<div dir="ltr"><h2 class="gmail-org-desc">
Department of Experimental Medical Science </h2>
<div class="gmail-company-top-desc">
<p><a href="https://lu.varbi.com/en/what:job/jobID:456054">https://lu.varbi.com/en/what:job/jobID:456054</a> <br></p><p>Lund University was founded in 1666 and is repeatedly ranked
among the world’s top 100 universities. The University has around 44 000
students and more than 8 000 staff based in Lund, Helsingborg and
Malmö. We are united in our efforts to understand, explain and improve
our world and the human condition.</p>
<p>Lund University welcomes applicants with diverse backgrounds and
experiences. We regard gender equality and diversity as a strength and
an asset.</p> </div>
<div class="gmail-subcompany-desc gmail-mb">
<p>
</p>
</div>
<div class="gmail-job-desc gmail-mb">
<p><strong>Background</strong></p><p>In the Atkinson lab we are
interested in making exciting discoveries about the evolution of protein
function and structure. We work mainly with bioinformatic methods,
developing our own tools and taking advantage of the wealth of available
genome and predicted proteome sequences. The Atkinson lab is based in
the Department of Experimental Medical Sciences in the Biomedical Centre
(BMC) in Lund. You can read more about our group on our lab website
here: <a href="https://atkinson-lab.com/">https://atkinson-lab.com/</a>, and about the department here:
<a href="https://www.medicine.lu.se/faculty-medicine-lund-university/departments/department-experimental-medical-science">https://www.medicine.lu.se/faculty-medicine-lund-university/departments/department-experimental-medical-science</a></p><p>One
of our main research directions concerns toxin-antitoxin (TA) systems
of bacteria and bacteriophages, which has led to papers in PNAS(1) and
Molecular Cell(2) on toxSAS enzymes that dramatically inhibit bacterial
growth though producing poisonous nucleotides, or modifying tRNA, as
well as a more recent preprint on the hyper promiscuous antitoxin domain
that we have named Panacea(3). Our work on toxin-antitoxins, and their
evolution, structure, function and biotechnological applications was
recently supported by a generous grant from the Knut and Alice
Wallenberg foundation (see
<a href="https://kaw.wallenberg.org/en/research/bacterias-emergency-stop-buttons">https://kaw.wallenberg.org/en/research/bacterias-emergency-stop-buttons</a>).
As a mechanism of defence against bacteriophages, TAs have significance
for developing new biotechnological tools, as well as understanding and
eventually overcoming natural barriers to phage therapy for treating
antibiotic resistant infections.</p><p>References</p><p> </p><ol><li>Jimmy, S.<em> et al.</em> <em>Proc Natl Acad Sci U S A</em> <strong>117</strong>, 10500-10510, (2020).</li><li>Kurata, T.<em> et al.</em> <em>Mol Cell</em> <strong>81</strong>, 3160-3170 e3169, (2021).</li><li>Kurata, T.<em>et al.</em> <em>Proc Natl Acad Sci U S A (in press) and </em><em>bioRxiv</em>, <a href="https://www.biorxiv.org/content/10.1101/2021.1105.1107.442387v442381">https://www.biorxiv.org/content/10.1101/2021.1105.1107.442387v442381</a>, (2021).</li></ol><p>In
our group, we strive for a supportive, respectful and stimulating
working environment that promotes personal and professional development
for all members.</p><p>We are looking for a PhD student to continue the
lab’s high impact work, driving new directions in toxin-antitoxin system
research. A significant part of the project will be the use of deep
learning methods for structural prediction such as AlphaFold2. The
employment is for 4 years at full time and the start date is by
agreement.</p><p><strong>Responsibilities</strong></p><p>In this PhD
project you will be using and developing computational tools to predict
the structure and biological function of toxin-antitoxin systems of
bacteria and bacteriophages. Bioinformatic predictions that come out of
this project will be verified experimentally through our collaborative
network. Much of the project will focus on toxin-antitoxin systems, but
you will also have opportunities to broaden your horizons to other
molecular systems. You will have the opportunity to attend and present
your work at international meetings.</p><p><strong>Qualifications</strong></p><p>Required qualifications:</p><ul><li>Coding skills (preferably in Python)</li><li>Experience in structural bioinformatics</li><li>Proficiency in spoken and written English</li><li>Background understanding of, and interest in molecular biology and evolution of microbes</li></ul><p>Desirable qualifications:</p><ul><li>Experience in creating pipelines for use with high performance computing clusters</li><li>Competence in large dataset handling</li><li>Previous
