PhD position in RNA structure computational analysis neural sublocalization of transcripts

KU-CENTER FOR SUNDHED OG SAMFUND; København; On-site; DKK 355,000 - 469,000; Full time

Job summary

KU-CENTER FOR SUNDHED OG SAMFUND, in the Gorodkin lab at the University of Copenhagen, invites applications for a PhD position focused on computational analysis of RNA structure and subcellular localization in neurons. The project combines sequence, structure, RBP interactions, and biology to predict RNA localization in health and disease.

The PhD is a three-year full-time program under the 5+3 scheme, with a February 1, 2027 start date, and requires formal enrolment as a PhD student.

Qualifications

• MSc in bioinformatics, computer science, computational biology or related field (equivalent to Danish two-year MSc).
• Proficient in Python.
• Strong Linux/Unix experience with command-line tools and scripting.
• Solid understanding of algorithms and data analysis; knowledge of machine learning theory and implementation.
• Familiarity with RNA structure algorithms and programs.
• Excellent written and spoken English; strong collaborative skills.

Responsibilities

• Develop and evaluate predictive models for neuronal RNA localization.
• Integrate RNA sequence, structure, and RBP interaction data with biological function.
• Collaborate across teams to combine datasets and validate predictive frameworks.
• Publish findings and contribute to teaching or dissemination of project results.

Skills

MSc in bioinformatics / computer sci /

Python

Linux/Unix

Algorithms & data analysis

Machine learning (theory & practice)

RNA structure knowledge

English proficiency

Collaboration / teamwork

Education

MSc degree equivalent to Danish master’s degree

Job description

PhD position in RNA structure computational analysis neural sublocalization of transcripts

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 February 1, 2027.

Principal supervisor is Professor Jan Gorodkin, Department of Public Health, [e-mail] phone [phone]

The project

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).

Your key tasks as a PhD student at SUND are:

• 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.

Who are we looking for

We are looking for a highly motivated candidate with a strong computational background and an interest in RNA biology and neuroscience. You will contribute to the development of computational methods for predicting neuronal RNA localization by integrating RNA sequence, RNA structure, and RNA-binding protein interactions. You will work in a cross-disciplinary and international research environment and collaborate closely with researchers working on computational and experimental aspects of the project. We value curiosity, independence, clear communication, and the ability to work constructively as part of a team.

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

Key selection criteria:

• Professional qualifications relevant for the position.
• Relevant work experience
• Fluency in English

Our research group

Our research group Computational Biology and Bioinformatics work 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 February 1, 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 31,850 DKK/Roughly 4,260 EUR (August 2026 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 may find this link useful: www.ism.ku.dk (International Staff Mobility).

Deadline for applications: 4 November 2026, 23.59pm CET

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