Senior Software Engineer II

Work on software that supports genomic testing end to end while partnering with scientific, clinical, and operational teams. At New York Genome Center, this senior individual contributor role focuses on building durable systems, improving product integrations and operational processes, and delivering reliable services for genomic-data workflows. The position is onsite in New York, NY.

What you’ll do

• 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, including integrations, APIs, data-processing services, and operational tooling.
• Build and improve systems supporting genomic testing, from sample accessioning through laboratory and sequencing workflows, computational analysis, clinical reporting, and secure genomic-data exchange.
• Work with scientific, clinical, and operational stakeholders to clarify needs, define requirements, and write specifications, translating them into clear technical designs and maintainable implementation plans.
• Contribute to product requirements and technical direction while improving recurring workflows and practices across related products and systems.
• Partner with teams including Computational Biology, Clinical Bioinformatics, Sequencing Operations, Project Management, Research Computing, and other stakeholders to deliver reliable, responsive services.
• Apply engineering best practices such as version control, code review, automated testing, release management, documentation, observability, data protection, and secure handling of sensitive information.
• Analyze cross-system technical and operational challenges, 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 outcomes.
• Use approved AI-enabled tools where appropriate to support software development, testing, documentation, and troubleshooting, and validate outputs for accuracy, security, privacy, and compliance with NYGC policies before relying on them.

What you bring

• Bachelor’s in Computer Science with 9+ years of relevant software engineering experience, or Master’s in Computer Science with 7+ years.
• Proven ability to lead multi-stakeholder software projects from needs definition and planning through delivery and support, including scope, dependency, and changing-constraint management.
• Technical judgment across multiple related areas and systems, with experience identifying cross-system issues and guiding 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 development practices.
• Experience designing or integrating APIs, databases or other data systems, and production services or workflows.
• Strong written and verbal communication skills, including collaboration 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 team.

Compensation

USD 155,000 - 182,000 per year.

Technologies you may work with

Google Cloud Platform (GCP), Amazon Web Services (AWS), Docker, Apptainer/Singularity, Kubernetes, Cloud Run, Nextflow, Snakemake, Workflow Description Language (WDL), Cromwell, Slurm, LSF, Grid Engine, Kafka, Pub/Sub, Python, PostgreSQL, GraphQL, AI-enabled development tools, HIPAA, NIST SP 800-171, CI/CD pipelines, infrastructure as code, event-driven architectures, version control, code review, automated testing, release management, observability, data protection.

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 such as Docker, Apptainer/Singularity, Kubernetes, or Cloud Run; workflow systems such as Nextflow, Snakemake, or WDL with Cromwell or similar engines; cluster job schedulers such as Slurm, LSF, or Grid Engine, or cloud batch services.
• Experience applying security and privacy practices to sensitive or regulated data, including familiarity with HIPAA and NIST SP 800-171 and experience 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.

How you’ll work

• Technical and Professional Skills: strong judgment, integrity, discipline, reliability, effective prioritization, expectation management, and consistent delivery.
• Collaborative & Communicative: clear communication, careful listening, relationship-building across functions, and trust through collaboration.
• Adaptable & Innovative: ability to embrace change, anticipate challenges, develop practical solutions, and continuously improve organizational effectiveness.