Junior Bioinformatics Scientist, Bureau of the Public Health Laboratory

City of New York • New York City, NY

2d • Hybrid

About The Position

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, contributing to the health and safety of NYC residents by providing clinical and environmental laboratory testing services. The PHL is seeking a qualified City Research Scientist II to serve as a Junior Bioinformatics Scientist.

Requirements

• 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.
• 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.
• Three years of responsible full-time research experience in the appropriate field of specialization (if appointed to Assignment Level II or above with a Master's degree).
• At least two years of experience described in '2' above (if appointed to Assignment Level II or above with a Master's degree).

Responsibilities

• Assist with conducting bioinformatics analyses for sequencing data that support public health efforts.
• Assist with developing or improving tools related to pathogen identification, outbreak tracking, mapping drug resistance determinants, variant analysis, genome annotation and phylogenetics, and genomics data visualization.
• Assist with strengthening 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 up to date with cutting edge scientific and epidemiological research and tools.
• Assist with mentoring and cross-training staff or research fellows at PHL.
• Collaborate with other 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).
• 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 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.
• 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.

Benefits

• Premium-free health insurance plan
• Additional health, fitness, and financial benefits may be available based on the position’s associated union/benefit fund.
• Public sector defined benefit pension plan
• Tax-deferred savings program
• Robust Worksite Wellness Program
• Job security
• Loan Forgiveness

What This Job Offers

• Job Type: Full-time
• Career Level: Entry Level