Principal Software Engineer

At the New York Genome Center (NYGC), the Principal Software Engineer is primarily an individual contributor who sets technical direction and leads the design and delivery of high-impact software across interconnected products and systems. The role applies engineering judgment to challenges with unclear or not-yet-defined requirements that span departments; builds and evolves reliable, secure, maintainable solutions; and remains hands-on in architecture, implementation, and production operations. Working across scientific, clinical, and operational teams, the Principal Software Engineer establishes durable engineering practices, guides technical decisions, and mentors engineers while partnering with engineering leaders on technical approach and delivery priorities. Supervisory responsibility for one or two direct reports may be assigned based on organizational needs and the individual's demonstrated experience and skill set.

Essential Duties and Responsibilities

* Set technical direction and architecture across the software product suite, services, data systems, and integrations; align design choices with organizational needs, system constraints, and long-term maintainability.

* Lead high-impact and ambiguous cross-functional projects from discovery through release and production support; set the technical execution approach and manage architecture, risk, dependencies, and delivery tradeoffs.

* Remain hands-on in designing, developing, reviewing, testing, deploying, documenting, and maintaining production software, APIs, data-processing services, scientific workflows, and operational tooling.

* Lead the design and evolution of interconnected operational systems that support genomic testing from sample accessioning through laboratory and sequencing workflows, computational analysis, clinical reporting, and secure genomic-data exchange; improve the integrations, reliability, and observability that enable those systems to operate at scale.

* Work with scientific, clinical, and operational stakeholders to determine needs and establish specifications where requirements are unclear or not yet defined; translate them into scalable technical approaches and clear implementation plans; explain tradeoffs and build agreement across teams and stakeholders.

* Partner with lab supervisors, clinical directors, computational biologists, Research Computing, and focused working groups to deliver dependable services and improve cross-system workflows.

* Establish and advance shared engineering practices for architecture, version control, code review, automated testing, release management, documentation, observability, data protection, and secure handling of sensitive information across related products and systems.

* Guide modernization and technical-debt work; identify opportunities to simplify systems, improve reliability and performance, and reduce operational burden through incremental, supportable changes.

* Diagnose system-wide quality, performance, capacity, integration, and production challenges; bring the right expertise together, evaluate options, and drive root-cause solutions across system boundaries.

* Mentor and coach engineers through design discussions, code reviews, and knowledge sharing; strengthen technical capability and shared practices, and support reliable delivery. When direct reports are assigned, provide regular supervision, coaching, and performance feedback.

* Communicate technical options, decisions, dependencies, risks, and progress to the Software Engineering team, stakeholders, and organizational leaders; provide evidence-based recommendations that inform technical roadmaps and shape major cross-functional initiatives.

* 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.

* Guide the technical evaluation and responsible adoption of AI tools and AI-enabled capabilities across related products and workflows, consistent with NYGC approval, security, privacy, and governance requirements. Establish practices for validation, security, privacy, compliance, reliability, and operational support.

Minimum Qualifications

* Bachelor's degree in Computer Science with 12+ years of relevant software engineering experience, or a Master's degree in Computer Science with 10+ years of relevant software engineering experience.

* Demonstrated success leading high-impact, cross-team software initiatives from problem definition and specification through delivery and ongoing production support.

* Demonstrated software architecture and engineering expertise across multiple related technical areas, including sound judgment in decisions that affect interconnected systems.

* Proficiency in one or more modern programming languages and object-oriented design, and a record of delivering extensible, well-tested, maintainable production software.

* Experience designing or integrating APIs, databases or other data systems, and production services or workflows.

* Demonstrated ability to improve engineering quality, reliability, security, and operational practices across a team or group of related systems.

* Strong written and verbal communication skills, including the ability to explain technical tradeoffs and influence decisions with scientific, technical, operational, and leadership stakeholders.

* Ability to work independently on broad technical problems, collaborate across functions, and develop expertise in new scientific and technical domains.

Preferred Qualifications

* Experience supporting scientific, clinical, bioinformatics, or other data-intensive software applications across multiple products or systems, 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 orchestration with tools such as Nextflow, Snakemake, Workflow Description Language (WDL) with Cromwell or similar engines, or Airflow; durable execution frameworks; cluster job schedulers such as Slurm, LSF, or Grid Engine, or cloud batch services; Python; PostgreSQL and other relational, document-store, graph, or analytical databases; GraphQL; FAIR (Findable, Accessible, Interoperable, Reusable) and AI-ready data, including Resource Description Framework (RDF); and event-driven architectures using tools such as Kafka or Pub/Sub.

* Experience with genomics, computational biology, clinical bioinformatics, sequencing operations, or high-throughput computing environments.

* Experience establishing and advancing security and privacy practices for sensitive or regulated data across multiple related systems, aligning those practices 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, and designing audit-ready processes and operational controls.

* 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.

* Experience evaluating or integrating AI tools or capabilities in production systems within established approval and governance processes, including validation, security, privacy, and operational support.

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 $183,000-$214,000 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.