PhD fellowship(s) in probabilistic modelling for RNA modifications

Department of Biology, Section for Computational and RNA Biology, University of Copenhagen invites applications for one, possibly two PhD fellowships focussed on developing computational methodologies for understanding the role of RNA modifications in gene regulation.

These positions are part of the Novo Nordisk Foundation–funded project “Probabilistic Modelling Approaches for Deciphering Post-Transcriptional Gene Regulation” led by Assistant Professor Sarah Rennie.

The expected start date is June 1, 2025, or as soon as possible thereafter.

The project
Modifications to RNA play central roles in many cellular processes, yet the specific mechanisms by which they influence RNA fate remain unclear. In this project, we aim to develop, test, and apply new computational methodologies for analysing RNA modification readouts from large transcriptomic datasets. The first position will focus on modelling single-cell datasets to unravel the regulatory dynamics of RNA modification. The second will focus on the development of robust deep learning frameworks to identify molecular determinants underlying modification patterns from short- and long-read sequencing data.

Who are we looking for?
We welcome candidates with strong backgrounds in computational biology, mathematics, statistics, or computer science. Prior experience in probabilistic modelling and/or deep learning will be a significant advantage. At a minimum, candidates must demonstrate a strong desire to learn these topics.

Required/Desired Qualifications

• Knowledge of statistical modelling and machine learning
• Prior experience analysing transcriptomic datasets, particularly single-cell and/or Nanopore long-read sequencing data would be beneficial
• Proficiency in Python or R, and familiarity with good coding practices (e.g., GitHub)
• Curiousity and interest in RNA-based gene regulation
• Excellent English language skills and willingness to present work in diverse settings, including international conferences and potential trips abroad
• Enthusiasm for working in an interdisciplinary environment; the Rennie Group works closely with several leading experimental labs locally and internationally

Our group and research- and what do we offer?
The Rennie group (https://rennielab.io/) is based in the Section for Computational and RNA Biology (SCARB, https://www1.bio.ku.dk/english/research/scarb/) at the Department of Biology, Faculty of SCIENCE, University of Copenhagen. Our group focuses on developing and applying computational and statistical modelling frameworks applicable to large transcriptomic datasets to derive key biological insights in the field of RNA Biology.

The department offers creative and stimulating working conditions in a dynamic and international research environment. SCARB is composed of 13 strong research groups, and the Rennie group works closely with with a number of computational-focussed groups (in particular Andersson and Sandelin groups), as well as groups specialising in RNA biology (Auxillos and Brodersen groups). PhD students also benefit from dedicated networking opportunities, scientific clusters and local clubs.

Principal supervisor: Associate Professor Robin Andersson, Co-supervisor Assistant Professor Sarah Rennie

Any inquires about the position can be made directly to Sarah Rennie, [email protected]

Qualifications needed for the regular 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. Bioinformatics, Statistics or Computer Science. For information of eligibility of completed programmes, see General assessments for specific countries 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.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

General responsibilities and tasks in the PhD programme

• Carry through an independent research project
• 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

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

Please include:

• Motivated letter of application (max. one page)
• Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
• Original diplomas for Bachelor of Science or Master of Science 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.
• Publication list (if possible)
• Reference letters (if available) or contact information for two scientific referees

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 and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected to be held during April 2025.

Questions
For specific information about the PhD fellowship, please contact Assistant Professor Sarah Rennie, [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.

Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.

Kontakt
Sarah Rennie
E-mail: [email protected]

Info
Ansøgningsfrist: 15-03-2025

Ansættelsesdato: 01-06-2025

Arbejdstid: Fuldtid

Afdeling/Sted: Department of Biology