Postdoc in computational RNA structure-based probe design

A two-year Postdoc position is 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 Postdoc position concerns developing computational design of RNA-based probes for detection of known pathogens. The position, funded by the Novo Nordisk Foundation, is available from September 1, 2022, or as soon as possible thereafter.

You will be an excellent and emphatic team player and pleasant for your colleagues to work with. You will work with great excitement and be a key person in the project essential for obtaining successful results. The Postdoc position will collaborate with other researchers in the group and with collaborating groups.

Background

Fast detection of multiple pathogens in one go is critical in many regards ranging from infections to food. In this project, the collaborative teams aim to develop a next-generation pathogen detection platform for massively parallel multiplex screening. This will be accomplished by using the non-enzymatic amplification technology (NISDA) in which RNA based probes are designed to capture the respective pathogens. The postdoc will be involved in RNA structure-based design while taking potential off-targets into account in the design process. This will involve not only employing RNA/DNA folding algorithms in the context of evolutionary conservation, but also to employ efficient algorithms to search for DNA-RNA interactions.

Job description

Your key tasks as a Postdoc at SUND will be:

• Access and evaluate the potential of DNA probes based on their folding and conservation patterns
• Develop an efficient DNA-RNA interaction search tool with outset in methodology in RIsearch2 for RNA-RNA interactions and CRISPRoff used in the context gRNA off-targeting on DNA
• Employ the screen to all representative bacterial and viral genomes
• Explore the further potential in developing the computational tools
• Teach and disseminate your knowledge

Required qualifications and selection criteria

The applicant should hold the professional as well as personal skills and qualifications stated below:

• A completed PhD degree in bioinformatics, computer science or in a similar area
• Strong knowledge of RNA folding and RNA-RNA interaction algorithms
• Strong knowledge of algorithms using suffix-arrays / suffix-trees for mapping (complementary) sequences to genomes
• Machine learning is a plus
• C++ or C and Perl or Python
• Strong experience with the Linux/Unix environment, command lines and shell scripting
• Good people skills and team player abilities

Critically important

In your enclosed cover letter, you must explain how you match each of the seven items listed under “Required qualifications and selection criteria “one by one. You should in your explanations include pointers to

• Previous publications
• Relevant work experience and specific projects
• Other professional activities
• Language skills

If such a letter is not enclosed or the items are not addressed one by one, your application may not be shortlisted (see “The further process” below).

Place of employment

RTH 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 37hours per week.

The position is a fixed-term position limited to a period of two years. The starting date is September 1, 2022, or after agreement.

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 starts at 35,624 DKK/approx. 4,781 EUR (April 2022 level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

International and Danish applicants may be eligible for tax reductions if they hold a PhD degree and have not been tax liable to Denmark the last 10 years.

The position 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] .

International applicants may find the following 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:

• Cover letter detailing your motivation and background for applying for the specific Postdoc project. This letter needs to include what is address under “Critically important” above
• CV
• Diploma and detailed transcripts of records 
• List of publications, clearly divided into peer reviewed journal papers and other papers
• Personal Recommendations. If none, please explain why it has not been possible to obtain
• Three relevant scientific works which the applicant wishes to be included in the assessment

The deadline for applications is June 30, 2022, at 23:59 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 above-mentioned 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. Once the assessment work has been completed each applicant may comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/ .

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

Interviews are expected to be held between July 10-22.

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