Bioinformatics Data Engineer: AI Pipelines & Data Versioning

Rivercell; Paris; Sur place; EUR 70 000 - 110 000; Plein temps

Avantages offerts par ce poste

Equity

Competitive salary

Career growth

Résumé du poste

Rivercell in Paris is seeking a Bioinformatics Data Engineer to build and operate data pipelines used to train and evaluate AI-driven cell models. You will process sequencing and imaging data, ensure versioned, analysis-ready datasets, and enable reproducible experiments.

You will collaborate with ML scientists, biologists, chemists and engineers on an ambitious biotech startup project, with an emphasis on scalable pipelines, cloud/HPC infrastructure, and rigorous data management.

Qualifications

• MSc or PhD in bioinformatics, computational biology, computer science, or related field.
• 3+ years of experience building and running bioinformatics pipelines in production.
• Processed single-cell RNA-seq data from raw reads and worked in AnnData/scverse ecosystem.
• Strong Python skills and engineering practices: workflows, containers, tests, CI, documentation.
• Experience with data versioning on large datasets, harmonizing heterogeneous datasets, and cloud/HPC infrastructure.
• Image processing at scale (microscopy) for feature/embedding extraction.
• Experience with high-performance data management (array/columnar formats) and PyTorch data loaders.
• Fluent in English; French helpful but not required.

Responsabilités

• Build bioinformatics pipelines from FASTQ to analysis-ready matrices and data versioning.
• Develop imaging pipelines for time-lapse data including segmentation and tracking.
• Harmonize and internalize public datasets with Rivercell data.
• Set up dataset versioning, lineage, and release management for reproducibility.
• Create tools to audit train/test splits for benchmarks.
• Manage data infrastructure including cloud storage and compute at scale.
• Collaborate with ML scientists, biologists, chemists and engineers.

Connaissances

Bioinformatics pipelines

Python

CI / workflow managers

Data versioning

Cloud / HPC

English communication

Research collaboration

Formation

MSc or PhD in bioinformatics / computational biology / CS

Outils

Cell Ranger

STARsolo

kallisto/bustools

alevin-fry

Cellpose

StarDist

CellProfiler

Zarr / Parquet / OME-Zarr

PyTorch

Description du poste

Rivercell in Paris is seeking a Bioinformatics Data Engineer to build and operate data pipelines used to train and evaluate AI-driven cell models. You will process sequencing and imaging data, ensure versioned, analysis-ready datasets, and enable reproducible experiments.

You will collaborate with ML scientists, biologists, chemists and engineers on an ambitious biotech startup project, with an emphasis on scalable pipelines, cloud/HPC infrastructure, and rigorous data management.