use of machine learning or artificial intelligence methods, especially
for structural prediction such as AlphaFold2 or RosettaFold</li></ul><p><strong>Eligibility</strong><br>Students
with basic eligibility for third-cycle studies are those who- have
completed a second-cycle degree- have completed courses of at least 240
credits, of which at least 60 credits are from second-cycle courses, or-
have acquired largely equivalent knowledge in some other way, in Sweden
or abroad.</p><p>The employment of doctoral students is regulated in
the Swedish Code of Statues 1998: 80. Only those who are or have been
admitted to PhD-studies may be appointed to doctoral studentships. When
an appointment to a doctoral studentship is made, the ability of the
student to benefit from PhD-studies shall primarily be taken into
account. In addition to devoting themselves to their studies, those
appointed to doctoral studentships may be required to work with
educational tasks, research and administration, in accordance with
specific regulations in the ordinance.</p><p><strong>Type of employment</strong><br>Limit of tenure, four years according to HF 5 kap 7§.</p><p> </p><p><strong>Include the following documents in your application:</strong></p><p>1. A cover letter (maximum 1 page) with the following sections:</p><p>a) Motivation</p><p> (explain your interest in the project, motivation for applying, and what you hope to learn)</p><p>b) Eligibility and experience</p><p>(explain
how you fulfil the eligibility and qualification requirements, describe
your previous relevant experience and outline how you will contribute
to the research group)</p><p>2. A CV (maximum 2 pages) with contact details of two referees</p><p>3. Bachelors and Masters certificates</p><p> </p></div>
<div class="gmail-subcompany-footer">
<p>
The Faculty of Medicine is a part of Lund University, and is
responsible for education and research within medicine and healthcare.
Our academic programs are closely linked with the healthcare system and
are firmly anchored in the faculty’s strong research tradition. Our
research spans a broad field within experimental preclinical research,
near-patient clinical research and health sciences research. The Faculty
of Medicine, with its 1,800 employees and 2,700 students in Lund and
Malmö, is a knowledge-intensive meeting place for students, teachers and
researchers from all over the world. </p>
</div>
<div class="gmail-company-footer">
<p>We kindly decline all sales and marketing contacts.</p> </div>
<table class="gmail-table gmail-table-condensed gmail-quick-info">
<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 longer than 6 months</td>
</tr>
<tr class="gmail-quick-info-admission">
<th scope="row" class="gmail-vth gmail-col-md-3">First day of employment</th>
<td>220301</td>
</tr>
<tr class="gmail-quick-info-pay">
<th scope="row" class="gmail-vth gmail-col-md-3">Salary</th>
<td>Monthly salary</td>
</tr>
<tr class="gmail-quick-info-number-of-positions">
<th scope="row" class="gmail-vth gmail-col-md-3">Number of positions</th>
<td>1</td>
</tr>
<tr class="gmail-quick-info-working-hours">
<th scope="row" class="gmail-vth gmail-col-md-3">Working hours</th>
<td>100</td>
</tr>
<tr class="gmail-quick-info-town">
<th scope="row" class="gmail-vth gmail-col-md-3">City</th>
<td>Lund</td>
</tr>
<tr class="gmail-quick-info-county">
<th scope="row" class="gmail-vth gmail-col-md-3">County</th>
<td>Skåne län</td>
</tr>
<tr class="gmail-quick-info-country">
<th scope="row" class="gmail-vth gmail-col-md-3">Country</th>
<td>Sweden</td>
</tr>
<tr class="gmail-quick-info-reference-number">
<th scope="row" class="gmail-vth gmail-col-md-3">Reference number</th>
<td>PA2021/3992</td>
</tr>
<tr class="gmail-quick-info-contact-list">
<th>Contact</th>
<td>
<ul class="gmail-contactList"><li>Gemma Atkinson, 046-2220000</li></ul>
</td>
</tr>
<tr class="gmail-quick-info-union-representative">
<th>Union representative</th>
<td>
<ul class="gmail-contactList"><li>OFR/ST:Fackförbundet ST:s kansli, 046-222 93 62</li><li>SACO:Saco-s-rådet vid Lunds universitet, 046-222 93 64</li><li>SEKO: Seko Civil, 046-222 93 66</li></ul>
</td>
</tr>
<tr class="gmail-quick-info-published">
<th>Published</th>
<td>07.Dec.2021</td>
</tr>
<tr class="gmail-quick-info-ends">
<th>Last application date</th>
<td>09.Jan.2022 11:59 PM CET</td></tr></tbody></table><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> Twitter: <a href="https://twitter.com/arneelof" target="_blank">https://twitter.com/arneelof</a></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>