PhD on Algorithms for co-transcriptional RNA folding

 

Applications are invited for a PhD fellowship/scholarship at Graduate School of Natural Sciences, Aarhus University, Denmark, within the Computer Science - incl. Bioinformatics at BiRC programme. The position is available from August 2022 or later.

Title:
Algorithms for co-transcriptional RNA folding

Research area and project description:
This project is concerned with RNA folding and prediction of RNA (secondary) structures. RNA folding was originally studied experimentally to derive thermodynamic parameters that be used to computationally prediction secondary structure. However, most often this approach cannot predict RNA structures found in Nature. The main reason for this discrepancy is the fact the biological RNA structures are not formed at thermodynamic equilibrium but by the kinetic non-equilibrium process known as co-transcriptional folding. A main problem is, however, that this folding process remain poorly understood and we are currently unable to reliably predict and/or design co-transcriptionally structures.

This PhD project, which is part of the larger COFOLD interdisciplinary research project concerned with co-transcriptional folding (https://inano.au.dk/about/research-centers-and-projects/cofold), will focus on the development and application of combinatorial and/or machine learning based algorithms and software tools with applications to understanding and prediction of co-transcriptional RNA folding. The PhD project will include algorithmic development, implementation, and experimentation within the larger area of co-transcriptional RNA folding. It will also involve collaboration with experimental researchers working on aspects of the co-transcriptional folding process within the larger COFOLD project.

The PhD candidate should therefore have an educational background that should include development of algorithms and software tools but could also include molecular biology in general and RNA folding in particular.

For technical reasons, you must upload a project description. When - as here - you apply for a specific project, please simply copy the project description above, and upload it as a PDF in the application. If you wish to, you can indicate an URL where further information can be found. Please note that we reserve the right to remove scientific papers, large reports, theses and the like.

Qualifications and specific competences:
The applicant must hold an MSc in Bioinformatics or related fields, or a BSc and have completed at least 1 year of MSc in Bioinformatics or related fields.

Place of employment and place of work:
The place of employment is Aarhus University, and the place of work is Department of Computer Science, Bioinformatics Research Centre (BiRC), Universitetsbyen 81, DK-8000 Aarhus C, Denmark. 

Contacts:
Applicants seeking further information for this project are invited to contact:

• Associate professor Christian Nørgaard Storm Pedersen, e-mail: cstorm@birc.au.dk
• Associate professor Ebbe Sloth Andersen, e-mail: esa@inano.au.dk

For information about application requirements and mandatory attachments, please see the  Application guide. Please read the Application guide thoroughly before applying and note the GSNS language skills requirement.

How to apply:
When ready to apply, go to https://phd.nat.au.dk/for-applicants/apply-here/ (Note, the online application system opens 1 March 2022)

1. Choose May 2022 Call with deadline 1 May 2022 at 23:59 CEST.
2. You will be directed to the call and must choose the programme “Computer Science - incl. Bioinformatics at BiRC”.
3. When filling in information about the project, please choose: “Algorithms for co-transcriptional RNA folding (AlcRNA)” in the dropdown menu in the box named “Study”.

Please note:

• The programme committee may request further information or invite the applicant to attend an interview.
• The project will only be initiated if final funding (from the graduate school/the faculty) is secured.

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants. All interested candidates are encouraged to apply, regardless of their personal background.