Bioinformatics Scientist , Bureau of the Public Health Laboratory

About the Role

The NYC Public Health Laboratory (PHL) seeks a Bioinformatics Scientist to work primarily in the Bioinformatics Unit. This position will develop and maintain analysis pipelines as well as perform bioinformatics analyses for high throughput 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.

Responsibilities

• 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 agencywide 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.

Qualifications

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.

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.

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 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.

Benefits

• Premium-free health insurance plan that saves employees over $10K annually, per a 2024 assessment.
• Additional health, fitness, and financial benefits may be available based on the position's associated union/benefit fund.
• Public sector defined benefit pension plan with steady monthly payments in retirement.
• Tax-deferred savings program.
• Robust Worksite Wellness Program that offers resources and opportunities to keep you healthy while serving New Yorkers.

Pay & Schedule

• Work From Home Policy: Depending on your position, you may be able to work up to two days during the week from home.
• Loan Forgiveness: As a prospective employee of the City of New York, you may be eligible for federal/state loan forgiveness and repayment assistance programs that lessen your payments or even fully forgive your full balance.
• Job Security: you could enjoy more job security compared to private sector employment and be able to contribute to making NYC a healthy place to live and work.