Bioinformatics Engineer

Excelra; Oost-Vlaanderen; Hybride; EUR 90 000 - 130 000; Plein temps

Avantages offerts par ce poste

Flexible hybrid work

International team

Attractive salary with extra-legal ben

Résumé du poste

Excelra is seeking a Scientific Manager to own ML pipelines and experimental design for genomic target prediction. You will shift scripts into a production-grade platform, automate workflows and ensure reproducibility, while collaborating with wet-lab and computational biology colleagues.

The role emphasizes building, automating and hardening pipelines, with hybrid work in Ghent and global collaboration. English fluency and strong coding practices are essential.

Qualifications

• PhD in bioscience engineering, bioinformatics, CS or ML – or MSc with 5+ years of equivalent experience.
• Strong Python, readable/reproducible code.
• Production-ready code: Git, packaging, containers, tests/CI.
• Experience with workflow orchestration (Nextflow, Snakemake).
• Cloud/HPC experience (AWS or SLURM).
• Solid ML methods for biology and experiment tracking.

Responsabilités

• Automate and professionalize ML and experimental design pipelines for genomic target prediction.
• Migrate scripts/notebooks to a production-ready, version-controlled codebase.
• Reduce manual steps in dataset prep, configs and execution.
• Integrate pipelines into AWS/HPC infrastructure.
• Enforce versioning, tests, and reproducibility across ML workflows.
• Collaborate with wet-lab and computational biology teams to meet requirements.
• Lead multiple projects and present results clearly to stakeholders.

Connaissances

Python

Git

Docker

CI/CD

Workflow orchestration

AWS

HPC/SLURM

ML modelling

Formation

PhD in bioscience engineering / bioinformatics / CS / ML

Outils

Nextflow

Snakemake

Singularity/Apptainer

MLflow / Weights & Biases

Terraform / IaC

Docker

Description du poste

Scientific Manager – Machine Learning Engineering (Computational Biology)

Ghent, Belgium (hybrid)

Who are we?

Excelra is a leader in biopharma data and analytics, that uniquely blends scientific understanding with technological expertise. This dual mastery empowers innovative drug discovery and development, transforming research data into actionable insights for groundbreaking discovery.

We have global locations in Ghent (Belgium), London (UK), Utrecht (The Netherlands), Boston/SFO (US) and Hyderabad (India).

www.excelra.com

About the role

We are hiring a Scientific Manager to take ownership of the machine learning and experimental design pipelines behind our customer’s genomic target prediction work. Much of this currently lives in individual scripts maintained by individual scientists. Your job is to turn it into an automated, version-controlled and reproducible platform the whole team can rely on – and to keep it scientifically sound by working shoulder to shoulder with our customer’s wet-lab and computational biology colleagues.

This is a hands-on engineering role in a scientific environment. You will spend more of your time building, automating and hardening pipelines than running individual analyses, so we are looking for someone who is as comfortable with Git, containers and workflow managers as with genomics data.

What will you do?

• Automate and professionalize internal ML and experimental design pipelines for genomic target prediction.
• Migrate existing scripts and notebooks into a production-ready, version-controlled codebase.
• Reduce the manual input required for dataset preparation, settings configuration and pipeline execution.
• Integrate pipelines into existing digital infrastructure, including AWS and HPC environments.
• Implement version control, testing and reproducibility standards across ML workflows, and help the team adopt them.
• Collaborate closely with wet-lab and computational biology colleagues to make sure pipelines meet real scientific requirements.
• Run several projects in parallel, (re)assigning tasks as priorities shift, and present results concisely to stakeholders inside and outside your domain.

What do you bring?

• A PhD in bioscience engineering, bioinformatics, computer science or machine learning engineering – or an MSc with 5+ years of equivalent experience. You can demonstrate this through peer-reviewed publications, contributions to public code repositories or relevant project work.
• Strong Python, and the habit of writing code that colleagues can read, test and re-run.
• Proven experience taking analysis code into production: version control with Git, code review, packaging, containerization (Docker, Singularity/Apptainer) and automated testing or CI/CD.
• Hands-on experience with workflow orchestration – Nextflow, Snakemake or equivalent.
• Experience running workloads on cloud infrastructure (AWS) and/or HPC clusters (e.g. SLURM).
• Solid grounding in statistical modelling and machine learning applied to biological data, including model evaluation and experiment tracking.
• The ability to translate between engineering and bench science, and to work with scientists who are not engineers.
• You are eligible to live and work in Belgium.

Nice to have

• Experience with genomics and transcriptomics data (RNAseq, single-cell, spatial, WES/WGS, …).
• R alongside Python.
• Experiment tracking and model registry tooling (MLflow, Weights & Biases) or infrastructure-as-code (Terraform).
• Experience in a client-facing, consulting or CRO setting.

Who are you?

• You enjoy project-based work and have a strong analytical mindset.
• You enjoy working in a multidisciplinary environment with people of diverse professional backgrounds (IT, (molecular) biology, genomics, engineering, etc.).
• You are communicative and customer focused.
• You are fluent in English, both written and verbally.
• You take initiative and have an eye for new opportunities.

What do we offer?

• A challenging job environment with advancement opportunities.
• Flexible hybrid working in an international (global) setting: largely home-based, with the option to work alongside colleagues in our Ghent office and occasional visits to our customers on site.
• A dynamic company with an open culture, easy communication and an ambitious vision.
• A rich & global team with a mix of backgrounds, experiences and expertise.
• Independence and flexibility.
• An attractive salary package with extra-legal benefits.