<div dir="ltr"><div><a href="https://jobportal.ku.dk/videnskabelige-stillinger/?show=162883">https://jobportal.ku.dk/videnskabelige-stillinger/?show=162883</a></div><div><br></div><div><h1>
Two PhD or Postdoc positions in computational off-target analysis of siRNA and small peptides
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<p>We have two positions each as either a three-year PhD or a three-year postdoc available in the Gorodkin lab (<a href="https://ivh.ku.dk/bioinformatics">https://ivh.ku.dk/bioinformatics</a>), Center for non-coding RNA in Technology and Health (RTH), (<a href="https://rth.dk/">http://rth.dk</a>) at Department of Veterinary and Animal Sciences (<a href="https://ivh.ku.dk/english">https://ivh.ku.dk/english</a>), Faculty of Health and Medical Sciences at University of Copenhagen.</p>
<p>The projects concern safety when siRNAs and small peptides are
applied as pesticides in plants and the aim is to develop the
computational tools and analyses that will contribute to an
environmental risk assessment framework for new bio-based plant
protection products (PPPs). The project is part of the Novo Nordic
Foundation Challenge project ENSAFE: “ENvironmental SAFEty of
biotechnological plant protection products based on short interfering
RNA and peptides” headed by Professor Nina Cedergreen. The title of the
two positions are:</p>
<ul><li>Computational methods to predict and analyze siRNA off-targets and their effects</li><li>Computational methods to predict and analyze small peptide off-targets and their effects</li></ul>
<p>Start date is February or March 2025 or as soon as possible thereafter.</p>
<p><strong>The project</strong><br>
The vision of ENSAFE is to develop the in silico and experimental
methods and tools needed to underpin an efficient evidence-based risk
assessment framework for new bio-based plant protection products (PPPs)
based on short double stranded RNA (dsRNA) or peptides. The two
positions will be filled as PhD students or postdocs working with each
their model compound of newly commercialised dsRNA or peptide-based
products:</p>
<ul><li>Position 1: Data analysis and computational tools for siRNA-RNA
interactions of the target and off-target organisms will be developed
with outset in established and in-house methods such as RIsearch2.</li><li>Position 2: Data analysis and computational tools for small peptide
interactions to proteins will be developed with outset in predicting
interactions between the peptides and the proteins of the target and
off-target organisms. The methodological framework will take outset in a
combination of sequence motif detection algorithms and 3D folding with
Alphafold for predicting the interactions.</li></ul>
<p>In both projects data structures or efficient initial omics-wide
searches will be constructed. The data obtained from the public domain
and from within the ENSAFE project will be used to build the search
tools, test its quality and guide the design of novel experiments. To
the extent data allows for it, the projects will further explore the
possibilities for modelling with machine/deep learning techniques. The
two positions will work close with collaborators of the Gorodkin lab on
computational elements and with the project partners of ENSAFE in
general.</p>
<p>If a position is offered as a PhD, your key tasks as a PhD student at SUND are:</p>
<ul><li style="text-align:justify">Carrying through an independent research project under supervision.</li><li style="text-align:justify">Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.</li><li style="text-align:justify">Participating in active research environments including a stay at another research team.</li><li style="text-align:justify">Obtaining experience with teaching or other types of dissemination related to your PhD project</li><li style="text-align:justify">Teaching and disseminating your knowledge.</li><li style="text-align:justify">Writing a PhD thesis on the grounds of your project</li></ul>
<p><strong>Who are we looking for</strong><br>
We are looking for highly motivated and enthusiastic candidates with a
strong technical background and experience in programming, algorithms,
data structures, machine learning and data analysis, in particular
omics, who are familiar and have experience with either RNA structure
and RNA-RNA interactions or protein structure and interactions. You will
work in a cross-disciplinary environment and collaborate with other
researchers internally in the group and with external groups working on
the experimental aspects. You will be an excellent and emphatic team
player and pleasant to work with. You will be highly dedicated, work
with great excitement and be a key person in the project essential for
obtaining successful results.</p>
<p>Essential experience and skills:</p>
<ul><li>For postdoc applicants: You have completed PhD degree in bioinformatics, computer science or in a similar area</li><li>For PhD applicants: You have completed MSc degree in
bioinformatics, in computer science or in a similar area. Please note
that your master’s degree must be equivalent to a Danish master’s degree
(two years)</li><li>You are highly experienced in Python</li><li>You have strong experience with the Linux/Unix environment, command lines and shell scripting</li><li>You are well familiar with machine learning algorithms both theoretically and practical implementation</li><li>You are proficient communication skills</li><li>You have excellent English skills, written and spoken</li><li>You have good people skills and is a strong team player</li></ul>
<p>Desirable experience and skills:</p>
<ul><li>Knowledge about RNA and / or protein structure and interactions</li><li>Knowledge about algorithms for RNA and/or protein structure and interaction prediction</li><li>Knowledge about omics e.g., transcriptomics / proteomics data analysis</li><li>Knowledge and experience with machine/deep learning</li><li>Knowledge with analysis of biological networks beyond basic applications through GUIs.</li></ul>
<p>For postdoc applicants we expect a general higher level of expertise
relative to PhD applicants, including (but not limited to) higher
experience research, programming, theoretical thinking and writing of
scientific articles. This higher experience for postdocs should be
reflected in having at least three additional years of experiences in
their scientific career including published and amount code written.</p>
<p>Key selection criteria for both PhD-student and postdoc:</p>
<ul><li>Publications</li><li>Professional qualifications relevant for the position</li><li>Relevant work experience</li><li>Language skills</li><li>Creativity</li></ul>
<p><strong>Our research group</strong><br>
Our research group Computational Biology and Bioinformatics
(<a href="https://ivh.ku.dk/bioinformatics">https://ivh.ku.dk/bioinformatics</a>) work with computational algorithms
and methods for molecular structure and interactions. We have excellent
computational infrastructure and further access to supercomputing when
needed. The research group is working on a range of bioinformatical
aspects both algorithm, data and omics-wise. The research group is
located on Frederiksberg Campus. Our research environment is highly
international and stimulating. We frequently organize seminars,
workshops, summer schools with international speakers and have retreats
with our international collaborators.</p>
<p><strong>Terms of employment </strong><br>
The average weekly working hours are 37 hours per week.</p>
<p>The position is a fixed-term position limited to a period of <strong>3</strong> years both as PhD-student and as postdoc. The starting date is February 1st, 2025, or as soon as possible thereafter.</p>
<p>Salary, pension and other conditions of employment are set in
accordance with the Agreement between the Ministry of Taxation and AC
(Danish Confederation of Professional Associations) or another relevant
organisation. Currently, the monthly salary for Postdocs starts at
35,000 DKK/approx. 4,700 EUR (October 2021 level). For PhD, the monthly
salary starts at 27,800 DKK/approx.. 3,700 EUR (October 2021 level).
