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 (http://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (http://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 (http://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 [email protected], phone +45 23375667 or for application procedure and formalities, please contact HR Officer, email [email protected] / 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:

1. 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”.
2. CV incl. education, work/research experience, language skills and other skills relevant for the position.
3. 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: http://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.