Chief of Bioinformatics, Bureau of the Public Health Laboratory

Job Description

The Division of Disease Control's mission is to safeguard the health of New Yorkers through identification, surveillance, treatment, control, and prevention of infectious diseases, which is achieved through varied and interrelated endeavors of its seven Bureaus. The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States where employees contribute to the health and safety of NYC residents by providing clinical and environmental laboratory testing services. PHL is committed to its mission to safeguard the health of all NYC residents by providing quality laboratory testing services that support the priorities of DOHMH and its community partners to prevent and respond to clinical and environmental public health concerns.

Position Summary: The Chief of Bioinformatics will provide strategic and scientific leadership for the development, implementation, and application of bioinformatics tools and data-driven approaches within the Public Health Laboratory (PHL). This role will oversee the analysis and interpretation of high-throughput sequencing and other complex laboratory data, ensuring timely, accurate, and actionable insights that support public health surveillance, outbreak response, and research.

The Chief will collaborate closely with epidemiologists, data scientists, and information technology teams across the Department of Health and Mental Hygiene (DOHMH) to integrate bioinformatics and data analytics into routine public health practice. Bioinformatics and data analytics play a vital role in PHL's mission and have been central to New York City's response to the COVID-19 pandemic as well as other respiratory, foodborne, and waterborne disease outbreaks. Reporting to PHL senior leadership, the Chief will lead a team of six scientists and guide the continued growth of the bioinformatics and data analytics program. This is an exceptional opportunity to join a multidisciplinary team of more than 200 laboratory professionals and collaborate with state, federal, and academic partners, including the New York State Wadsworth Center and the Centers for Disease Control and Prevention (CDC). Selected publications and news: Legionella: https://www.nytimes.com/2025/08/27/nyregion/legionnaires-disease-new-york-lab.html Mpox: https://www.nature.com/articles/s41467-025-60486-x COVID-19: https://pmc.ncbi.nlm.nih.gov/articles/PMC9949853/ Wastewater surveillance: https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-025-22306-1

DUTIES WILL INCLUDE BUT NOT BE LIMITED TO:
- Supervise and mentor a team of bioinformatics and data analytics scientists, providing technical guidance and performance oversight.
- Train and develop staff in bioinformatics tools, pipelines, and analytical best practices.
- Design, implement, and apply state-of-the-art computational methods for high-throughput sequencing (HTS) data analysis, including pathogen identification, outbreak tracking, detection of drug-resistance determinants, variant analysis, genome annotation, and phylogenetics.
- Support the development of innovative computational solutions to software and analytical challenges across diverse projects involving microbial, viral, fungal, and parasitic HTS data.
- Maintain rigorous quality assurance and quality control (QA/QC) processes to ensure the accuracy, reproducibility, and integrity of HTS data and downstream analyses.
- Promote best practices in code development, version control, documentation, and data management to support transparency and reproducibility.
- Educate and provide expert guidance to internal staff and Department of Health and Mental Hygiene (DOHMH) partners on data interpretation and the application of bioinformatics results to public health investigations.
- Lead data modernization initiatives.
- Contribute to the development and implementation of policies, procedures, and standards for clinical and public health testing that incorporate bioinformatics analyses.
- Lead and participate in research studies involving HTS technologies; oversee staff in the design, execution, and analysis of research projects.
- Communicate findings and results clearly and effectively through technical reports, scientific presentations, and peer-reviewed publications.

PREFERRED SKILLS:
- Demonstrated ability to develop complex bioinformatics solutions independently and with minimal supervision.
- Advanced proficiency in at least one scripting language (e.g., Python, Perl, or Bash) and experience working in a Linux computing environment.
- Experience with containerization technologies such as Docker, Podman or Singularity.
- Proficiency in SQL for data querying and management.
- Proficiency in Git.
- Strong experience with statistical and data analysis tools, including R and associated packages.
- Proven ability to provide expert guidance and technical leadership during the design, development, validation, and implementation of bioinformatics projects.
- Experience contributing to the preparation of high-quality scientific manuscripts, presentations, and grant proposals.
- Ability to mentor, train, and supervise junior or mid-level bioinformatics and data analytics staff.

Why you should work for us:

- Benefits: City employees are entitled to unmatched benefits such as:
o a premium-free health insurance plan that saves employees over $10K annually, per a 2024 assessment.
o additional health, fitness, and financial benefits may be available based on the position’s associated union/benefit fund.
o a public sector defined benefit pension plan with steady monthly payments in retirement.
o a tax-deferred savings program and
o a robust Worksite Wellness Program that offers resources and opportunities to keep you healthy while serving New Yorkers.
- Work From Home Policy: Depending on your position, you may be able to work up to two days during the week from home.
- Job Security - you could enjoy more job security compared to private sector employment and be able to contribute to making NYC a healthy place to live and work.

Established in 1805, the New York City Department of Health and Mental Hygiene (NYC Health Department) is the oldest and largest health department in the U.S., dedicated to protecting and improving the health of NYC. Our mission is to safeguard the health of every resident and cultivate a city where everyone, regardless of age, background, or location, can achieve their optimal health. We provide a wide array of programs and services focused on food and nutrition, anti-tobacco support, chronic disease prevention, HIV/AIDS treatment, family and child health, environmental health, mental health, and social justice initiatives. As the primary population health strategist and policy authority for NYC, with a rich history of public health initiatives and scientific advancements, from addressing the 1822 yellow fever outbreak to the COVID-19 pandemic, we serve as a global leader in public health innovation and expertise.

Come join us and help to continue our efforts in making a difference in the lives of all New Yorkers!

The NYC Health Department is an inclusive equal opportunity employer committed to providing access and reasonable accommodation to all individuals. To request reasonable accommodation to participate in the job application or interview process, contact Sye-Eun Ahn, Director of the Office of Equal Employment Opportunity, at [email protected] or 347-396-6549.

CITY RESEARCH SCIENTIST - 21744

Qualifications

1. For Assignment Level I (only physical, biological and environmental sciences and public health) A master's degree from an accredited college or university with a specialization in an appropriate field of physical, biological or environmental science or in public health.
To be appointed to Assignment Level II and above, candidates must have:
1. A doctorate degree from an accredited college or university with specialization in an appropriate field of physical, biological, environmental or social science and one year of full-time experience in a responsible supervisory, administrative or research capacity in the appropriate field of specialization; or
2. A master's degree from an accredited college or university with specialization in an appropriate field of physical, biological, environmental or social science and three years of responsible full-time research experience in the appropriate field of specialization; or
3. Education and/or experience which is equivalent to "1" or "2" above. However, all candidates must have at least a master's degree in an appropriate field of specialization and at least two years of experience described in "2" above. Two years as a City Research Scientist Level I can be substituted for the experience required in "1" and "2" above.

NOTE:
Probationary Period
Appointments to this position are subject to a minimum probationary period of one year.

Additional Information

The City of New York is an inclusive equal opportunity employer committed to recruiting and retaining a diverse workforce and providing a work environment that is free from discrimination and harassment based upon any legally protected status or protected characteristic, including but not limited to an individual's sex, race, color, ethnicity, national origin, age, religion, disability, sexual orientation, veteran status, gender identity, or pregnancy.