Junior Bioinformatics Scientist, Bureau of the Public Health Laboratory

About the role

The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States, safeguarding the health of all NYC residents by providing quality laboratory testing services that support the priorities of the NYC Department of Health and Mental Hygiene (DOHMH) and its community partners to prevent and respond to clinical and environmental public health concerns. PHL seeks a City Research Scientist II to serve as a Junior Bioinformatics Scientist.

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 up to date 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)
• 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

Preferred Skills

• Strong skills in Linux command line and BASH shell scripting
• Proficiency in R, Python, C, Java, or other programming languages
• Experience in 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 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, interpersonal, and written communication skills

Qualifications

• For Assignment Level II and above:
  • A doctorate degree with one year of full-time experience in a responsible supervisory, administrative, or research capacity in an appropriate field; or
  • A master’s degree with three years of responsible full-time research experience in an appropriate field; or
  • Education and/or experience equivalent to the above.
• All candidates must have at least a master’s degree in an appropriate field and at least two years of experience as described above.
• Two years as a City Research Scientist Level I can substitute for the required experience.