In addition membrane
proteins are quite difficult to handle experimentally, therefore prediction
methods are important to gain information about these protein.  We have
developed many of the leading methods for prediction of membrane protein
structures. For a full list of publication see http://bioinfo.se/papers/ .

The primarily aim of this project is to obtain detailed structural
information about large biological complexes and networks, such as membrane
protein translocases, by integrating different types of genomic sequence
data. The information from a sufficient number of homologous sequences is
often sufficient to predict the fold of soluble globular proteins or
membrane proteins.

Two types of information will primarily be used. First, the identification
of co-evolving residues can be used to predict interacting residue pairs.
Secondly the use of structural homology combined with analysis of
interaction surfaces can be used to identify potentially interacting
proteins. These purely computational methods will then, if needed, be
combined with experimental data from Cryo-EM and other techniques.

A general interest in protein, programming and machine learning methods and
a solid background in bioinformatics, physics or computer science is
suitable for this position.

This position is a part of a European Union Marie Skłodowska Curie Initial
Training Network named “protein factory”.  The overall aim of this network
is to develop new protein production systems that can deliver secreted
enzymes and membrane proteins in greater yields, with higher quality and at
lower costs. The network consists of 11 partners from 7 different European
countries and in total 15 PhD students will be recruited. All these
students will participate in several workshops, meetings and courses.  This
provides a unique possibility to form a network of fewllow scientists with
a common research interest.

The position is funded by a European Union Marie Skłodowska Curie Initial
Training Network. Therefore, potential candidates must not have resided or
carried out their main activity (work, studies, etc.) in Sweden for more
than 12 months in the 3 years immediately prior to the recruitment, and
have no more than 4 years of research experience.

Include a short motivation, a CV (plus diplomas and certificates/date when
you expect to finish your studies), an example of computer code you have
written and the contact details of at least 2 references in your
application.

References:

1)      Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G.
and  Elofsson, A. (2008) Prediction of membrane-protein topology from
first principles. Proc Natl Acad Sci U S A 105 (20) : 7177-718

2)      Bendz, M., Skwark, M., Nilsson, D., Granholm, V., Cristobal, S.,
Kall, L. and Elofsson, A. (2013) Membrane protein shaving with  thermolysin
can be used to evaluate topology predictors. Proteomics 13 (9) : 1467-1480.

3)      Peters, C. and Elofsson, A. (2014) Why is the biological
hydrophobicity scale more accurate than earlier experimental hydrophobicity
scales? Proteins 82 (9) : 2190-2198.

4)      Skwark, M.J., Raimondi, D., Michel, M. and Elofsson, A. (2014)
Improved contact predictions using the recognition of protein like contact
patterns. PLoS Comput Biol 10 (11) : e1003889.

5)


*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.


*Selection *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 *A PhD education at Stockholm University is four years
(48 months). The four-year PhD program includes at least three years of
research and at most one year of course work. The position may be extended
by up to one year if up to 20% teaching assistance or administration is
included in the contract. During the beginning of the PhD education, the
student receives a study grant ("utbildningsbidrag"), and after at most one
year she/he acquires a PhD studentship ("doktorandanställning"). From July 1
st, 2015 employment will be the only option.
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 at dbb.su.se). General information about
the PhD training program may be requested from the director of graduate
studies, Stefan Nordlund (stefan at dbb.su.se) or from Lena Mäler, Head of
Department (*prefekt*) (lenam at dbb.su.se).
Faculty of Science: www.science.su.se/english

*Union representatives*
Anqi Lindblom-Ahlm (Saco-S) and Lisbeth Häggberg (Fackförbundet ST),
telephone +46-(0)8-162000 (switch board), and Gunnar Stenberg (SEKO),
telephone +46-(0)70-316 43 41.


*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.

*The application, labelled with Ref. No. SU FV-0263-15 – SU FV-0270-15,
should be sent no later than February 23, 2015 by email to
registrator at su.se <registrator at su.se>. Please note that the reference
number should be stated in the subject line of your email.*





Yours

Arne

-----------------------------------------
  Arne Elofsson                Science for Life Laboratory
  Tel:+46-(0)852481531     Stockholm University
  http://bioinfo.se/             Box 1031,
  Email: arne at bioinfo.se   17121 Solna, Sweden
  Twitter:   https://twitter.com/arneelof
  Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ
  ORCID: 0000-0002-7115-9751
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