Bioinformatics Scientist, Bureau of the Public Health Laboratory

About the role

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. 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 that support DOHMH priorities and community partners in preventing and responding to public health concerns.

Responsibilities

• Conduct bioinformatics analyses for sequencing data that support 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 from clinical and environmental samples (e.g., wastewater).
• Conduct literature reviews and stay current with cutting-edge scientific and epidemiological research and tools.
• Mentor and cross-train staff or research fellows at PHL.
• Collaborate with team members and partners on genomics data management (e.g., SQL databases, public repository uploads, other datasets).
• 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 to non-bioinformaticians (e.g., epidemiologists, virologists, microbiologists).
• 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 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.

Preferred Skills

• Strong skills in Linux command line and BASH shell scripting.
• Proficiency in R, Python, C, Java, or other programming languages.
• Experience with 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.
• MS or PhD degree in biological sciences, evolutionary biology, genomics, or related fields.
• Strong analytical and organizational skills.
• Excellent oral, interpersonal, and written communication skills.

Qualifications

• Assignment Level I: 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.
• Assignment Level II and above:
  • 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
  • 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
  • Education and/or experience equivalent to the above.
• All candidates must have at least a master’s degree in an appropriate field of specialization and at least two years of experience as described above.
• Two years as a City Research Scientist Level I can substitute for the experience required above.

Appointment is subject to a minimum probationary period of one year.