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<p class="MsoNormal"><b><span style="font-size:14pt;color:rgb(0,112,192)">PhD position at
the Department of Biochemistry and Biophysics<br>
</span></b><b>Reference numbers SU FV-0267.15<br>
Deadline for application: February 23, 2015</b></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><b>Ref No. SU FV-0267-15<br>
Project title: Prediction and studies of membrane protein interactions<br>
</b>Project leader: Arne Elofsson,
<a href="mailto:arne@bioinfo.se" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=arne@bioinfo.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">arne@bioinfo.se</a>, Homepage: <a href="http://bioinfo.se/">http://bioinfo.se/</a></p>
<p class="MsoNormal" style="text-indent:13.5pt">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 <span lang="SV"><a href="http://bioinfo.se/papers/"><span lang="EN-US">http://bioinfo.se/papers/</span></a></span> .</p>
<p class="MsoNormal" style="text-indent:13.5pt">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.</p>
<p class="MsoNormal" style="text-indent:13.5pt">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.</p>
<p class="MsoNormal" style="text-indent:13.5pt">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. </p>
<p class="MsoNormal">This position is a part of a European Union <span lang="EN-GB">Marie </span><span lang="FR-BE">Skłodowska</span><span lang="EN-GB"> Curie
Initial Training Network named “protein factory”. The overall aim of this network is to develop
new protein production systems that can deliver </span>secreted enzymes and membrane proteins<span lang="EN-GB"> 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.</span></p>
<p class="MsoNormal">The position is funded by a European Union <span lang="EN-GB">Marie </span><span lang="FR-BE">Skłodowska</span><span lang="EN-GB"> Curie
Initial Training Network. </span>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. </p>
<p class="MsoNormal" style="text-indent:13.5pt">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.</p>
<p class="MsoNormal" style="text-indent:13.5pt"><span lang="SV">References: </span></p>
<p class="" style="margin:0in 0in 0.0001pt;text-indent:13.5pt"><span lang="SV">1)<span style="font-stretch:normal;font-size:7pt;font-family:'Times New Roman'">
</span></span><span lang="SV">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</span></p>
<p class="" style="margin:0in 0in 0.0001pt;text-indent:13.5pt"><span lang="SV">2)<span style="font-stretch:normal;font-size:7pt;font-family:'Times New Roman'">
</span></span><span lang="SV">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.</span></p>
<p class="" style="margin:0in 0in 0.0001pt;text-indent:13.5pt"><span lang="SV">3)<span style="font-stretch:normal;font-size:7pt;font-family:'Times New Roman'">
</span></span><span lang="SV">Peters, C. and Elofsson, A. (2014)
Why is the biological hydrophobicity scale
more accurate than earlier experimental hydrophobicity scales? Proteins 82 (9)
: 2190-2198.</span></p>
<p class="" style="margin:0in 0in 0.0001pt;text-indent:13.5pt"><span lang="SV">4)<span style="font-stretch:normal;font-size:7pt;font-family:'Times New Roman'">
</span></span><span lang="SV">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.</span></p>
<p class="" style="margin:0in 0in 0.0001pt;text-indent:13.5pt"><span lang="SV">5)<span style="font-stretch:normal;font-size:7pt;font-family:'Times New Roman'">
</span></span><span lang="SV"> </span></p>
<p class="MsoNormal"><b>Requirements<br>
</b>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 <i>curriculum vitae</i> (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. </p>
<p class="MsoNormal"><b>Selection<br>
</b>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.</p>
<p class="MsoNormal"><b>Terms of employment<br>
</b>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<sup>st</sup>, 2015 employment
will be the only option. <br>
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.</p>
<p class="MsoNormal"><b>More information<br>
</b>More
information about the project can be provided by the project leader. General
information about the application procedure can be provided by Haidi Astlind (<a href="mailto:haidi@dbb.su.se" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=haidi@dbb.su.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">haidi@dbb.su.se</a>). General information about
the PhD training program may be requested from the director of graduate
studies, Stefan Nordlund (<a href="mailto:stefan@dbb.su.se" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=stefan@dbb.su.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">stefan@dbb.su.se</a>)
or from Lena Mäler, Head of Department (<i>prefekt</i>)
(<a href="mailto:lenam@dbb.su.se" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=lenam@dbb.su.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">lenam@dbb.su.se</a>).<br>
Faculty of Science: <a href="http://www.science.su.se/english">www.science.su.se/english</a></p>
<p class="MsoNormal"><b>Union
representatives</b><br>
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.<b></b></p>
<p class="MsoNormal" style><strong>Application<br>
</strong>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. </p>
<p><b><span style="font-size:11pt">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 <a href="mailto:registrator@su.se" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=registrator@su.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">registrator@su.se</a>. Please note that the
reference number should be stated in the subject line of your email.</span></b></p>
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<div><div class="gmail_signature"><div dir="ltr"> <br>Yours<br><br>Arne<br><i><br></i>-----------------------------------------<br> Arne Elofsson Science for Life Laboratory<br> Tel:+46-(0)852481531 Stockholm University<br> <a href="http://bioinfo.se/" target="_blank">http://bioinfo.se/</a> Box 1031, <br> Email: <a href="mailto:arne@bioinfo.se" target="_blank" onclick="window.open('https://mail.google.com/mail/?view=cm&tf=1&to=arne@bioinfo.se&cc=&bcc=&su=&body=','_blank','location=yes,menubar=yes,resizable=yes,width=800,height=600');return false;">arne@bioinfo.se</a> 17121 Solna, Sweden<br> Twitter: <a href="https://twitter.com/arneelof" target="_blank">https://twitter.com/arneelof</a><br> Scholar: <a href="http://scholar.google.se/citations?user=s3OCM3AAAAAJ" target="_blank">http://scholar.google.se/citations?user=s3OCM3AAAAAJ</a><br> ORCID: 0000-0002-7115-9751</div></div></div>
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