PhD in RNA structure computational analysis neural sublocalization of transcripts

University of Copenhagen; København; On-site; DKK 323,000 - 387,000; Full time

Job summary

We have a PhD position available in the Gorodkin lab at the Section for Health Data Science and AI at the Department of Public Health, Faculty of Health and Medical Sciences at University of Copenhagen. The project concerns the development of a predictive computational framework for understanding the subcellular localization of polyadenylated RNAs in neurons, including mRNAs and long noncoding RNAs.

Start date is February1,2027.

Qualifications

• MSc degree in bioinformatics, computer science, computational biology, or a related field.
• Master’s degree must be Danish-equivalent (180+120 ECTS).
• Strong Python experience.
• Experience with Linux/Unix and shell scripting.
• Excellent written and spoken English.

Responsibilities

• Carry out an independent research project under supervision.
• Complete PhD courses (~30 ECTS).
• Participate in active research environments including a stay at another team.
• Teaching or dissemination experience related to the PhD project.
• Write a PhD thesis based on the project.

Skills

Python

Linux/Unix

Algorithms

English

Education

MSc in bioinformatics / computational biology / CS

Job description

We have a PhD position available in the Gorodkin lab at the Section for Health Data Science and AI at the Department of Public Health, Faculty of Health and Medical Sciences at University of Copenhagen. The project concerns the development of a predictive computational framework for understanding the subcellular localization of polyadenylated RNAs in neurons, including mRNAs and long noncoding RNAs. The project will integrate RNA sequence, structure, RNA‑binding protein interactions, and biological function to uncover the rules governing RNA localization in healthy, degenerating, and regenerating neurons. Start date is February1,2027. Principal supervisor is Professor JanGorodkin, Department of Public Health, [e-mail] phone [phone]

We have a PhD position available in the Gorodkin lab at the Section for Health Data Science and AI at the Department of Public Health, Faculty of Health and Medical Sciences at University of Copenhagen. The project concerns the development of a predictive computational framework for understanding the subcellular localization of polyadenylated RNAs in neurons, including mRNAs and long noncoding RNAs. The project will integrate RNA sequence, structure, RNA‑binding protein interactions, and biological function to uncover the rules governing RNA localization in healthy, degenerating, and regenerating neurons. Start date is February1,2027. Principal supervisor is Professor JanGorodkin, Department of Public Health, [e-mail] phone [phone]

The project aims to develop a predictive computational framework for neuronal RNA localization by combining RNA sequence and structure information with RNA‑binding protein (RBP) interactions and biological function. The framework will use data on endogenous and designed RNAs in healthy, degenerating, and regenerating neurons. The project will integrate existing datasets on neuronal RNA localization, including Frac‑seq and N‑zip data, with RNA structure and RBP‑binding information. Computational approaches will include feature‑based classifiers and machine/deep learning methods, including sequence models such as convolutional neural networks and transformers. You will help develop and evaluate models that predict whether RNAs localize to neuronal cell bodies or neurites, combine complementary experimental datasets, and identify sequence and structural features that contribute to localization. The work will also explore how RNA localization changes in neurodegeneration and regeneration, with a focus on disease‑relevant models such as amyotrophic lateral sclerosis (ALS).

Key tasks

• Carrying through an independent research project under supervision.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

PhD Programme description

The PhD programme is a three‑year full‑time research education within the framework of the 5+3 scheme, intended for candidates holding a relevant academic degree within the project’s subject area.

Qualifications: If you have completed your academic education in Denmark, the admission to the PhD programme requires a relevant Master’s degree (equivalent to 180 ECTS BSc + 120 ECTS MSc). If you have an academic education from abroad, you must have either a degree equivalent to a Danish master's degree (180 ETCS + 120 ECTS MSc), or at a minimum, a bachelor’s degree equivalent to a Danish bachelor's degree (180 ECTS) and be academically qualified at master's level. As part of the assessment of whether you meet the educational requirements, you must also achieve a positive academic evaluation and be assessed as the best qualified for the position.

Essential experience and skills

• You have completed an MSc degree in bioinformatics, computer science, computational biology, or a related area.
• Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).
• You are highly experienced in Python.
• You have strong experience working in a Linux/Unix environment, including command‑line tools and shell scripting.
• You have a solid understanding of algorithms and data analysis, and knowledge of machine learning including theory and practical implementation.
• You are well familiar basic RNA structure algorithms and programs.
• You have excellent written and spoken English skills.
• You communicate well and are a strong collaborative team player.

Desirable experience and skills

• Strong knowledge and experience working with RNA biology, RNA sequence or structure, or RNA–protein interactions.
• Substantial experience with machine learning or deep learning methods.
• Experience with high‑throughput sequencing, transcriptomics, CLiP or other omics data analysis.
• Experience developing computational methods or predictive models.
• Professional qualifications relevant for the position.
• Relevant work experience.
• Fluency in English.

Our research group is a Computational Biology and Bioinformatics group that works with computational algorithms and methods for molecular structure and interactions. We have excellent computational infrastructure and further access to supercomputing when needed. The research group is working on a range of bioinformatical aspects both algorithm, data and omics‑wise. The research group is currently located on Frederiksberg Campus but will move physically to the Department of Public Health at City Campus at the Municipal Hospital on Øster Farimagsgade. Our research environment is highly international and stimulating. We frequently organize seminars, workshops, summer schools with international speakers and have retreats with our international collaborators.

Terms of employment

The average weekly working hours are 37 hours per week. The position is a fixed‑term position limited to a period of 3 years as PhD‑student. The starting date is February1,2027. The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant. The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 31,850DKK/Roughly 4,260EUR (August2026 level) plus pension. You can read more about salary levels in the state sector www.loenoverblik.dk (in Danish). The position is covered by the Job Structure for Academic Staff at Universities 2025.

Questions

For further information about the scientific content of the position please contact Professor Jan Gorodkin, email [e-mail] or for application procedure and formalities, please contact HR Officer, email [e-mail] / www.sund.ku.dk.

Foreign applicants

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility).

Selection process

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement. Once the assessment work has been completed, each applicant has the opportunity to comment on the part of the assessment that relates to the applicant himself and herself.

Diversity statement

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background. 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.