A two-year Postdoc position is available in the Gorodkin lab (ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (rth.dk) at Department of Veterinary and Animal Sciences (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 October 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:
1)Access and evaluate the potential of DNA probes based on their folding and conservation patterns
2)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
3)Employ the screen to all representative bacterial and viral genomes
4)Explore the further potential in developing the computational tools
5)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).
Application procedure
Your online application must be submitted in English by the UCPH jobsite: employment.ku.dk/faculty/?show=156385. Only application submitted via this site will be taken into consideration.
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 July 31, 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.