<div dir="ltr"><div><br></div><div><div id="gmail-:6eq" class="gmail-Am gmail-aiL gmail-Al editable gmail-LW-avf gmail-tS-tW gmail-tS-tY" aria-label="Message Body" role="textbox" aria-multiline="true" style="direction:ltr;min-height:327px" tabindex="1" aria-controls=":74h" aria-expanded="false"><div><br clear="all"></div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"> <br><p>PhD Position at Stockholm University in "Using Deep Learning to Understand Protein Structure Evolution". </p><p><br class="gmail-ProseMirror-trailingBreak"></p><p><span class="gmail-autolink"><a href="https://su.varbi.com/en/what:job/jobID:830925/">https://su.varbi.com/en/what:job/jobID:830925/</a></span></p><p><span class="gmail-autolink"><br></span></p><div class="gmail-banner-wrap">
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<h1 tabindex="0" class="gmail-pull-left">PhD student in Bioinformatics</h1>
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<p><strong>The Department of Biochemistry and Biophysics</strong> <br>SciLifeLab (<a href="https://www.scilifelab.se/" target="_blank" rel="noopener">SciLifeLab</a>)
is a national center for molecular biosciences with a focus on health
and environmental research. The center combines frontline technical
expertise with advanced knowledge of translational medicine and
molecular bioscience. SciLifeLab is a national resource hosted by
Karolinska Institutet, KTH Royal Institute of Technology, Stockholm
University and Uppsala University. The center also collaborates with
several other universities.</p><p>The employment will be placed at the Department of biochemistry and biophysics, at Stockholm university.</p><p>More information about us, please visit: <a href="http://www.dbb.su.se/" target="_blank" rel="noopener noreferrer">the Department of Biochemistry and Biophysics</a>.</p><h2>Project description</h2><p><strong> </strong>Your studies in Bioinformatics will be in the project: "Using Deep Learning to Understand Protein Structure Evolution”.</p><p>We
have studied domain evolution and observed that structural change is
roughly linear with sequence change. However, larger structural changes
might also occur within a domain during evolution, particularly within
transporters3. Further, domains can be combined to create multi-domain
proteins. Most domain architectures arise from adding or removing a
single domain at the N- or C-terminal regions, while certain
repeat-domain families undergo more internal duplications. We also
demonstrated that eukaryotic proteins harbour substantially more
disordered and linker regions, which expand more rapidly than globular
domains. Most phylogenetic studies of proteins, including ours, have
primarily focused on changes in the amino-acid sequences. Today,
accurate structural models from AlphaFold make it possible to integrate
structure into large-scale phylogenetic and sequence analyses.
Therefore, in this application, we propose revisiting earlier studies,
scaling them up, and adding structural information to the analysis. This
study will provide a detailed structural understanding of changes
within domains, how novel protein architectures emerge, and why certain
domains and architectures continue expanding and diversifying in
specific lineages. We believe this study will provide fundamental
insights into protein structure evolution and how evolutionary
mechanisms and selective pressures have shaped proteins. Together, the
three aims of this project will reveal how domain changes their
structure and how rearrangements shape structural protein diversity
across the tree of life.</p><p>The Elofsson group is located at the
Science for Life Laboratory. Elofsson has worked on protein structure
predictions and evolution for over two decades. He has worked on various
techniques using machine learning and other computational techniques.
Our most important contributions to this work are the methods he has
developed to identify the quality of protein models, Pcons, and various
versions of ProQ. The group comprises 5 PhD students, one postdoc, and
one senior researcher.</p><h2>Qualification requirements</h2><p>In order
to be admitted to postgraduate education, the applicant must have the
general and specific entry requirements. The qualification requirements
must be met by the deadline for applications.</p><p>You meet <strong>general entry requirements</strong>
if you have completed a second-cycle degree, or 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.</p><p>In order to meet <strong>the specific entry requirements</strong>,
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).</p><h2>Selection</h2><p>The selection amongst the
eligible candidates will be based on their capacity to successfully
complete the program. Important criteria when assessing this capacity
are; documented knowledge and skill in the field of the thesis project,
written and oral proficiency in English, the capacity for analytical
thinking, the ability to collaborate, as well as creativity, initiative,
and independence. The assessment will be based on previous experience
and grades, the quality of the degree project, references, relevant
experience, interviews and the candidate’s written motivation for
seeking the position.</p><p><a href="https://medarbetare.su.se/en/our-su/governance/rules--regulations/education/admission-regulations-for-third-cycle-study-programmes" target="_blank" rel="noopener noreferrer">Admission Regulations for Doctoral Studies at Stockholm University.</a></p><h2>About the post</h2><p>We
offer a fixed-term employment as a doctoral student according to
Chapter 5 of the Higher Education Ordinance (1993:100). The period of
