Bioinformatics Scientist , Bureau Public Health Laboratory

The New York City (NYC) Department of Health and Mental Hygiene(DOHMH) is a public health leader serving over 8.4 million New York City residents from diverse ethnic, cultural, and economic backgrounds. The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States offering a dynamic and innovative work environment where employees contribute to the health and safety of NYC residents by providing clinical and environmental laboratory testing services.

With more than 100 years of leadership in public health, a team of over 200 scientific and support staff that are committed to its mission to safeguard the health of all NYC residents by providing quality laboratory testing services that support the priorities of the NYC DOHMH and its community partners to prevent and respond to clinical and environmental public health concerns.

PHL seeks a qualified candidate to serve as a Bioinformatics Scientist. This position will work primarily in PHL’s Bioinformatics Unit. This position will develop and maintain analysis pipelines as well as perform bioinformatics analyses for high through put sequencing (HTS) data. It will play an integral role in genomics analysis aimed at responding to public health threats, including but not limited to COVID-19, vaccine preventable diseases, HIV, Legionella as well as respiratory, foodborne, and waterborne disease outbreaks.

• 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 and phylogenetics, genomics data visualization.
• Strengthening the application of genomic tools to support public health diagnostic testing for pathogens such as Mycobacterium tuberculosis and mpox.
• Conducting literature reviews and stay up to date with cutting edge scientific and epidemiological research and tools.
• 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).
• Supervising 1-2 staff in conducting research projects.
• Representing the agency in meetings and conferences.
• Drafting written protocols and maintain accurate records of software tools design.
• Writing original manuscripts for publication based on data analyses and product development.
• Maintaining quality assurance and control of HTS data generated by PHL to ensure reproducibility and accuracy of downstream bioinformatics analyses. This includes 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 (knowledge of open source and commercial microbial NGS analysis pipelines) and genome annotation.
• Demonstrated work in public health genomics research.
• A PhD degree in the biological sciences with extensive…