Machine Learning Engineer â AI & Bioinformatics
Machine Learning Engineer â AI & Bioinformatics
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1 Vacancy
Job Description
ProQR Therapeutics is a NASDAQ-listed biotechnology company headquartered in Leiden the Netherlands with an office in and Cambridge Massachusetts USA.
At ProQR we are on a mission to edit RNA treat disease and change lives. A team of 180 enthusiastic ProQRians from all walks of life and more than 30 different nationalities is committed to pioneering transformative RNA therapies to make a difference in the lives of the communities we serve.
Our proprietary Axiomer RNA editing technology platform enables the editing of specific single nucleotides in RNA using the cells own editing machinery. Axiomer RNA editing technology harnesses ADAR (Adenosine Deaminase Acting on RNA) a protein which is present in all human cells to repair G-to-A mutations modulate protein and enable protective mutation functions. Axiomer could potentially yield a new class of innovative medicines and treat currently untreatable diseases. By harnessing the power of RNA editing we aim to create a world where genetics inform your health - but never limit it.
Our R&D department is currently looking for an experienced ML Engineer - AI & Bioinformatics to join our team in Leiden. The ML Engineer will contribute to the development of robust scalable pipelines that transform complex experimental biology data into AI-ready datasets. This role supports both scientific modeling initiatives and the automation of critical bioinformatics workflows contributing to a standardized and reproducible data infrastructure.
This position is ideal for someone with a strong foundation in machine learning and data engineering who is eager to apply those skills to real-world biological challenges and data-driven decision-making. You will work closely with laboratory and computational scientists bioinformaticians and domain experts to ensure seamless integration of data and models.
We expect our ML Engineer to have:
- MSc in Computer Science Bioinformatics Data Science or a related quantitative discipline
- At least 2 years of relevant work experience in Data engineering Machine learning Generative AI models Deep learning (industry or advanced academic research)
- Strong proficiency in Python for data processing scripting and model development
- Practical experience with JAX or PyTorch for training and evaluating machine learning models
- Hands-on experience with Linux-based environments and command-line tools
- Familiarity with Docker (strongly preferred) or similar containerization tools for reproducible environments
- Demonstrated experience or interest in handling biological datasets (e.g. RNA-Seq HTS Assay data)
- Knowledge of software engineering best practices including version control (Git) modular code design and documentation
- Exposure to R for statistical workflows
- Curiosity and adaptability to explore the best tools and approaches for each project
Key Responsibilities
- Design build and maintain modular reproducible data pipelines that transform raw experimental data into standardized AI-ready datasets
- Automate and optimize data flows to reduce manual steps and improve scalability using scripting and containerized tools (e.g. Docker)
- Develop train and evaluate AI models using JAX or PyTorch for biological prediction tasks
- Benchmarking model performance across diverse biological tasks and contributing to model selection and improvement
- Collaborate cross-functionally with domain scientists bioinformaticians and project leads to align computational outputs with experimental context
- Contribute to data infrastructure initiatives including FAIR-compliant schema development metadata standards and integration with platforms.
- Support statistical analyses and data exploration using Python and/or R
- Ensure reproducibility through modular code design version control (Git) thorough documentation and adherence to best practices
- Engage in technical discussions retrospectives and team knowledge-sharing sessions to foster learning and continuous improvement
Skills and competencies that are required for making the difference:
- Analytical and accurate
- Creative thinker
- Flexible and adaptable
- Hands-on mentality
- Pro-active and pragmatic self-starter with a result-oriented mindset
- Team player
- Autonomous and coachable
- Being able to work in a fast-paced environment
- Being able to prioritize multiple tasks
- Patient-oriented attitude
- Excellent knowledge of spoken and written English
- A nice person
ProQR as an employer
As an employer we value a diverse workforce in which people are encouraged to develop themselves both personally and professionally. We believe that when people are happy energized and supported by an environment in which they can thrive they can achieve extraordinary things.
We are committed to ensuring that no employee candidate or job applicant receives less favorable treatment on the grounds of race age disability pregnancy religion gender identity and expression sexual orientation marriage or civil partnership status. At ProQR we want to create an inclusive culture where everyone can be valued for who they are and in which individual differences and contributions in all forms are recognized and valued.
We offer an exciting and innovative working environment in a very committed organization with the following benefits:
- 8% holiday allowance
- 30 vacation days
- An annual performance bonus
- Stock options
- A premium-free pension plan
- A commuting allowance
- A subsidized staff restaurant
- Unlimited (un)healthy snacks and drinks
- Employee events (boot camp Coffee and Collaboration Caf and other social events)
We are looking for people who are inspired by our mission to edit RNA treat disease and change lives. Are you up for the challenge
Submit your application via the Apply button below. Please contact Silvia Catellani via if you have any questions.
#LI-SC1
Employment Type
Full Time
