Postdoc in CRISPR Bioinformatics in the Gorodkin lab
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 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 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.
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.
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
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 on average 37 hours 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.
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 position is covered by the Job Structure for Academic Staff at Universities 2020.
For further information about the scientific content of the position please contact Professor Jan Gorodkin, email firstname.lastname@example.org, phone +45 23375667 or for application procedure and formalities, please contact HR Officer, email email@example.com.
International applicants may find the following link useful www.ism.ku.dk (International Staff Mobility).
Apply by clicking "Apply online" 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” above
- 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 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 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 July 10-22, 2022.
The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.