Industrial PhD in Cancer Multi -omics & Machine Learning

Let’s shape the future - University of Antwerp

The University of Antwerp is a dynamic, forward-thinking university. We offer an innovative academic education to more than 20,000 students; conduct pioneering scientific research and play an important service-providing role in society. With more than 6000 employees from 100 different countries, we are helping to build tomorrow's world every day. Together we push back boundaries and set a course for the future – a future that you can help to shape.

The University of Antwerp’s Center of Medical Genetics, in collaboration with Qurin PCR B.V. (Leiden, Netherlands), is looking for a full-time, skilled and motivated Ph.D. student to join our dynamic team. We are offering an exciting industrial Ph.D. position focused on developing scalable, Machine Learning (ML) pipelines for genomic and epigenomic biomarker discovery from Oxford Nanopore Technologies (ONT) long-read sequencing data. The project begins with bladder cancer detection from urine-derived DNA and expands towards a broader set of urologic and related cancers, ultimately supporting precision diagnostics from urine to clinic.

Position

The position includes the following tasks:

• Bioinformatics Pipeline Development: Design, build, and maintain a robust, scalable bioinformatics pipeline for ONT long-read sequencing data preprocessing and analysis.
• Advanced Analytics: Implement analysis modules for methylation calling, structural variant detection, fragmentation-based signatures and multi-omics integration.
• Machine Learning for Biomarker Discovery: Develop and fine-tune machine learning algorithms for biomarker discovery, cancer classification, and exploring omics features.
• Collaborative Research: Work in a multidisciplinary setting with scientists, clinical manager, AI researchers, and industry experts at the interface of academia and biotech.
• Knowledge Dissemination: Contribute to peer-reviewed publications, conference presentations, IP generation, and knowledge transfer between academic and industrial partners.

Profile

We are looking for a motivated and curious researcher with the following attributes:

• Master’s degree (or equivalent) in Bioinformatics, Computational Biology, Computer Science, or a related field from an institution in the EEA or Switzerland.
• Strong interest in translational cancer research, bioinformatics, and machine learning.
• Strong proficiency with R/Python and machine learning frameworks (e.g., PyTorch, TensorFlow).
• Prior experience with workflow management tools (e.g., Snakemake, Nextflow).
• Familiarity with cloud computing environments (AWS preferred).
• Demonstrated independence and problem-solving ability.
• Eager to engage in cutting-edge research and work at the interface of academia and industry.
• Open-minded and effective in a collaborative, interdisciplinary environment.
• Prior experience with ONT data or epigenomic datasets is an advantage but not required.

What we offer

• A fully funded, 4-year industrial PhD position within a high-impact startup environment, upon positive evaluation after one year.
• Joint supervision by leading scientists at the University of Antwerp and Qurin PCR B.V., ensuring both academic rigor and industrial relevance.
• Access to state-of-the-art sequencing, clinical samples, and high-performance cloud computing infrastructure.
• Training in cutting-edge computational biology, machine learning, and cancer genomics, with opportunities for workshops, seminars, and conferences.
• Hands-on exposure to translational R&D, and IP development in a biotech setting. A dynamic, innovation-driven workplace with the mission to improve lives through early cancer detection.
• As part of this industrial PhD, you will gain valuable experience in a truly multicultural, cross-border research environment, moving between the Netherlands (Leiden) and Belgium (Antwerp), offering a unique opportunity to collaborate, learn, and build a strong international network.
• Your monthly scholarship amount is calculated according to the scholarship amounts for doctoral scholarship holders.
• You will receive ecocheques, internet-connectivity allowance, and a bicycle allowance or a full reimbursement of public transport costs for commuting.
• You will have 40 days of annual leave and collective leave for 1 week when the university is closed, between Christmas and New Year.
• Starting date: Q1 2026, with a convenient date will be discussed with the successful candidate

Find out more about working at the University of Antwerp here.

Want to apply?

• You can apply for this job through the University of Antwerp’s online job application platform up to and including 20 November 2025 (by midnight Brussels time). Click on the 'Apply' button and complete the online application form. Be sure to include the following attachments:
  • a detailed CV
  • a letter of motivation explaining why you are interested in this PhD position in particular
  • the names and contact details of 2 referees
• The selection committee reviews all applications as soon as possible after the application deadline. As soon as a decision is made, we will notify you. If you are still eligible after the pre-selection, you will be informed about the possible next step(s) in the selection procedure. Interviews will take place on the 2^nd week of January 2026.
• If you have any questions about the position itself, please contact Prof. Dr. Ken Op de Beeck at [emailprotected] or Dr. Joe Ibrahim at [emailprotected]. If you have any questions about the online application form, please check the Frequently Asked Questions or send an email to [emailprotected].

The University of Antwerp is a sustainable, family-friendly organisation which invests in its employees’ growth. We encourage diversityand attach great importance to an inclusive working environment and equal opportunities, regardless of gender identity, disability, race, ethnicity, religion or belief, sexual orientation or age. We encourage people from diverse backgrounds and with diverse characteristics to apply.