National Center of Excellence looking for Data Engineer in Multi-Omics and Machine Learning

The National Center of Excellence PREDICT, based at the Department of Clinical Medicine, Aalborg University Copenhagen, is looking to recruit a highly skilled data engineer to join our international and interdisciplinary center. Start of employment: 1 November 2025 or shortly after.

The role is initially a full-time (37 hours per week), two-year appointment, with the possibility of extension. We welcome international applicants who need relocation or work-permit support – over half of our colleagues are international.

Your work tasks

We are conducting a large-scale study investigating the molecular profiles of individuals who develop inflammatory bowel disease (IBD) up to 20 years before diagnosis. We will comprehensively profile pre-diagnostic patient samples using deep multi-omics techniques. Our goal is to leverage these data to uncover the mechanisms underlying the development of IBD and to establish robust models for predicting the disease before diagnosis.

The Data Engineer is integral to the production and analysis efforts for this study and will have a 360° overview of the analytical efforts in this project and will bridge the efforts across several research teams. We are looking to recruit an excellent candidate to build scalable pipelines that go from raw omics files into QC-checked, normalized datasets ready for statistical and ML analyses, and facilitate these analyses by working with the PhDs and postdocs from the research teams. Ability to drive independent computational projects can be discussed.

The data engineer will report to Center Director, Professor Tine Jess and be co-hosted and supervised by the Head of Genomics and AI, Dr. Aleksejs Sazonovs. They will work closely with the Head of Metabolomics, Dr. Filip A Ottosson, and Head of Statistics, Dr. Gry J Poulsen.

Your competencies

The data engineer will assume primary responsibility for data-processing, analytical and machine learning pipelines across the core work packages of this ambitious project. From writing multi-stage pipelines to interpreting data quality and working on machine learning problems, you will be working with domain specialists to ensure the quality and compatibility with best field practices.

Qualification requirements

We are looking for a candidate with excellent skills in computational data processing, especially applied to machine learning or (multi-)omics.

The ideal candidate has:

•  A Master’s degree in a computational discipline and 2+ years of relevant professional experience. Alternatively, a PhD in a STEM discipline and demonstrable professional experience in machine learning or multi-omics. For post-PhD candidates, please provide a list of publications. 
• High proficiency and 3+ years of day-to-day work experience in a scripting language like Python, including the Python scientific and ML stack. Other scripting and compiled languages are an advantage.
• Experience in high-performance and scalable compute is an advantage.   
• Practical experience with pipeline management systems (e.g., Snakemake, Nextflow) and cluster scheduling systems is highly desired. 
• Experience implementing and validating multi-stage and multi-tool pipelines. These need to be robust, maintainable and reusable across many future projects.
• Skilled in end-to-end ML lifecycle – data prep, ETL/ELT pipelines, baseline modelling, rigorous validation with robust metrics and stratified splits, experiment tracking.
• Ideally, experience in processing and analyzing multi-omics data: handling missing; batch effects and population structure; association and prediction work. Examples can be drawn from both smaller cohorts and analyzing public biobanks. Candidates excelling in one omics type analysis are also encouraged to apply.
• Excellent writing and communication skills in English.
•  Excellent collaborative skills.

Who we are   

PREDICT National Center of Excellence for Molecular Prediction of Inflammatory Bowel Disease was founded in 2021 with the purpose of studying and unravelling the cause and prognosis of inflammatory bowel diseases (IBD), which are chronic and disabling diseases that affect millions of people worldwide. 
PREDICT has grown to become a world-renowned center, organized as a broad, national and interdisciplinary collaboration between Aalborg University, Aalborg University Hospital, and University of Copenhagen, with a multidisciplinary team of immunologists, geneticists, data scientists, clinicians and many more disciplines. PREDICT also has strong international collaborations across the world.

You will be an integral part in a large-scale and ambitious multi-omics project, and build out a unique set of skills applicable in both academia and industry. We work in a dynamic, informal, high-performing environment with dedicated, friendly colleagues.

Learn more about PREDICT here: 

www.predictibd.dk
Bluesky: @predictibd.bsky.social‬ 
LinkedIn: https://www.linkedin.com/company/center-for-molecular-prediction-of-inflammatory-bowel-disease-predict

About the Department of Clinical Medicine:

The Department of Clinical Medicine delivers research-based teaching across all
disciplines of the medical degree programme and conducts research within the clinical
specialties. We collaborate closely with hospitals in the North Denmark Region and with
general practice in both teaching and research. Medical students receive instruction at
multiple hospital locations and in general practice throughout the region.
The department is affiliated with approximately 40 research units, each representing a
specific medical specialty, and is also associated with several other research centres and
collaborative units. Most of the department’s staff hold concurrent clinical positions
alongside their academic appointments.
Read more about the Department of Clinical Medicine here.  

How to apply

Your application must contain the following: 

• A brief motivated application describing your professional and personal competences and the experience qualifying you particularly for the position 
• Curriculum Vitae (CV) 
• Examination certificate 
• Any other relevant appendices 

You can read more about the requirements for your application here.  

The application must be submitted via Aalborg University’s recruitment system, which can be accessed under the job advertisement on Aalborg University's website. 
 
Aalborg University wants to reflect the surrounding society and has diversity as a core value. Therefore, everyone, regardless of personal background and orientation, is encouraged to apply for the position.

Do you have any questions?  
 
If you have any questions about the position, you are more than welcome to contact us.

Further information 

Read more about our recruitment process here.

The hiring process at Aalborg University may include a risk assessment as a tool to identify potential risks associated with new hires, ensuring the safety, compliance, and integrity of the workplace.  

Salary and terms of employment

Employment and salary are in accordance with the Collective Agreement for Academic Staff Employed in the State Sector (in Danish). Qualification-based supplements may be granted, subject to negotiation. 

There is a 3-month mutual trial period.