Postdoc in computational CRISPR guide RNA design

A two-year Postdoc position is available 1 March 2023 or as soon as possible thereafter in the Gorodkin lab (http://ivh.ku.dk/bioinformatics  Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk ) at Department of Veterinary and Animal Sciences (http://ivh.ku.dk/english ), Faculty of Health and Medical Sciences at University of Copenhagen. The CRISPR field is developing rapidly and is continuously providing novel technological possibilities by several types of applications including gene editing and gene surgery. An understudied key challenge in these types of applications is off-targets. These are guide RNAs (gRNAs) which edit or operate on other genes than the intended one. This postdoc position precisely addresses this problem by developing computational tools for guide RNA (gRNA) design that do not only take off-targets into account but also how these are affected by DNA modifications. The position is funded by the Independent Research Fund Denmark.

Our research

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 an 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. 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.

Your job

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-target
• Explore further possibilities for improving the computational prediction and modelling
• Teach and disseminate your knowledge

Profile

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 work in a cross-disciplinary environment and collaborate with other researchers internally in the group and with collaborating groups working on the experimental aspects.

We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

• You have completed PhD degree in bioinformatics, computer science or in a similar area
• You are well familiar and experienced with C++ or C and Perl or Python
• You have strong experience with the Linux/Unix environment, command lines and shell scripting
• You are well familiar with machine learning algorithms
• You are proficient communication skills
• You have excellent English skills written and spoken
• You have good people skills and is a strong team player

Desirable experience and skills:

• Knowledge of RNA folding and RNA-RNA interaction algorithms
• Knowledge of algorithms using suffix-arrays / suffix-trees and data structures

Key selection criteria:

• Publications
• Professional qualifications relevant for the position
• Relevant work experience
• Language skills
• Creativity

Terms of employment

The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 years. The starting date is 1 March 2023 or as soon as possible thereafter.

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 35,700 DKK/approx. 4,800 EUR (October 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 lived in Denmark the last 10 years.

The position is covered by the Job Structure for Academic Staff at Universities 2020.

 You have completed a PhD degree in bioinformatics or computer science.

Questions

For further information about the scientific content of the position 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 ];www.sund.ku.dk

Foreign applicants may find this 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:

Deadline for applications: December 18th, 2023, 23.59pm 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 has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at http://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 from January 4th take approximately a week

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

Apply for position

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.