Senior Software Engineer II

The Senior Software Engineer II (SSEII) at the New York Genome Center is a senior individual contributor who guides software efforts from planning through delivery and ongoing support. The role applies technical judgment to build durable systems that improve products, integrations, maintenance, and operational processes supporting genomic testing workflows.

Key Responsibilities

• Lead cross-functional projects from requirements clarification and scope definition through release and production support, managing technical and operational tradeoffs, dependencies, and delivery planning.
• Design, develop, test, deploy, document, and maintain production-quality software, integrations, APIs, data-processing services, and operational tooling.
• Develop and improve software supporting genomic testing from sample accessioning through laboratory and sequencing workflows, computational analysis, clinical reporting, and secure genomic-data exchange, partnering with teams who use these systems daily.
• Collaborate with scientific, clinical, and operational stakeholders to clarify needs, define requirements, and write specifications; translate requirements into technical designs, implementation plans, and maintainable software solutions.
• Contribute to product requirements and technical direction, improving recurring workflows and practices across related products and systems.
• Partner with Computational Biology, Clinical Bioinformatics, Sequencing Operations, Project Management, Research Computing, and other stakeholders to deliver reliable, responsive services.
• Apply approved engineering practices including version control, code review, automated testing, release management, documentation, observability, data protection, and secure handling of sensitive information.
• Analyze technical and operational challenges across related products and systems, evaluate alternatives, and propose practical, cost-effective solutions.
• Mentor engineers through design discussions, code reviews, and knowledge sharing to strengthen shared practices and support reliable delivery.
• Communicate progress, risks, decisions, and delivery expectations clearly, seeking relevant expertise and contributing constructively to shared outcomes.
• Use approved AI-enabled tools when appropriate for software development, testing, documentation, and troubleshooting, validating outputs for accuracy, security, privacy, and compliance with NYGC policies before relying on them.

Required Qualifications

• Bachelor’s degree in Computer Science with 9+ years of relevant software engineering experience, or a Master’s degree in Computer Science with 7+ years of relevant software engineering experience.
• Demonstrated ability to lead multi-stakeholder software projects from needs definition and planning through delivery and support, managing scope, dependencies, and changing constraints.
• Demonstrated ability to apply technical judgment across multiple related areas and systems, identify cross-system issues, evaluate alternatives, and guide practical solutions.
• Proficiency in one or more modern programming languages and object-oriented design, with experience building extensible, well-tested, maintainable software.
• Experience with version control, code review, automated testing, technical documentation, and collaborative software development practices.
• Experience designing or integrating APIs, databases or other data systems, and production services or workflows.
• Strong written and verbal communication skills, including the ability to work effectively with scientific, technical, and operational stakeholders.
• Ability to learn new scientific and technical domains quickly and work effectively independently and as part of a small, collaborative team.

Technology Environment

• Cloud and infrastructure: Google Cloud Platform (GCP), Amazon Web Services (AWS), Docker, Kubernetes, Cloud Run, infrastructure as code
• Workflow and orchestration: Nextflow, Snakemake, Workflow Description Language (WDL), Cromwell, Slurm, LSF, Grid Engine
• Data and messaging: Kafka, Pub/Sub, PostgreSQL
• Development and security: Python, GraphQL, CI/CD pipelines, event-driven architectures, version control, code review, automated testing, release management, observability, data protection
• Container and scientific workflow support: Apptainer/Singularity
• Compliance and regulated data: HIPAA, NIST Special Publication (SP) 800-171
• AI-enabled development tools

Benefits

• Medical/Dental/Vision
• Vacation, Holidays, Sick, and Other Leave, including a paid winter break
• 401(k) match
• Life Insurance
• Flexible Spending Accounts
• Employee Tuition Reimbursement
• Employee Assistance Program
• Generous time off

Preferred Qualifications

• Experience supporting scientific, clinical, bioinformatics, or other data-intensive software applications, including analysis workflows, data repositories, laboratory information systems, enterprise integrations, and large-scale data movement.
• Experience with cloud platforms such as GCP or AWS; infrastructure as code; CI/CD pipelines; containerized services including Docker, Apptainer/Singularity, Kubernetes, or Cloud Run; and workflow systems such as Nextflow, Snakemake, or WDL with Cromwell or similar engines.
• Experience with cluster job schedulers such as Slurm, LSF, or Grid Engine, or cloud batch services; plus Python, PostgreSQL, and other data stores.
• Experience applying security and privacy practices to sensitive or regulated data, including familiarity with HIPAA and NIST SP 800-171, and supporting audit-ready operational processes.
• Experience with genomics, computational biology, clinical bioinformatics, or high-throughput computing environments.
• Experience using AI-enabled development tools or integrating AI capabilities into software workflows, including evaluating output quality, applying data-classification requirements, and protecting against inappropriate disclosure of data.

Competencies

• Technical and Professional Skills: Strong judgment, integrity, discipline, and reliability; prioritizes work appropriately, manages expectations, and delivers on commitments.
• Collaborative & Communicative: Builds strong relationships across functions; communicates clearly and thoughtfully; listens carefully; fosters collaboration and trust.
• Adaptable & Innovative: Embraces change, anticipates challenges, develops practical solutions, and continuously seeks opportunities to improve organizational effectiveness.