Postdoc in RNA degradation machine learning

Department of Biology
Faculty of Science
University of Copenhagen

The Sandelin group is looking to recruit a talented postdoctoral researcher to our highly dynamic research group working in the interface of computational biology and genomics. The position is for two years with possible extension, in an interdisciplinary project focused nuclear RNA degradation. Our previous work in this area include:

Chen et al, Nature Genetics 2016, DOI: 10.1038/ng.3616

Thiefry et al, Plant Cell 2020, DOI: 10.1105/tpc.19.00815

Andersson et al, Nature Reviews Genet 2020,   DOI: 10.1038/s41576-019-0173-8

Wu et al, NAR Genom Bioinform, 2022 DOI: 10.1093/nargab/lqac071

Nuclear RNA degradation is essential for all cells. Together with transcription, it determines RNA expression levels, which underlies all major cellular transitions in development in disease. Different transcripts have widely different half-lives, which means nuclear RNA degradation is a key process in gene-specific expression regulation. Therefore, understanding nuclear RNA degradation is necessary to understand the biology of cells.

Classical bioinformatics methods used by us and others have been helpful in identifying sequence signals and processing events that are important for nuclear degradation, but it has up to now not been possible to link these into a biologically relevant and predictive model for nuclear RNA degradation. This is needed to go from just describing RNA degradation biology to quantitatively understand it.

To this end, this postdoc project aims to take RNA degradation research the next level by combining state of the art transcriptomic readouts from cells - already produced, using diverse sequencing methods including long-read nanopore-sequencing with a protocol developed by the group -   with of machine learning methods. We aim to identify sequence signals that are predictive of diverse aspects of nuclear RNA degradation, and others in the group will test the causality of these predictions in the laboratory.

Applicants must hold a PhD or equivalent in bioinformatics or related fields, e.g. computer science or statistics. Candidates finishing their PhD before May 2024 will also be considered.  We require:

• Experience in machine learning methods, especially based on biological sequences. We are particularly interested in candidates with a deep learning model or neural network background.
• Knowledge of cellular biology, RNA degradation and genomics in general is an advantage but not a strict requirement. However, an interest in the area is necessary.  
• Excellent English skills including conference presentations and scientific writing.
• One or more first authorships in well-respected in bioinformatics/genomics and/or machine learning journals, or in the case of computer science, conference proceedings
• A passion for working in a highly interdisciplinary environment: the Sandelin group is both experimental and computational and the postdoc will work with scientists from both disciplines, from within and outside the group.

The postdoc’s duties will include research within the field as well as limited teaching.

Further information on the Department is linked at https://www.science.ku.dk/english/about-the-faculty/organisation/ . Inquiries about the position can be made to prof Albin Sandelin, [email protected]

The position is open from June 1, 2024, or as soon as possible thereafter.

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

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.

Negotiation for salary supplement is possible.

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

Please include

• Curriculum Vitae
• Diplomas (Bachelor, Master, and PhD degree or equivalent)
• Letter of interest, outlining your motivation for applying and your suitability for the position
• Complete publication list

The deadline for applications is March 30, 2024, 23:59 GMT +1.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/ .

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.