Depending on qualifications, a supplement for both PhD-student and
postdoc may be negotiated. The employer will pay an additional 17.1 % to
your pension fund.</p>
<p>Foreign and Danish applicants may be eligible for tax reductions, if
they hold a PhD degree and have not lived in Denmark the last 10 years.</p>
<p><span style="color:black">The position either as PhD-student or as postdoc is covered by the Job Structure for Academic Staff at Universities 2020. </span></p>
<p><strong>Questions</strong><br>
For further information about the scientific content of the position please contact Professor Jan Gorodkin, email <a href="mailto:gorodkin@sund.ku.dk">gorodkin@sund.ku.dk</a>, phone +45 23375667 or for application procedure and formalities, please contact HR Officer, email <a href="mailto:sund-hr-ivh@sund.ku.dk">sund-hr-ivh@sund.ku.dk</a> /<strong> </strong><a href="https://www.sund.ku.dk/"><strong>www.sund.ku.dk</strong></a></p>
<p>Foreign applicants may find this link useful: <a href="https://www.ism.ku.dk/">www.ism.ku.dk</a> (International Staff Mobility).</p>
<p><strong>Application procedure</strong><br>
Your online application must be submitted in English by clicking ‘Apply
now’ below. Furthermore, your application must include the following
documents/attachments – all in PDF format:</p>
<ol><li>Motivation letter of application. In this letter you must briefly
detail, one by one, how you meet the requirements for each item listed
under “Essential experience and skills” and “Desirable experience and
skills”.</li><li>CV incl. education, work/research experience, language skills and other skills relevant for the position.</li><li>A certified/signed copy of:</li></ol>
<ul><li><strong>a)</strong> For the postdoc position: PhD certificate. If the PhD is not completed, a written statement from the supervisor will do.</li><li><strong>b</strong>) For the PhD position: Certified copy of
original Master of Science diploma and transcript of records in the
original language, including an authorized English translation if issued
in other language than English or Danish. If not completed, a
certified/signed copy of a recent transcript of records or a written
statement from the institution or supervisor is accepted. As a
prerequisite for a PhD fellowship employment, your master’s degree must
be equivalent to a Danish master’s degree. We encourage you to read more
in the assessment database: <a href="https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database">https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database</a>.
Please note that we might ask you to obtain an assessment of your
education performed by the Ministry of Higher Education and Science<br>
<br>
4. List of publications.<br>
5. Personal Recommendations. If none, please explain why it has not been possible to obtain.</li></ul>
<p><strong>Deadline for applications: 1 December</strong><strong> 2024, 23.59pm CET </strong></p>
<p>We reserve the right not to consider material received after the
deadline, and not to consider applications that do not live up to the
abovementioned requirements.</p>
<p><strong>The further process </strong><br>
After the expiry of the deadline for applications, the authorized
recruitment manager selects applicants for assessment on the advice of
the hiring committee. All applicants are then immediately notified
whether their application has been passed for assessment by an unbiased
assessor.</p>
<p style="text-align:justify">The assessor makes a non-prioritized assessment of the academic qualifications and experience <span style="color:black">with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.</span></p>
<p>Once the assessment work has been completed each applicant has the
opportunity to comment on the part of the assessment that relates to the
applicant him/herself.</p>
<p>You find information about the recruitment process at: <a href="https://employment.ku.dk/faculty/recruitment-process/">https://employment.ku.dk/faculty/recruitment-process/</a></p>
<p>The applicants will be assessed according to the Ministerial Order
no. 242 of 13 March 2012 on the Appointment of Academic Staff at
Universities.</p>
<p><em><span style="color:black">The University of Copenhagen wish to
reflect the diversity of society and encourage all qualified candidates
to apply regardless of personal background.</span></em></p>
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<p>Københavns Universitet giver sine knap 10.000 medarbejdere
muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt
miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri
forskning på højt internationalt niveau. Vi søger svar og løsninger på
fælles problemer og gør ny viden tilgængelig og nyttig for andre.</p>
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<h3>Info</h3>
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<strong>Ansøgningsfrist:</strong> 01-12-2024
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<strong>Ansættelsesdato:</strong>
01-02-2025
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<strong>Arbejdstid:</strong> Fuldtid
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<strong>Afdeling/Sted:</strong> Department of Veterinary and Animal Sciences
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</div></div></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: @arneelof.bsky.social </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>