Bioinformatics Scientist , Bureau of the Public Health Laboratory

About the role

The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States, providing clinical and environmental laboratory testing services to over 8.4 million New York City residents. The Bioinformatics Unit is seeking a Bioinformatics Scientist to develop and maintain analysis pipelines and perform bioinformatics analyses for high-throughput sequencing (HTS) data, contributing to genomics analysis aimed at responding to public health threats such as COVID-19, vaccine-preventable diseases, HIV, Legionella, and various outbreaks.

Responsibilities

• Conduct bioinformatics analyses for sequencing data supporting public health efforts.
• Develop or improve tools related to pathogen identification, outbreak tracking, mapping drug resistance determinants, variant analysis, genome annotation, phylogenetics, and genomics data visualization.
• Strengthen the application of genomic tools to support public health diagnostic testing for pathogens such as Mycobacterium tuberculosis and mpox.
• Conduct literature reviews and stay current with cutting-edge scientific and epidemiological research and tools.
• Participate in agency-wide WGS journal club and genomic data exchange working groups.
• Develop tools (e.g., dashboards) or strategies (e.g., Docker-based pipelines) to improve accessibility of bioinformatics analyses for non-bioinformaticians (e.g., epidemiologists, virologists, microbiologists).
• Supervise 1–2 staff in conducting research projects.
• Represent the agency in meetings and conferences.
• Draft written protocols and maintain accurate records of software tools design.
• Write original manuscripts for publication based on data analyses and product development.
• Maintain quality assurance and control of HTS data to ensure reproducibility and accuracy of downstream bioinformatics analyses, including writing and designing SOPs and validation/verification protocols.
• Use best practices for code development and documentation.
• Lead and participate 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.

Requirements

• A PhD degree in the biological sciences with extensive experience in the technical and administrative operations of a Clinical or Public Health Laboratory.

Qualifications

• Strong skills in Linux command line and BASH shell scripting.
• Proficient in R, Python, C, Java, or other programming languages.
• Experience in SQL.
• Experience 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, de novo sequencing analysis, knowledge of open-source and commercial microbial NGS analysis pipelines, and genome annotation.
• Demonstrated work in public health genomics research.
• Strong analytical and organizational skills.
• Excellent oral, interpersonal, and written communication skills.

Preferred Skills

• Strong skills in Linux command line and BASH shell scripting.
• Proficient in R, Python, C, Java, or other programming languages.
• Experience in SQL.
• Experience 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.