Bioinformatics Data Engineer for AI Cell Modeling

Rivercell; Paris; Hybrid; EUR 70,000 - 120,000; Full time

Benefits offered by this job

Equity package

Competitive salary

Job summary

Rivercell is seeking a Bioinformatics Data Engineer to join our team and help turn sequencing and imaging data into analysis-ready, versioned datasets. You will collaborate with ML scientists, biologists, chemists and engineers to improve data quality, harmonization and reproducibility across experiments.

You will build end-to-end pipelines for single-cell omics and imaging, implement dataset versioning and release processes, and ensure data infrastructure scales to tens of terabytes in the

Qualifications

• MSc or PhD in bioinformatics, computational biology, CS, or related field.
• 3+ years building bioinformatics pipelines in production.
• Processed single-cell RNA-seq data from raw reads (Cell Ranger, STARsolo, kallisto/bustools, alevin-fry, or equivalent).
• Strong Python and software engineering: containers, tests, CI, and documentation.
• Experience with data versioning on large datasets and cloud/HPC infrastructure.
• Experience with image processing at scale, ideally microscopy (segmentation/tracking/feature extraction).
• Experience with high-performance data management (Zarr, Parquet, OME-Zarr).
• Fluent in English; French helpful but not required.

Responsibilities

• Build omics pipelines from FASTQ to analysis-ready matrices: alignment, quantification, cell calling, ambient RNA handling, quality control.
• Build imaging pipelines for live-cell data: illumination correction, segmentation, tracking, feature/embedding extraction.
• Harmonize public datasets with Rivercell data.
• Set up dataset versioning, lineage, and release management for reproducibility.
• Build tooling for contamination-controlled train/test splits for benchmarks.
• Manage data infrastructure: cloud storage/compute for tens of terabytes, cost control.
• Develop data side of closed lab-in-a-loop: experiments proposed by models, retraining-ready data.

Skills

Python

Bioinformatics pipelines

Single-cell RNA-seq

Data versioning

Cloud computing

Image processing at scale

English fluency

Education

MSc or PhD in bioinformatics/computational biology/CS

Tools

Cell Ranger

STARsolo

kallisto/bustools

alevin-fry

AnnData/scverse

Cellpose

StarDist

CellProfiler

Zarr/OME-Zarr

Parquet

Job description

Rivercell is seeking a Bioinformatics Data Engineer to join our team and help turn sequencing and imaging data into analysis-ready, versioned datasets. You will collaborate with ML scientists, biologists, chemists and engineers to improve data quality, harmonization and reproducibility across experiments.

You will build end-to-end pipelines for single-cell omics and imaging, implement dataset versioning and release processes, and ensure data infrastructure scales to tens of terabytes in the