Senior Software Engineer II

At the New York Genome Center (NYGC), the Senior Software Engineer II (SSEII) is a senior individual contributor who leads software projects from planning through delivery and support. The role applies sound judgment across related technical areas and systems, designs durable solutions, mentors engineers, and improves products, integrations, maintenance, and operational processes while anticipating effects on adjacent departments and shared services.

Essential Duties and Responsibilities

● Lead cross-functional projects from requirements clarification and scope definition through release and production support; manage 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.

● Build and improve the software that supports genomic testing from sample accessioning through laboratory and sequencing workflows, computational analysis, clinical reporting, and secure genomic-data exchange; work directly with the teams who rely on these systems each day. ● Work with scientific, clinical, and operational stakeholders to clarify needs, define requirements, and write specifications; translate them into clear technical designs, implementation plans, and maintainable software solutions.

● Contribute to product requirements and technical direction, and improve 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 sound 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; incorporate appropriate expertise, evaluate alternatives, and propose practical, cost-effective solutions.

● Mentor engineers through design discussions, code reviews, and knowledge sharing; help teammates resolve difficult technical decisions, strengthen shared practices, and deliver reliable work. ● Communicate progress, risks, decisions, and delivery expectations clearly; seek relevant expertise and contribute constructively to collective outcomes.

● Use approved AI-enabled tools, where appropriate, to support software development, testing, documentation, and troubleshooting. Validate outputs for accuracy, security, privacy, and compliance with NYGC policies before relying on them.

Minimum 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 while 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, and experience developing 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. ● Effective written and verbal communication skills, including the ability to work productively with scientific, technical, and operational stakeholders.

● Ability to learn new scientific and technical domains quickly and to work effectively both independently and as part of a small, collaborative team.

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 Google Cloud Platform (GCP) or Amazon Web Services (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 Workflow Description Language (WDL) with Cromwell or similar engines; cluster job schedulers such as Slurm, LSF, or Grid Engine, or cloud batch services; Python; PostgreSQL and other relational, document-store, or graph databases; GraphQL; and event-driven architectures using tools such as Kafka or Pub/Sub.

● Experience applying security and privacy practices to sensitive or regulated data, demonstrating familiarity with applicable requirements such as the Health Insurance Portability and Accountability Act (HIPAA) and the National Institute of Standards and Technology (NIST) Special Publication (SP) 800-171, along with 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.

Competencies Technical and Professional Skills: Demonstrates strong judgment, integrity, discipline, and reliability; appropriately prioritizes work, manages expectations, and consistently 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. Salary & Benefits The pay range for this position is $155,000-182,000 per year; the base pay offered may vary depending on job-related knowledge, skills, and experience.

In addition, NYGC offers a full range of medical, financial, and other benefits as well as generous time off. This includes Medical/Dental/Vision for employees & dependent(s); Vacation, Holidays, Sick, and Other Leave, including a paid winter break; a 401(k) match; Life Insurance; Flexible Spending Accounts; employee Tuition Reimbursement; an Employee Assistance Program; and much more.

About the New York Genome Center The New York Genome Center (NYGC) is an independent, nonprofit, academic research organization dedicated to advancing genomic research. NYGC scientists and staff are furthering new approaches to diagnosing and treating neurological diseases and cancer through their unique capabilities in whole genome sequencing, RNA sequencing, state-of-the art analytics, and the development of genomic tools.

NYGC concentrates specifically on disease-based research in the following areas: neuropsychiatric disease (autism, schizophrenia, bipolar); neurodegenerative disease (ALS, Alzheimer’s, Parkinson’s, Huntington’s), and cancer. Located in Lower Manhattan, the New York Genome Center was founded by and remains closely affiliated with the leading academic medical centers and research universities in the New York region, engaging in research projects with and for these institutions.

Essential to our collaborative work is an outstanding faculty, whose members typically hold a joint appointment at NYGC and a partner university. They support our scientific mission by conducting independent research in areas of mutual interest to us and the wider scientific community. Equal Opportunity We are committed to fostering a workplace environment that is welcoming and fair to all, ensuring that every employee has the opportunity to thrive.

We believe that bringing together individuals with diverse backgrounds, experiences, and perspectives leads to greater collaboration, innovation, and discovery. Valuing and supporting each employee in reaching their full potential strengthens our organization and enhances our collective success. We recognize that creating an environment where all employees feel valued and included requires sustained effort and dedication from the entire organization.

The New York Genome Center is a VEVRAA Federal Contractor. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, creed, color, gender, religion, national origin, sexual orientation, age, disability, genetic predisposition or carrier status, protected veteran or military status, domestic violence victim status, partnership status, caregiver status, alienage or citizenship status, marital status, or any other characteristic protected by applicable law.

NYGC takes affirmative action in support of its policy to hire and advance in employment individuals who are protected veterans and individuals with disabilities.