PhD Fellowship in Dynamics of Chromatin Organization at Novo Nordisk Foundation Center for Protein Research

One three-year PhD fellowship is available in the Krietenstein group at the Novo Nordisk Foundation Center for Protein Research (NNF-CPR - https://www.cpr.ku.dk/) at the University of Copenhagen.

The successful candidate is scheduled to start 1 December 2023 or soon after.

Our Group
Our group aims is to elucidate the mechanisms and dynamics of 3D genome organization to better understand the role of spatial chromosome structure in genome regulation. The candidate should have a strong interest in applied bioinformatics and machine learning. Our group is located at The Novo Nordisk Center for Protein Research (NNF-CPR) which was established in 2007 at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied research. NNF-CPR is located in central Copenhagen and provides an international, interdisciplinary, collaborative environment. NNF-CPR is a highly collaborative environment, therefore a strong interest in collaborative work by the PhD candidate is highly valued. We encourage enthusiastic and motivated candidates to apply to this call.

About the PI
Nils Krietenstein has a long-standing interest in chromatin biology. During his PhD at the University of Munich he studied the 1D organization of chromatin organization biochemically with in vitro reconstitution experiments in the lab of Philipp Korber. In his latest research at the University of Massachusetts Medical School he studied mammalian genome organization in 3D using high-resolution spatial genomics tools with Oliver Rando. For more information about Nils Krietenstein, please visit: https://scholar.google.com/citations?user=kCFN_2sAAAAJ&hl=en

https://www.researchgate.net/profile/Nils-Krietenstein

Project Description
The PhD candidate will focus on developing novel computational tools to analyze 3D genomics data, in particular Micro-C. We use health-relevant cell culture systems and biochemical approaches to study 3D chromatin structure. We also aim to develop novel tools to gain insights into structural changes of genome organization system using state-of-the-art sequencing technologies. The PhD candidate should have a strong interest to work in collaborative projects. The PhD candidate should be interested to develop computational pipelines and tools to analyze and correlate 3D genomics data with transcriptional outputs of genomes. Importantly, the candidate should have a strong understanding of mechanistic principals of genome regulation. Our group is part of the Protein Memory Program that Anja Groth leads. The program is interested in understanding how chromatin regulates the function of genomes, what epigenetic states are involved in this role and how these states are memorized through cell divisions. The program provides access to cutting-edge core facilities, such as genomics, proteomics and imaging platforms. The candidate will be able to participate in a highly collaborative research environment.

Required qualifications
As an applicant you must have:

• Obtained (or expect to have obtained) a Master’s degree (equivalent to a Danish Master’s degree) in Informatics, Biology, Biochemistry, Biophysics or related areas prior to the starting date
• Fluency in English and excellent written and oral communication skills
• Experience in working with genomics data
• Experience in working on shared high-performance computing clusters (experience with Slurm, LSF, etc.)
• Experience in working with computational pipelines (nextflow, snakemake, etc.)
• Experience in R and/or Python programming.

Preferred qualifications
Experience with Machine learning

Job description
Your key tasks as a PhD fellow at the Faculty are to:

• Carry through an independent research project under supervision
• Write scientific articles and the PhD thesis on the grounds of your research project
• Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points
• Obtain experience with teaching or other types of dissemination related to your PhD project
• Participate in national and international congresses and scientific meetings
• Stay at an external research institution, preferably abroad

Terms of employment
The employment as PhD fellow is full time and for 3 years.
It is 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. Enrolment at the Graduate School requires submission and acceptance of an application for the specific project formulated by the applicant (for more information, please see https://healthsciences.ku.dk/phd/guidelines/) .

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2019) and the Faculty’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins around 27,568 DKK /approx. 3.700 EUR (February 2021-level) plus pension.

Questions
For further information, please Nils Krietenstein, [email protected]. For administrative information please contact the HR Center, [email protected].

Application procedure

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

1. Motivated letter of application (max. one page)

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: 24th of September 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 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. 1443 of 11 December 2020 on the Appointment of Academic Staff at Universities.

Kilde: Jobnet.dk