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 bioinformatic tools regarding guide RNA (gRNA) design in the CRISPR system taking off-target and DNA modifications into account. The position, funded by the Independent Research Fund Denmark, 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. You will collaborate with other researchers in the group and with collaborating groups.
Background
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
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
Application procedure
Apply by clicking "Apply online" on the UCPH jobsite: employment.ku.dk/faculty/?show=156384 . 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” 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 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. 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 may read about the recruitment process at 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 in August.
The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.