PhD or Postdoc in computational CRISPR guide RNA design targeting network modules

We have a three-year PhD or three-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 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 position, whether it is carried out by a PhD-student or a postdoc 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. 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
In the project you will work with a combination of gRNA on- and off-target data and biological networks of genetic interactions such as functional redundancy. The combination of these two areas will move into next generation CRISPR design which address modules of multiple genes connected through functional redundancy for tomorrow’s function studies using CRISPR.

Your key tasks as a PhD-student or 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.
• To explore further possibilities for improving the computational prediction and modelling
• Teach and disseminate your knowledge

Furthermore your key tasks as a PhD-student will also include:

• Carrying through an independent research project under supervision.
• 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

Profile of the PhD or postdoc
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:

• For postdoc applicants: You have completed PhD degree in bioinformatics, computer science or in a similar area
• For PhD applicants: You have completed MSc degree in bioinformatics, computer science or in a similar area. 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
• You have experience with analysis biological networks beyond basic applications through GUIs.
• You are highly experienced in Python
• 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 about CRISPR
• Knowledge of RNA folding and RNA-RNA interaction algorithms
• Strong knowledge of biological networks

For postdoc applicants we expect a general higher level of expertise relative to PhD applicants, including (but not limited to) higher experience research, programming, theoretical thinking and writing of scientific articles. This higher experience for postdocs should be reflected in having at least three additional years of experiences in their scientific career including published and amount code written.

Key selection criteria for both PhD-student and postdoc:

• 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 both as PhD-student and as postdoc. The starting date is August 1st, 2024, 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 for Postdocs starts at 35,000 DKK/approx. 4,700 EUR (October 2021 level). 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.

For PhD, the monthly salary starts at approximately 27,800 DKK/Roughly 3,700 EUR (October 2021 level) plus pension.

Depending on qualifications, a supplement for both PhD-student and postdoc may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

The positions as PhD student or postdoc are covered by the Job Structure for Academic Staff at Universities 2020.

The employment as PhD student is furthermore conditioned upon the applicant’s success­ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

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.

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:

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. 
   For postdoc position: A certified/signed copy of a) a PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
   For PhD position: 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. List of publications. (For PhD students, if possible)

5. Personal Recommendations. If none, please explain why it has not been possible to obtain.

Deadline for applications: 19 May, 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.

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: https://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.