211-2108/25-2H PhD fellowship in n gene regulation and single cell methodology

PhD fellowship in PhD fellowship in gene regulation and single cell methodology
PhD project on gene regulation in single cells across development
Department of Biology
Faculty of SCIENCE
University of Copenhagen

The Department of Biology invites applicants for a PhD fellowship in single cell-resolved gene regulation to understand tissue development.

The start date is (expected to be) the 1st of August 2025 or as soon as possible thereafter.

The position is offered within the Tissue Gene Regulation lab headed by Robert Krautz.

We are also advertising for a postdoc position within the same area. Only one of the positions will be filled.


The project
The development of human tissues relies on the regulated activation of subsets of genes in tissue-specific cell types. Tens of thousands of short DNA-sequences called enhancers are spread across the human genome and regulate the extent to which genes are activated in different cell types. Despite their role, it has so far been impossible to measure activity levels of enhancers in single cells. Hence, the successful candidate will have the opportunity to work on a project aiming to establish a novel method to directly measure the activity of enhancers and promoters in single cells and apply it to disentangle the differentiation of cell types in developing tissues. This will allow to identify key gene regulatory mechanisms that define how cell types and tissues emerge.

The project is highly interdisciplinary and will include primarily experimental work (i.e., single cell method development, high throughput sequencing and library preparation, molecular biology, organoid culture). However, interest for or previous experience with single cell data analysis and statistical modeling are more than appreciated.

Who are we looking for?
We are seeking a genuinely motivated individual with a MSc (or equivalent documentation) in Molecular Biology, Biochemistry, Biotechnology, Biomedicine, or a comparable field with extensive experience in experimental lab-work. A strong background in RNA and chromatin laboratory work, sequencing library preparation and single cell technologies are expected from the candidate. Importantly, the applicant should have a strong interest in gene regulation and a desire to work on an interdisciplinary and highly collaborative project bridging single-cell genomics, genetics and developmental biology. Continuous scientific discussions and a strong dedication for ongoing research questions within the group and amongst collaborators also require proactive participation and enthusiasm for problem solving.

In particular, we are looking for candidates with:

• A MSc (or equivalent) in Molecular Biology, Biochemistry, Biotechnology, Biomedicine, or a related discipline with extensive experience in experimental lab-work
• Documented experience in usage and preferably development or optimization of single cell methods
• Documented experience in preparation of high-throughput sequencing libraries, sequencing method development and optimization
• A high proficiency in spoken and written English

Our group and research
The Tissue Gene Regulation lab bridges the gap between gene regulatory mechanisms, transcriptional activation of enhancers and promoters in single cells on the one hand and the development of tissues and its dysregulation during disease on the other. For this, we devise new genomics methods and single cell techniques - both experimentally and computationally - to profile enhancers and promoters, model their activities and decode their interactions. In this way, we can pinpoint the time point and cell type where genetic variants begin to disrupt normal development – crucial information to develop new diagnostic approaches and identify therapeutic targets. As a young group in an established environment, we bring our great enthusiasm for science and making a difference for future patients into an already established environment with all the necessary equipment and facilities. For more information, see http://tgrlab.org.

The Tissue Gene Regulation lab adheres to the #MentorFirst (see https://mentorfirst.org) principle that emphasizes the value of the researcher behind the work. A productive, successful project is an emergent property of motivated, well mentored lab members that feel freedom in and ownership of their projects. The hope is that empowered and successful lab members will continue contributing to academia and society with sound scientific work after their stint in the lab.

The Tissue Gene Regulation lab is based in a highly collaborative environment in the Section for Computational and RNA Biology, which is currently composed of 13 strong research groups. The Department of Biology is located at the Biocenter in central Copenhagen, Denmark. Due to its close proximity to the Biotech Research & Innovation Centre (BRIC) as well as the Faculty of Health and Medical Science, collaborations across disciplines, groups and institutes are a natural part of the efforts in the lab. We are especially connected to the Andersson lab in the same section due to our shared interest in gene regulation and several ongoing collaborations. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and computational infrastructures.

Principal and administrative supervisor is Associate Professor Robin Andersson. Robert Krautz, Assistant Professor and Group Leader of the Tissue Gene Regulation lab, will supervise all technical and experimental work. For inquiries regarding the position, please contact Robert Krautz, [email protected].

The PhD programme

Qualifications needed for the PhD programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. e.g. Molecular Biology, Biochemistry, Biotechnology, Biomedicine. For information of eligibility of completed programmes, see General assessments for specific czountries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The terms of employment and salary are in accordance to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

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Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page)
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Original diplomas for Bachelor of Science or Master of Science (or equivalent documentation) and transcript of records in the original language, including an authorized English translation if issued in another 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.
4. A list of publications (if any)
5. Reference letters (if available)

Application deadline:

The deadline for applications is 31st of March 2025, 23:59 GMT +2.

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 deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Questions
For specific information about the PhD fellowship, please contact the Robert Krautz, [email protected].

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.