Sr. Bioinformatics Developer

Job ID: 1162892_RR00120928

Facility: NYU Grossman School of Medicine

Position Type: Full-Time/Regular

Shift: Day

Schedule: 9am-5pm

Department: IT/Health IT/Informatics, MCIT-Research-DataCore (S1724), NYU Grossman School of Medicine,

NYU Grossman School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU Langone Health, the Grossman School of Medicine at its core is committed to improving the human condition through medical education, scientific research, and direct patient care. At NYU Langone Health, equity and inclusion are fundamental values. We strive to be a place where our exceptionally talented faculty, staff, and students of all identities can thrive. We embrace inclusion and individual skills, ideas, and knowledge.

For more information, go to med.nyu.edu (Opens in a new window), and interact with us on LinkedIn (Opens in a new window), Glassdoor (Opens in a new window), Indeed (Opens in a new window), Facebook (Opens in a new window), X (Opens in a new window) and Instagram (Opens in a new window).

Position Summary:
We have an exciting opportunity to join our team as a Sr. Bioinformatics Developer.

NYU Langone Health seeks an experienced Bioinformatics Developer to design, develop, and implement end-to-end molecular testing data integration pipelines. This role will focus on harmonizing multi-vendor genomic data from clinical molecular testing platforms and building automated data transformation pipelines to load standardized datasets into cBioPortal, OMOP Genomics Extensions, and other analytics platforms. The ideal candidate combines strong software engineering skills with deep domain expertise in cancer genomics, clinical molecular testing, and bioinformatics data standards.

Job Responsibilities:

Genetic Data Harmonization & Integration

• Harmonize and standardize molecular testing data from multiple vendors including Foundation Medicine, Guardant Health, Tempus, and in-house PACT testing platforms
• Process and integrate VCF, XML, and BAM format files across all vendors and test types (somatic, germline, liquid biopsy, solid tumor) at gene and alteration levels
• Convert vendor-specific formats (Foundation Medicine CNV/rearrangements, Guardant data) to common standardized formats
• Map genomic variants to common standards including HGVS nomenclature
• Implement annotation pipelines to uniformly annotate variants, enabling clear distinction between clinically relevant and other variants
• Build automated data transformation and loading pipelines to ingest harmonized molecular testing data into cBioPortal, OMOP-CDM and its relevant genomics extensions, and Tableau
• Develop end-to-end workflows that orchestrate the complete process from data harmonization through loading into multiple analysis systems
• Design scalable, extensible, and modular pipeline architectures that facilitate future integration of new data sources
• Implement robust data validation and quality control processes to ensure data integrity throughout the pipeline
• Coordinate with NYU engineering teams to deploy and test solutions in production environments

Precision Medicine & Translational Research Support

• Support development and validation of AI/ML-based risk assessment models using integrated genomic and clinical data from harmonized molecular testing datasets
• Contribute to deep phenotyping initiatives by linking molecular testing results with comprehensive clinical phenotype data to enable genotype-phenotype correlation studies
• Build and maintain precision medicine decision support pipelines that integrate genetic and molecular testing data to inform treatment selection and clinical trial matching
• Develop data transformation workflows to support translational research studies linking molecular alterations to clinical outcomes and treatment responses
• Create data marts and analytical datasets from harmonized molecular testing data to enable precision oncology research and biomarker discovery
• Collaborate with clinical and research teams to validate clinical utility of genomic variants and support evidence-based precision medicine initiatives

Architecture & Requirements Analysis

• Lead business analysis and requirements gathering to document systems arc…