Senior Genomics Data Integration Engineer

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

Job summary

NYU Langone Health invites applications for a Sr. Bioinformatics Developer to design end-to-end molecular testing data integration pipelines.

The role focuses on harmonizing multi-vendor genomic data from clinical platforms and loading standardized datasets into cBioPortal, OMOP Genomics Extensions, and analytics tools. The ideal candidate combines strong software engineering with deep cancer genomics knowledge, experience with cBioPortal, and collaboration with NYU engineering teams to deploy

Qualifications

• Master's degree in bioinformatics or related field is required; PhD preferred.
• 5+ years creating bioinformatics pipelines for genomic data processing.
• Proven experience with cBioPortal data integration, loading, and validation.
• Experience building multi-vendor data harmonization pipelines for clinical data.
• Experience with clinical cancer genomics data from vendors (Foundation Medicine, Guardant, Tempus).

Responsibilities

• Harmonize and standardize molecular testing data from multiple vendors.
• Process VCF, BAM, XML files across somatic, germline, and liquid biopsy tests.
• Map variants to HGVS nomenclature and standard formats.
• Build automated pipelines to load data into cBioPortal, OMOP-CDM, and Tableau.
• Develop end-to-end workflows from harmonization to loading into analysis systems.
• Collaborate with NYU engineering teams to deploy solutions in production.

Skills

Python programming

Genomics knowledge

Data integration

Analytical skills

Written communication

Education

Master's in Bioinformatics

PhD preferred

Tools

Nextflow

Snakemake

Apache Airflow

Docker

Kubernetes

Tableau

Java

SQL

OMOP-CDM

Job description

NYU Langone Health invites applications for a Sr. Bioinformatics Developer to design end-to-end molecular testing data integration pipelines.

The role focuses on harmonizing multi-vendor genomic data from clinical platforms and loading standardized datasets into cBioPortal, OMOP Genomics Extensions, and analytics tools. The ideal candidate combines strong software engineering with deep cancer genomics knowledge, experience with cBioPortal, and collaboration with NYU engineering teams to deploy