Bioinformatics Scientist, Bureau Public Health Laboratory

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, 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.

• Conducting bioinformatics analyses for sequencing data that support public health efforts.
• Developing or improving tools related to pathogen identification, outbreak tracking, mapping drug resistance determinants, variant analysis, genome annotation, phylogenetics, and genomics data visualization.
• Strengthening the application of genomic tools to support public health diagnostic testing for pathogens from clinical and environmental samples (e.g., wastewater).
• Conducting literature reviews and staying up to date with cutting‑edge scientific and epidemiological research and tools.
• Mentoring and cross‑training staff or research fellows at PHL.
• Collaborating with other team members and partners on genomics data management (e.g., SQL databases, public repository uploads, other datasets).
• Participating in agency‑wide WGS journal club and genomic data exchange working groups.
• Developing tools (e.g., dashboards) or strategies (e.g., Docker‑based pipelines) to improve accessibility of bioinformatics analyses to non‑bioinformaticians (e.g., epidemiologists, virologists, microbiologists).
• Representing the agency in meetings and conferences.
• Drafting written protocols and maintaining accurate records of software tool design.
• Writing original manuscripts for publication based on data analyses and product development.
• Maintaining quality assurance and control of high‑throughput sequencing data generated by PHL to ensure reproducibility and accuracy of downstream bioinformatics analyses, including writing and designing SOPs and validation/verification protocols.
• Using best practices for code development and documentation.
• Leading and participating in presentations and workshops with Quality Management (QM) at PHL to improve understanding and tracking of sequencing data and analyses quality control measures, data security and data management using resources from APHL, ASM, and others.

• Strong skills in Linux command line and BASH shell scripting.
• Proficient in R, Python, C, Java, or other programming languages.
• Experience in SQL.
• Experience in utilizing multi‑core server resources, automating processes, containerization, and workflow languages.
• Experience with common tools for next generation sequencing analysis (NGSA), including reference‑based analysis and de‑novo sequencing analysis and genome annotation.
• Demonstrated work in public health genomics research.
• MS or PhD degree in the biological sciences, evolutionary biology, genomics, or related fields.
• Strong analytical and organizational skills with excellent oral, inter‑personal and written communication skills.

For Assignment Level I (physical, biological and environmental sciences and public health) a master’s degree from an accredited college or university in a relevant field of physical, biological or environmental science or in public health is required. For Assignment Level II and above, candidates must meet one of the following:

• A doctorate degree from an accredited institution 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.
• A master’s degree from an accredited institution with specialization in an appropriate field of physical, biological,…