PhD fellowship in computational CRISPR guide RNA design

Faculty of Health and Medical Sciences
University of Copenhagen

A PhD fellowship is available in the Computational Biology and Bioinformatics research group (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. A key challenge is to pick the most efficient on-target guide RNA (gRNA) among several possible ones in a specific target region while taking the possible off-targets, i.e., unintended edits elsewhere in the genome, into account. This PhD project aims to make computational methods for on-target gRNA design while taking the off-target potential into account. The position is funded by the Novo Nordisk Foundation.

Start date is November 1st, 2023 or as soon as possible thereafter.

The Bioinformatics group and research
The Computational Biology and Bioinformatics research group holds a long-standing interest in Computational RNA biology and transcriptomics but works in general on many different topics covering computational, algorithmic and biological aspects. Over the recent years CRISPR bioinformatics has evolved from the group’s interest in RNA-RNA interactions through gRNA-DNA interactions. The group is located on Frederiksberg Campus. Our research environment is highly international and stimulating. We are involved in organizing seminars, workshops, summer schools with international speakers and have retreats with our international collaborators.

Project description
The PhD project is focused on designing computational methods for gRNA design while taking the off-target landscape, developed by others in the group, into account. The PhD project will take outset in the in-house deep learning (DL) model, CRISPRon, to be applied on data generated by project collaborator Prof Yonglun Luo. The initial model will encode both on- and off-target data (as ranked by our CRISPRoff method) to predict gRNA efficiency while also being used for model-driven data generation of novel gRNA efficiency data by collaborator. The downstream computational models will explore machine and deep learning techniques for further enhancement, and they will subsequently be used to make a multiplex version to simultaneously target multiple genes taking their genetic interactions into account. Throughout the project, methodological advances will be incorporated in the available CRISPR design web interface.

Principal supervisor is Professor, Jan Gorodkin, Department of Veterinary and Animal Sciences, Phone: +45 23375667, Email: [email protected].

Start: November 1, 2023 or as soon as possible thereafter.
Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision, with content as outlined above in the project description.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project such as Bioinformatics, Computer Science or similar areas. Most importantly that you meet the technical requirements in bullet #2 below. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

• The grade point average achieved
• Professional qualifications relevant to the PhD project. This include (but not limited to):
  For the following criteria the level has to be at level where you are able to work independently:
  • A solid knowledge of Machine and Deep learning algorithms
  • Python (or Perl) and knowledge of C/C++, shell scripting and Unix/Linux operating system
• Previous publications
• Relevant work experience
• Demonstrate that you can work independently while keeping the team up to date
• Pro-active in the project and its planning
• Other professional activities
• Language skills

Additional knowledge of (RNA and Cas) structural bioinformatics is an advantage. Applicants are encouraged to explain in their motivation letter how they match the specific requirements listed in bullet #2 and other relevant qualifications.

Place of employment
The place of employment is at the Computational Biology and Bioinformatics group, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen. The work environment in the lab is highly dynamic and international with good synergy among the different research projects. The group has access to all the necessary computational infrastructure and high-performance computing needed for the project.

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 start date is November 1, 2023 or as soon as possible thereafter.

The employment is conditioned upon the applicant’s success¬ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agree¬ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 28,800 DKK/Roughly 3,800 EUR (April 2023 level) plus pension.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.
For specific questions regarding the HR process of recruitment, you can contact [email protected].

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:

1. Motivation letter of application
2. CV incl. education, experience, language skills and other skills relevant for the position
3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science
4. Publication list (if possible)

Application deadline: September 20, 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.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

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 find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/

The applicants 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.