Bioinformatics Software Engineer Jobs in New York

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.
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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 architecture and software design for molecular testing data flows

• Produce detailed technical specifications and design documents for scalable data integration solutions

• Develop project plans with clear implementation, testing, validation, and deployment milestones

• Architect solutions that support future extensibility to additional data sources and analysis platforms

Documentation, Training & Knowledge Transfer

• Create comprehensive technical documentation for all pipelines, data transformations, and system configurations

• Deliver source code, configuration files, and documentation organized in designated repositories (e.g., Git)

• Provide training and handoff to NYU informatics teams to enable ongoing maintenance after deployment

• Ensure all digital artifacts are well-organized and accessible for future extensions

• Work with NYU molecular oncology and informatics teams to validate data transformations and confirm usability in cBioPortal

Minimum Qualifications:

• Master's degree in Bioinformatics, Computational Biology, Computer Science, or related field required; PhD preferred
• 5+ years of hands-on experience developing bioinformatics pipelines for genomic data processing
• Demonstrated experience with cBioPortal data integration, including file format specifications, data loading, and validation
• Proven track record building data harmonization pipelines for multi-vendor clinical molecular testing data
• Experience working with clinical cancer genomics data from commercial testing vendors (Foundation Medicine, Guardant, Tempus, or similar)
• Experience supporting translational research or precision medicine initiatives in academic medical center or clinical research setting
• Expert proficiency in Python for bioinformatics pipeline development and data transformation
• Strong experience with genomic file formats: VCF, BAM, XML, and variant annotation formats
• Solid understanding of HGVS nomenclature and genomic variant standardization
• Experience with cBioPortal data models, file formats, and data loading procedures
• Proficiency with SQL and relational databases (MySQL, PostgreSQL)
• Experience with version control systems (Git/GitHub) and collaborative software development
• Knowledge of OMOP Common Data Model concepts and implementation

Preferred Qualifications:

• Experience with workflow orchestration tools (Nextflow, Snakemake, Apache Airflow, or similar)
• Familiarity with containerization (Docker, Kubernetes) for reproducible pipeline deployment
• Knowledge of Tableau or other business intelligence platforms for genomic data visualization
• Experience with Java for cBioPortal backend customization
• Understanding of cloud platforms (AWS, GCP, Azure) for bioinformatics infrastructure
• Experience with machine learning frameworks (scikit-learn, TensorFlow, PyTorch) for clinical prediction models
• Knowledge of statistical analysis tools (R, Python pandas/scipy) for biomarker analysis
• Domain Knowledge:
• Deep understanding of cancer genomics: somatic mutations, copy number variations, structural rearrangements, germline variants
• Knowledge of clinical molecular testing workflows and laboratory data management
• Familiarity with variant annotation databases and clinical relevance classification (OncoKB, CIViC, ClinVar)
• Understanding of solid tumor vs. liquid biopsy testing methodologies
• Knowledge of precision oncology applications and clinical genomics data integration
• Understanding of genotype-phenotype relationships and molecular tumor boards
• Awareness of pharmacogenomics and targeted therapy selection principles
• Strong analytical and problem-solving skills with attention to detail in data quality and validation
• Excellent written and verbal communication skills for technical documentation and cross-functional collaboration
• Ability to work independently and manage complex projects with multiple stakeholders
• Experience translating scientific and clinical requirements into technical specifications
• Commitment to software engineering best practices including testing, documentation, and code quality

Qualified candidates must be able to effectively communicate with all levels of the organization.
NYU Grossman School of Medicine provides its staff with far more than just a place to work. Rather, we are an institution you can be proud of, an institution where you'll feel good about devoting your time and your talents. At NYU Langone Health, we are committed to supporting our workforce and their loved ones with a comprehensive benefits and wellness package. Our offerings provide a robust support system for any stage of life, whether it's developing your career, starting a family, or saving for retirement. The support employees receive goes beyond a standard benefit offering, where employees have access to financial security benefits, a generous time-off program and employee resources groups for peer support. Additionally, all employees have access to our holistic employee wellness program, which focuses on seven key areas of well-being: physical, mental, nutritional, sleep, social, financial, and preventive care. The benefits and wellness package is designed to allow you to focus on what truly matters. Join us and experience the extensive resources and services designed to enhance your overall quality of life for you and your family.
NYU Grossman School of Medicine is an equal opportunity employer and committed to inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration. We require applications to be completed online.
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NYU Langone Health provides a salary range to comply with the New York state Law on Salary Transparency in Job Advertisements. The salary range for the role is $84,577.93 - $135,224.49 Annually. Actual salaries depend on a variety of factors, including experience, specialty, education, and hospital need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.

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