Bioinformatics Scientist, Bureau of the Public Health Laboratory

Bioinformatics Scientist, Bureau of the Public Health Laboratory

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, which is achieved through varied and interrelated endeavors of its seven Bureaus. The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States where employees contribute to the health and safety of NYC residents by providing clinical and environmental laboratory testing services. PHL is committed to its mission to safeguard the health of all NYC residents by providing quality laboratory testing services that support the priorities of DOHMH and its community partners to prevent and respond to clinical and environmental public health concerns.

Duties will include but not be limited to:

• 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 from clinical and environmental samples (e.g., wastewater).
• Conducting literature reviews and stay up to date with cutting edge scientific and epidemiological research and tools.
• Mentoring and cross-training staff or research fellow sat PHL.
• Collaborating with other team members and partners on genomics data management (e.g., SQL data bases, public repository uploads, other datasets).
• 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).
• 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.

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.
• MS or PhD degree in the biological sciences, evolutionary biology, genomics, or related fields.
• Strong analytical and organizational skills; Excellent oral, inter-personal and written communication skills

Why you should work for us:

• 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.
• Benefits: City employees are entitled to unmatched benefits such as: a 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. A public sector defined benefit pension plan with steady monthly payments in retirement. A tax-deferred savings program and a robust Worksite Wellness Program that offers resources and opportunities to keep you healthy while serving New Yorkers.
• Work From Home Policy: Depending on your position, you may be able to work up to two days during the week from home.
• 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.

The City of New York is an inclusive equal opportunity employer committed to recruiting and retaining a diverse workforce and providing a work environment that is free from discrimination and harassment based upon any legally protected status or protected characteristic, including but not limited to an individual's sex, race, color, ethnicity, national origin, age, religion, disability, sexual orientation, veteran status, gender identity, or pregnancy.