Bioinformatics Scientist, Bureau of the Public Health Laboratory

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 staying up to date with cutting edge scientific and epidemiological research and tools
• Mentoring and cross-training staff or research fellows at PHL
• Collaborating with other team members and partners on genomics data management (e.g., SQL databases, public repository uploads, other datasets)
• Participating in agency-wide 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 maintaining accurate records of software tool 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 producibility 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 (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

Why You Should Work for Us:

• Loan Forgiveness: Federal/state loan forgiveness and repayment assistance programs that lessen your payments or fully forgive your full balance.
• Benefits: Premium-free health insurance plan, additional health, fitness, and financial benefits, public sector defined benefit pension plan, tax-deferred savings program, and a robust Worksite Wellness Program.
• Work From Home Policy: Ability to work up to two days during the week from home.
• Job Security: Enjoy more job security compared to private sector employment and be able to contribute to making NYC a healthy place to live and work.

Preferred Skills:

• Experience managing competitive procurements for a government agency
• Experience writing specifications or scopes of work (SOWs) for competitive procurements or contracts
• Experience using the PASSPort system
• Superior writing skills
• Ability to manage a wide range of projects in a fast-paced environment

Minimum 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:
• 1. 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;
• 2. 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;
• 3. 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.