employment may not be longer than what corresponds to full-time doctoral
education for four years. As a doctoral student, you should primarily
devote yourself to your own doctoral education, but the employment may
include work with education, research and administration to a limited
extent (maximum 20 %).</p><p>A new employment as a doctoral student is
for a maximum of one year, the employment is then renewed for a maximum
of two years at a time.</p><p>Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.</p><h2>Contact</h2><p>For more information, please contact Professor Arne Elofsson, <a href="mailto:arne.elofsson@dbb.su.se" target="_blank" rel="noopener noreferrer">arne.elofsson@dbb.su.se</a>.</p><h2>Application</h2><p>Apply
for the PhD student position at Stockholm University's recruitment
system. Attach a personal letter and CV as well as the attachments
requested in the application form. It is the responsibility of the
applicant to ensure that the application is complete in accordance with
the instructions in the job advertisement, and that it is submitted
before the deadline.</p><p>The instructions for applicants are available at: <a href="https://www.su.se/english/about-the-university/work-at-su/how-to-apply-for-a-position" target="_blank" rel="noopener noreferrer">How to apply for a position</a>.</p></div>
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<p>Stockholm University contributes to the development of
sustainable democratic society through knowledge, enlightenment and the
pursuit of truth.</p> </div>
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<tbody>
<tr class="gmail-quick-info-type-of-employment">
<th scope="row" class="gmail-vth gmail-col-md-3">Type of employment</th>
<td>Temporary position</td>
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<th scope="row" class="gmail-vth gmail-col-md-3">Contract type</th>
<td>Full time</td>
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<th scope="row" class="gmail-vth gmail-col-md-3">Salary</th>
<td>Fixed salary</td>
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<th scope="row" class="gmail-vth gmail-col-md-3">Number of positions</th>
<td>1</td>
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<tr class="gmail-quick-info-working-hours">
<th scope="row" class="gmail-vth gmail-col-md-3">Full-time equivalent</th>
<td>100 %</td>
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<tr class="gmail-quick-info-town">
<th scope="row" class="gmail-vth gmail-col-md-3">City</th>
<td>Stockholm</td>
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<th scope="row" class="gmail-vth gmail-col-md-3">County</th>
<td>Stockholms län</td>
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<th scope="row" class="gmail-vth gmail-col-md-3">Country</th>
<td>Sweden</td>
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<tr class="gmail-quick-info-reference-number">
<th scope="row" class="gmail-vth gmail-col-md-3">Reference number</th>
<td>SU FV-2178-25</td>
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<th>Union representative</th>
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<ul class="gmail-contactList"><li>ST/OFR, <a href="mailto:st@st.su.se">st@st.su.se</a></li><li>Saco-S, <a href="mailto:saco@saco.su.se">saco@saco.su.se</a></li><li>Seko, <a href="mailto:seko@seko.su.se">seko@seko.su.se</a></li></ul>
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<th>Published</th>
<td>23.May.2025 </td>
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<th>Last application date</th>
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13.Jun.2025 </td>
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<h3><br></h3></div></div></div><p><br></p>Yours<br><br>Arne<br><i><br></i>-----------------------------------------<br> Arne Elofsson Science for Life Laboratory<br> Tel:+46-(0)70 695 1045 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">arne@bioinfo.se</a> 17121 Solna, Sweden<br></div><div>Bluesky: @<a href="http://bioinfo.se" target="_blank">bioinfo.se</a> </div><div dir="ltr">Twitter/X: @arneelof<br></div><div dir="ltr"> Mastodon: @<a href="mailto:arneelof@fediscience.org" target="_blank">arneelof@fediscience.org</a><br></div><div dir="ltr"> Zoom: <span style="display:inline-flex"><a href="https://stockholmuniversity.zoom.us/my/arneelof/" target="_blank">https://stockholmuniversity.zoom.us/my/arneelof/</a><span></span></span><br> Scholar: <a href="http://scholar.google.se/citations?user=s3OCM3AAAAAJ" target="_blank">http://scholar.google.se/citations?user=s3OCM3AAAAAJ</a><br> ORCID: <a href="https://orcid.org/0000-0002-7115-9751" target="_blank">0000-0002-7115-9751</a></div></div></div></div></div></div><br clear="all"></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"> <br>Yours<br><br>Arne<br><i><br></i>-----------------------------------------<br> Arne Elofsson Science for Life Laboratory<br> Tel:+46-(0)70 695 1045 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">arne@bioinfo.se</a> 17121 Solna, Sweden<br></div><div>Bluesky: @<a href="http://bioinfo.se" target="_blank">bioinfo.se</a> </div><div dir="ltr">Twitter/X: @arneelof<br></div><div dir="ltr"> Mastodon: @<a href="mailto:arneelof@fediscience.org" target="_blank">arneelof@fediscience.org</a><br></div><div dir="ltr"> Zoom: <span style="display:inline-flex"><a href="https://stockholmuniversity.zoom.us/my/arneelof/" target="_blank">https://stockholmuniversity.zoom.us/my/arneelof/</a><span></span></span><br> Scholar: <a href="http://scholar.google.se/citations?user=s3OCM3AAAAAJ" target="_blank">http://scholar.google.se/citations?user=s3OCM3AAAAAJ</a><br> ORCID: <a href="https://orcid.org/0000-0002-7115-9751" target="_blank">0000-0002-7115-9751</a></div></div></div></div></div></div>