Bioinformatics Scientist

About the Role

The NYC Public Health Laboratory (PHL) seeks a qualified candidate to serve as a Bioinformatics Scientist. This position will work primarily in PHL's Bioinformatics Unit.

Key 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, and phylogenetics.
• Develop or improve tools for 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 up to date with cutting-edge scientific and epidemiological research and tools.
• Participate in agency-wide WGS journal clubs 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).
• 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 high throughput sequencing (HTS) data generated by PHL to ensure reproducibility and accuracy of downstream bioinformatics analyses.
• Write and design 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.

Requirements & Tech Stack

• 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 experience in the technical and administrative operations of a Clinical or Public Health Laboratory.
• Strong analytical and organizational skills.
• Excellent oral, inter-personal, and written communication skills.

Qualifications

For Assignment Level I (only physical, biological and environmental sciences and public health)

• 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.

To be appointed to Assignment Level II and above, candidates must have:

• 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 which is equivalent to "1" or "2" above.
• However, all candidates must have at least a master's degree in an appropriate field of specialization and at least two years of experience described in "2" above.
• Two years as a City Research Scientist Level I can be substituted for the experience required in "1" and "2" above.

Note

• Probationary Period: Appointments to this position are subject to a minimum probationary period of one year.