The Sandelin group is looking to recruit a talented assistant professor to our highly dynamic research group working in the interface of computational biology and genomics. The position is for two years in an interdisciplinary project focused on nuclear RNA degradation.

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 project aims to take RNA degradation research to 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 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 and have had at least one postdoctoral period in bioinformatics. We require:

• Strong experience in analysis of genomics data in particular experience in analyzing CAGE Nanopore long read cDNA bulk and spatial transcriptomics data is strictly required. This includes mapping quantification and statistical analysis of data.
• Experience in Long read sequencing methods development
• Knowledge of cellular biology in particular transcriptional regulation RNA processing and degradation.
• Experience with transcription factor and RNA binding protein binding site data such as ChIP-Seq and eCLIP data. This includes binding site prediction techniques such as position weight matrices.
• A strong understanding of modelling techniques especially linear regression or non-linear methods and a proficiency in associated statistical methods and tools to assess model performances (such as receiver operating characteristics and precision-recall curve).
• Proficiency in both R and python programming languages. Fluency with Linux servers Linux commands and programming in bash.
• Excellent English skills including conference presentations and scientific writing.
• One or more first authorships in well-respected in bioinformatics/genomics journals
• Previous experience 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 assistant professors duties will primarily include research including obligations with regard to publication/scientific communication and research-based teaching with associated examination obligations within Assistant Professor of Computational biology. To a limited extent this may also include performance of other duties.

Assessment of applicants will primarily consider their level of documented internationally competitive research. The ability to attract external funding will be considered together with outreach qualifications. Teaching qualifications are not mandatory but documented teaching qualifications and teaching experience will be considered.

Six overall criteria apply for assistant professor appointments at the University of Copenhagen. The six criteria (research teaching societal impact organisational contribution external funding and leadership) are considered a framework for the overall assessment of candidates. Furthermore each candidate must be assessed according to the specific requirements stated in the job advertisement. Please read more at https://jobportal.ku.dk/videnskabelige-stillinger/kriterier-for-videnskabelige-stillinger/dokumenter-til-meritering/5a_Criteria_for_recognising_merit_-Assistant_professors.pdf .

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 Professor Albin Sandelin (albin@binf.ku.dk).

The position is open from 1 July 2024 or as soon as possible thereafter. It is a full-time position for a period of 2 years.

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 (Master and PhD degree or equivalent)

- Research plan description of current and future research plans

- If available description and documentation of teaching and supervision experience and qualifications - please describe and document:

o Experience with supervision of BSc and MSc students

o Teaching experience

o Formal pedagogical training

- Complete publication list

- Separate reprints of 5 particularly relevant papers

The deadline for applications is Friday 15 March 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/.

Interviews/trial lectures will be held in late April and early May.

Please refer to the following no. in future communication in this case: 211-0401/24-2A.