Bioinformatics Software Engineer II, Pathology and Lab Medicine

About the role

The Pathology and Laboratory Medicine Department at Memorial Sloan Kettering Cancer Center (MSK) is seeking a Bioinformatics Software Engineer to support state-of-the-art molecular diagnostics and cancer genomics programs. This role involves building web applications and APIs that enable genomic data visualization and clinical reporting, collaborating with bioinformaticians, laboratory scientists, researchers, and clinicians to develop robust software solutions, and ensuring data quality, reproducibility, and proper documentation.

Responsibilities

• Build web applications and APIs that enable genomic data visualization and clinical reporting
• Collaborate closely with bioinformaticians, laboratory scientists, researchers, and clinicians to translate workflow needs into software solutions
• Develop, optimize, and maintain computational workflows for Next Generation Sequencing (NGS) data processing
• Improve performance, scalability, and reliability of existing pipelines and tools
• Ensure data quality, reproducibility, and proper documentation across all projects

Requirements

• BS in Bioinformatics, Computer Science, or related field + 5 years of experience OR MS in Bioinformatics, Computer Science, or related field + 2 years of experience
• Strong programming skills in Python
• Experience in web development (e.g., Flask, Django, React)
• Experience with relational databases (PostgreSQL, MySQL) and/or NoSQL (MongoDB)
• Hands-on experience with containerization (Docker, Kubernetes)
• Familiarity with version control (Git/GitHub) and CI/CD workflows
• Understanding of NGS data analysis workflows
• Strong debugging, analytical, and problem-solving skills

Preferred Experience

• Knowledge of cancer genomics, variant calling, and annotation
• Experience with cloud computing (AWS, GCP, or Azure)

Core Skills

• Ability to translate scientific and clinical needs into maintainable, well-designed software
• Strong communication skills and comfort collaborating with multidisciplinary teams
• Ability to work in fast-paced research and clinical environments
• Commitment to reproducible, traceable, and well-documented work

Additional Information

• Schedule: hybrid, at least 2 days a week in office, must reside in the NYC metro area
• Location: Joy Building, 321 E 61st Street, NYC
• Reporting to: Manager, Bioinformatics

Compensation and Benefits

Pay Range: $100,600.00 - $161,000.00
FSLA Status: Exempt