RCI-ABBV-31464 Bioinformatics Scientist (Omics Data/Python/SQL/R Programming/HPC/Nextflow/Snakemake/PostgreSQL/Metadata/Git)

Hybrid – Cambridge, MA Through End of Year Top 3–5 Skills Needed: • Strong programming and data engineering skills (Python, SQL, R) • Experience with large-scale omics data management and integration • Knowledge of metadata standards and ontologies for biological data • Experience designing or maintaining bioinformatics data pipelines or repositories • Understanding of data governance, permissions, and FAIR data principles Job Description: • We are seeking a highly motivated Data Scientist to design and implement an internal GEO-like system for managing the Immune Discovery omics data assets. • The successful candidate will build a centralized platform that integrates raw, processed, and metadata layers of multi-omics datasets (e.g., bulk and single-cell RNA-seq, spatial omics, CyTOF) and ensures that they are findable, accessible, well-documented, and permission-controlled. • This role bridges bioinformatics, data engineering, and data governance, enabling researchers to efficiently submit, query, and reuse internal datasets while maintaining data quality and compliance. Key Responsibilities: • Design and implement scalable pipelines for ingestion, curation, and storage of raw and processed omics data. • Build and maintain a searchable data catalog or portal to enable dataset discovery and visualization of metadata and QC metrics. • Implement access controls and permission management systems to ensure appropriate data security and compliance. • Work closely with Immunology Discovery, and IR teams to integrate the system with existing compute and storage infrastructure. • Develop and enforce metadata standards, ontologies, and schema to ensure consistency and interoperability across studies. Impact: • By developing this internal data platform, the candidate will transform how omics data are organized and shared across client. • The system will improve data visibility and reuse, enhance reproducibility, and accelerate scientific insights by enabling streamlined access to all relevant data layers, raw, processed, and annotated. Qualifications: • BS (5+ years) or MS (0–3 years) in Bioinformatics, Computational Biology, Data Science, Computer Science, or related field. • Proficiency in Python and SQL, with experience in data wrangling, ETL pipelines, and automation. • Hands-on experience managing large omics datasets. • Strong understanding of metadata models, data provenance, and FAIR data principles. • Excellent communication skills and ability to collaborate with cross-functional teams. Preferred Technical Skills: • Experience with cloud storage or compute environments (AWS, GCP, or on-prem HPC). • Experience with workflow orchestration tools (Nextflow, Snakemake). • Familiarity with relational and NoSQL databases (PostgreSQL). • Familiarity with public repositories such as GEO, or SRA and their metadata standards. • Proficiency with Git for version control and collaboration. Additional Technical Skills (a plus): • Experience with containerization (Docker/Singularity) and CI/CD workflows. • Understanding of web application frameworks or dashboarding tools for data portals. • Exposure to single-cell or multi-omics integration workflows. • Experience implementing data access and permission systems integrated with organizational identity management.