Postdoc In Computational Crispr Guide Rna Design Targeting Network Modules

A three-year postdoc position is available 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 commencing 15 May 2024 or as soon as possible hereafter..

The development of CRISPR field is very rapidly and novel technological possibilities are continuously emerging. Some aspects address multiplex gene editing opening the possibility to, in one go, target entire modules in gene networks, such as those made from gene genetic interactions. gRNA design in this context a requires incorporating such networks into the design both concerning on- and off-targets. Project includes collaborators Prof Lars Juhl Jensen on molecular networks and Prof Yonglun Luo on data generation. This postdoc position addresses these challenges in the context of constructing an interactive user interface. The position is funded by the Novo Nordic Foundation.

Our research
Genome editing is to a very large degree driven by developments of the CRISPR technology of which the computational strategies key in both data analysis and algorithm for optimization experimental design of data and gene editing itself. In the current project methods for multiplex gRNA design targeting network modules will be developed taking outset in existing computational strategies, e.g. (Xiang et. al., Nat Comm, 2021; Corsi et al., Nat Comm, 2022). The research group is involved in several computational CRISPR projects, while working on a range of bioinformatical aspects both algorithm, data and omics-wise. The research group 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:

• Develop the multiplex-based gRNA design strategy to target network modules
• Involvement in gRNA on- and off-target efficiency prediction methods.
• Involvement in construction of networks genetic interactions.
• Involvement in designing a user interface.
• 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 be highly dedicated, 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 highly experienced in Python
• You are well familiar C++/C
• You have strong experience with the Linux/Unix environment, command lines and shell scripting
• You are well familiar with machine learning algorithms both theoretically and practically in implementing them
• 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 biological networks

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 3 years. The starting date is 15 May 2024 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 36,000 DKK/approx. 4,800 EUR (October 2023 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.

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

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:

1. Motivation letter of application. In this letter you must briefly detail, one by one, how you meet the requirements for each item listed under “Essential experience and skills” and “Desirable experience and skills”.
2. CV incl. education, work/research experience, language skills and other skills relevant for the position.
3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
4. List of publications.
5. Letters of Recommendations. 

Deadline for applications: 5 March, 2024, 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.

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.