PhD Fellow in RNA Biotechnology

University of Copenhagen Department of Plant and Environmental Sciences

PhD fellow in RNA Biotechnology

Department of Plant and Environmental Sciences, Faculty of Science at University of Copenhagen is offering a PhD scholarship in RNA Biotechnology commencing 01.01.2022 or as soon as possible thereafter.

Description of the scientific environment

The Department of Plant and Environmental Sciences constitutes a stimulating and international research environment. The current position is financially supported by a Novo Nordisk Foundation Ascending Investigator Grant to Associate Professor Sebastian Marquardt. The position will be located at Copenhagen Plant Science Centre (CPSC) with state-of-the-art research facilities. The aim of CPSC is to create a cross-disciplinary scientific environment that links plant scientists and advances research from bench to application.

Project description

Plants have an amazing ability to deal with changing environments through molecular mechanisms that facilitate adaptation. We are looking for an exceptionally motivated Ph. D. student to elucidate temperature-sensing properties of short promoter-proximal RNAs (sppRNAs) that are connected to temperature responsive plant gene expression. sppRNAs are transcript isoforms resulting from partial RNA polymerase II (RNAPII) transcription of plant genes, linked to promoter-proximal stalling of RNAPII during gene expression. For detailed information on sppRNAs and project background please see: The project operates at the interface between the research areas of: epigenetics, RNA biology, RNAPII transcription and genomics. You will be based in the laboratory of Sebastian Marquardt, University of Copenhagen, Denmark, and visit the laboratory of Zachary Lippman, Cold Spring Harbor Laboratory, USA, to perform the parts of your project, particularly elements in tomato.

You will characterize temperature-sensitive characteristics of plant gene expression in Arabidopsis and tomato. A key element of your project will be the characterization of molecular mechanisms triggering sppRNA formation during plant gene expression during changing temperature with a focus on cold. This Ph.D. project involves design, execution and analysis of transcriptomics and epigenomics Next-Generation Sequencing (NGS) data. Expertise and enthusiasm to analyze NGS data characterize candidates that match the profile for this position. You will examine sppRNAs in tomato, which will involve targeted genetic engineering of tomato using CRISPR/Cas9. Tomato is sensitive to cold temperatures, which affects yield. Your project will test the hypothesis that part of the cold sensitivity of tomato may be rooted in differences of sppRNA-based cold sensing compared to plants that are more resistant to cold (i.e. Arabidopsis).  This project could thus help to inform on RNA-based molecular solutions to help plants to adjust to a changing climate.

Principal supervisor is Associate Professor, Copenhagen Plant Science Centre, Sebastian Marquardt, E-mail: , Direct Phone: +4535331305.

Job description

The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project 
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • To stay at an external research institution (Cold Spring Harbor Laboratory, USA) for a few months
  • Work for the department

Formal requirements

Applicants should hold an MSc degree in Biology/Biochemistry/Molecular Biology/Bioinformatics or related fields with very good results and good English skills. As criteria for the assessment of your qualifications emphasis will also be laid on previous publications (if any) and relevant work experience, particular in the area of NGS data analysis.

Terms of employment

The position is covered by the Memorandum on Job Structure for Academic Staff.
Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 333,464 (approx. €44,461) including annual supplement (+ pension at a minimum DKK 54,191). Negotiation for salary supplement is possible.

Application Procedure

The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include

  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project.
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Other information for consideration, e.g. list of publications (if any)
  • 1-3 reference letters (if any)

Reference letters must be uploaded by the applicant him/herself. The recruiting person must NOT  obtain reference letters which content is not known to the applicant him/herself. This is against Danish law.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is Sunday 4 July 2021, 23:59 GMT +2.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.

The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science.

You can read more about the recruitment process at . 


For specific information about the PhD scholarship, please contact the principal supervisor Associate Professor, Copenhagen Plant Science Centre, Sebastian Marquardt, E-mail: , Direct Phone: +4535331305.

General information about PhD programmes at SCIENCE is available at


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.


Sebastian Marquardt


Application deadline: 04-07-2021
Employment start: 01-01-2022
Working hours: Full time
Department/Location: Department of Plant and Environmental Sciences