Bioinformatics Scientist , Bureau of the Public Health Laboratory

City of New York • New York City, NY

7d

About The Position

The NYC Public Health Laboratory (PHL), part of the New York City Department of Health and Mental Hygiene, seeks a Bioinformatics Scientist to work primarily in its Bioinformatics Unit. The role develops and maintains analysis pipelines and performs bioinformatics analyses of high-throughput sequencing (HTS) data. Its work supports genomics analyses responding to public health threats, including COVID-19, vaccine-preventable diseases, HIV, Legionella, and respiratory, foodborne, and waterborne disease outbreaks.

The scientist develops and improves genomic tools for pathogen identification, outbreak tracking, drug-resistance mapping, variant analysis, genome annotation, phylogenetics, and data visualization. The role also strengthens genomic tools for public health diagnostic testing, supervises one to two staff, represents the agency at meetings and conferences, and produces protocols, records, and manuscripts. It maintains quality assurance and control for PHL-generated HTS data, including developing SOPs and validation or verification protocols, and works with Quality Management to improve understanding and tracking of sequencing quality control, data security, and data management. The position is subject to a minimum one-year probationary period.

The NYC Health Department offers public-service benefits and describes a work-from-home policy under which employees may be able to work from home up to two days a week, depending on position.

Requirements

• Meet the City Research Scientist qualifications: for Assignment Level I, a master's degree from an accredited college or university specializing in an appropriate field of physical, biological, or environmental science, or public health.
• For Assignment Level II and above, qualify through one of the stated routes: a doctorate in an appropriate field plus one year of full-time responsible supervisory, administrative, or research experience; a master's degree in an appropriate field plus three years of responsible full-time research experience; or equivalent education and/or experience. Candidates must have at least a master's degree and at least two years of the specified research experience. Two years as a City Research Scientist Level I may substitute for the experience required in the first two routes.
• Strong analytical and organizational skills.
• Excellent oral, interpersonal, and written communication skills.

Nice To Haves

• Strong Linux command-line and BASH shell scripting skills.
• Proficiency in R, Python, C, Java, or other programming languages.
• Experience with SQL.
• Experience using multicore server resources, process automation, containerization, and workflow languages.
• Experience with common next-generation sequencing analysis tools, including reference-based and de novo sequencing analysis, microbial NGS pipelines, and genome annotation.
• Demonstrated work in public health genomics research.
• A PhD in biological sciences and extensive experience in the technical and administrative operations of a clinical or public health laboratory.

Responsibilities

• Conduct bioinformatics analyses of sequencing data supporting public health efforts.
• Develop or improve tools for pathogen identification, outbreak tracking, drug-resistance mapping, variant analysis, genome annotation, phylogenetics, and genomics data visualization.
• Strengthen the application of genomic tools to public health diagnostic testing for pathogens such as Mycobacterium tuberculosis and mpox.
• Conduct literature reviews and stay current with scientific and epidemiological research and tools.
• Participate in agencywide whole-genome sequencing journal club and genomic data exchange working groups.
• Develop tools or strategies, such as dashboards or Docker-based pipelines, to make bioinformatics analyses more accessible to non-bioinformaticians.
• Supervise one to two staff conducting research projects.
• Represent the agency in meetings and conferences.
• Draft written protocols and maintain accurate records of software tool design.
• Write original manuscripts for publication based on data analyses and product development.
• Maintain quality assurance and control of HTS data generated by PHL to ensure reproducible and accurate downstream analyses.
• Write and design SOPs and validation or verification protocols.
• Use best practices for code development and documentation.
• Lead and participate in presentations and workshops with PHL Quality Management to improve understanding and tracking of sequencing quality control measures, data security, and data management.

Benefits

• Potential eligibility for federal or state loan forgiveness and repayment assistance programs.
• Premium-free health insurance plan.
• Additional health, fitness, and financial benefits may be available depending on the position’s associated union or benefit fund.
• Public-sector defined-benefit pension plan.
• Tax-deferred savings program.
• Worksite Wellness Program.
• Potential to work from home up to two days during the week, depending on the position.
• Job security compared with private-sector employment.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior