Two Postdoc positions of two years are available in the Gorodkin lab, Center for non-coding RNA in Technology and Health (RTH), at Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences at University of Copenhagen. The first Postdoc position concerns developing bioinformatic tools regarding guide RNA (gRNA) design in the CRISPR system taking off-target and DNA modifications into account. The second position concerns developing computational design of RNA-based probes for detection of known pathogens.The positions, are funded by the Independent Research Fund Denmark, and the Novo Nordisk Foundation respectively. They are 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. You will collaborate with other researchers in the group and with collaborating groups.
Position 1 - Postdoc in CRISPR Bioinformatics
The CRISPR technology has become a key tool for genome editing with all the applications that follows. However, unintended edits elsewhere in the genome, off-targets, can have detrimental effects, resulting in additional and irrelevant gene activity not related to intended target. In this project, off-targets will be addressed systematically by developing a computational framework, with outset in energy-based and deep learning models recently published by the lab. In the project, DNA modifications will be considered in the gRNA design using data generated explicitly in the project.
Job description
Your key tasks as a Postdoc at SUND will be to:
- Extend an existing energy model for the CRISPR-Cas9 system and implement in conjunction of existing code
- Integrate methylation data into the off-target mapping algorithm and implement the pipeline
- Implement a hybrid energy model and machine or deep learning framework for predicting off-targets
- Explore further possibilities for improving the computational prediction and modelling
- Teach and disseminate your knowledge
Required qualifications and selection criteria
The applicant should hold the professional as well as personal skills and qualifications as 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
- 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
Position 2 - Postdoc in computational RNA structure-based probe design
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
Terms of employment
The average weekly working hours are on average 37 hours per week. The positions are fixed-term positions 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.
Foreign 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 positions are covered by the Job Structure for Academic Staff at Universities 2020.
Questions
For further information about the scientific content of the positions please contact Professor Jan Gorodkin, email gorodkin@sund.ku.dk, phone +45 23375667 or for application procedure and formalities, please contact HR Officer, email sund-hr-ivh@sund.ku.dk.
International applicants may find the following link useful www.ism.ku.dk (International Staff Mobility).
Application procedure
Apply by clicking "Apply for Position" below. Please note that only online applications will be accepted. Applications - in English - must include:
- Cover letter detailing your motivation and background for applying for the specific Postdoc project. This letter needs to include what is addressed under “Critically important” below
- 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
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).
Application Deadline: 31 July 2022