[SocBiN] Two PhD or Postdoc positions in computational off-target analysis of siRNA and small peptides

[Arne Elofsson]

https://jobportal.ku.dk/videnskabelige-stillinger/?show=162883

 Two PhD or Postdoc positions in computational off-target analysis of siRNA
and small peptides

We have two positions each as either a three-year PhD or a three-year
postdoc available in the Gorodkin lab (https://ivh.ku.dk/bioinformatics),
Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk)
at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english),
Faculty of Health and Medical Sciences at University of Copenhagen.

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:

    Computational methods to predict and analyze siRNA off-targets and
their effects
    Computational methods to predict and analyze small peptide off-targets
and their effects

Start date is February or March 2025 or as soon as possible thereafter.

The project
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:

    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.
    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.

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.

If a position is offered as a PhD, your key tasks as a PhD student at SUND
are:

    Carrying through an independent research project under supervision.
    Completing PhD courses or other equivalent education corresponding to
approximately 30 ECTS points.
    Participating in active research environments including a stay at
another research team.
    Obtaining experience with teaching or other types of dissemination
related to your PhD project
    Teaching and disseminating your knowledge.
    Writing a PhD thesis on the grounds of your project

Who are we looking for
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.

Essential experience and skills:

    For postdoc applicants: You have completed PhD degree in
bioinformatics, computer science or in a similar area
    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)
    You are highly experienced in Python
    You have strong experience with the Linux/Unix environment, command
lines and shell scripting
    You are well familiar with machine learning algorithms both
theoretically and practical implementation
    You are proficient communication skills
    You have excellent English skills, written and spoken
    You have good people skills and is a strong team player

Desirable experience and skills:

    Knowledge about RNA and / or protein structure and interactions
    Knowledge about algorithms for RNA and/or protein structure and
interaction prediction
    Knowledge about omics e.g., transcriptomics / proteomics data analysis
    Knowledge and experience with machine/deep learning
    Knowledge with analysis of biological networks beyond basic
applications through GUIs.

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.

Key selection criteria for both PhD-student and postdoc:

    Publications
    Professional qualifications relevant for the position
    Relevant work experience
    Language skills
    Creativity

Our research group
Our research group Computational Biology and Bioinformatics (
https://ivh.ku.dk/bioinformatics) 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.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years both
as PhD-student and as postdoc. The starting date is February 1st, 2025, or
as soon as possible thereafter.

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.

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.

The position either as PhD-student or as postdoc is covered by the Job
Structure for Academic Staff at Universities 2020.

Questions
For further information about the scientific content of the position please
contact Professor Jan Gorodkin, email gorodkin at sund.ku.dk, phone +45
23375667 or for application procedure and formalities, please contact HR
Officer, email sund-hr-ivh at sund.ku.dk / www.sund.ku.dk

Foreign applicants may find this link useful: www.ism.ku.dk (International
Staff Mobility).

Application procedure
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:

    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”.
    CV incl. education, work/research experience, language skills and other
skills relevant for the position.
    A certified/signed copy of:

    a) For the postdoc position: PhD certificate. If the PhD is not
completed, a written statement from the supervisor will do.
    b) 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:
https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database.
Please note that we might ask you to obtain an assessment of your education
performed by the Ministry of Higher Education and Science

    4. List of publications.
    5. Personal Recommendations. If none, please explain why it has not
been possible to obtain.

Deadline for applications: 3 January 2025, 23.59pm CET

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.

The further process
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.

The assessor makes a non-prioritized assessment of the academic
qualifications and experience with respect to the above-mentioned area of
research, techniques, skills and other requirements listed in the
advertisement.

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.

You find information about the recruitment process at:
https://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242
of 13 March 2012 on the Appointment of Academic Staff at Universities.

The University of Copenhagen wish to reflect the diversity of society and
encourage all qualified candidates to apply regardless of personal
background.

Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for
at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer
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