Senior Bioinformatics Developer – Multi-Vendor Genomics Pipelines

NYU Langone Health; New York (NY); On-site; USD 85,000 - 135,000; Full time

Job summary

NYU Langone Health seeks a Sr. Bioinformatics Developer to design, build, and deploy end-to-end molecular testing data integration pipelines.

You will harmonize multi-vendor genomic data and load standardized datasets into cBioPortal, OMOP Genomics Extensions, and analytics platforms. The role blends software engineering with cancer genomics, requiring deep domain knowledge in clinical molecular testing, HGVS standardization, and data quality control.

Qualifications

• Master's degree in Bioinformatics, Computational Biology, Computer Science or related field is required.
• 5+ years of hands-on experience developing bioinformatics pipelines for genomic data processing.
• Experience with cBioPortal data integration, including file formats, loading and validation.
• Proven track record building data harmonization pipelines for multi-vendor clinical molecular testing data.
• Experience with clinical cancer genomics data from Foundation Medicine, Guardant, Tempus, or similar.
• Proficiency in Python for pipeline development and data transformation.
• Strong knowledge of HGVS nomenclature and genomic variant standardization.
• Experience with cBioPortal data models, data loading procedures, and SQL databases.

Responsibilities

• Lead genetic data harmonization and integration across multiple vendors (Foundation Medicine, Guardant, Tempus, in-house).
• Process and integrate VCF, BAM, XML formats across test types and map variants to HGVS nomenclature.
• Develop automated data transformation and loading pipelines into cBioPortal, OMOP-CDM and genomics extensions.
• Coordinate with NYU engineering teams to deploy and test solutions in production environments.
• Design scalable, modular pipelines for future data source integration.
• Implement robust data validation and quality control throughout pipelines.
• Provide training and handoff to NYU informatics teams for ongoing maintenance.

Skills

Python

Genomics data formats

HGVS nomenclature

cBioPortal integration

SQL

Git/GitHub

OMOP

Education

Master's in Bioinformatics/Computational Biology/CS

PhD preferred

Tools

Nextflow

Snakemake

Apache Airflow

Docker

Kubernetes

Tableau

Java

Cloud platforms (AWS/GCP/Azure)

ML frameworks (scikit-learn, TensorFlow, PyTorch)

Job description

NYU Langone Health seeks a Sr. Bioinformatics Developer to design, build, and deploy end-to-end molecular testing data integration pipelines.

You will harmonize multi-vendor genomic data and load standardized datasets into cBioPortal, OMOP Genomics Extensions, and analytics platforms. The role blends software engineering with cancer genomics, requiring deep domain knowledge in clinical molecular testing, HGVS standardization, and data quality control.