Bioinformatics Scientist , Bureau of the Public Health Laboratory The New York City (NYC) Department of Health and Mental Hygiene(DOHMH) is a public health leader serving over 8.4 million New York City residents from diverse ethnic, cultural, and economic backgrounds. The NYC Public Health Laboratory (PHL) is one of the largest local public health laboratories in the United States offering a dynamic and innovative work environment where employees contribute to the health and safety of NYC residents by providing clinical and environmental laboratory testing services. With more than 100 years of leadership in public health, a team of over 200 scientific and support staff that are committed to its mission to safeguard the health of all NYC residents by providing quality laboratory testing services that support the priorities of the NYC DOHMH and its community partners to prevent and respond to clinical and environmental public health concerns. PHL seeks a qualified candidate to serve as a Bioinformatics Scientist. This position will work primarily in PHL's Bioinformatics Unit. This position will develop and maintain analysis pipelines as well as perform bioinformatics analyses for high through put 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. DUTIES WILL INCLUDE BUT NOT BELIMITED 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 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. 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. - 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. For more information, please visit the U.S. Department of Education's website (https://studentaid.gov/pslf/) - Benefits: City employees are entitled to unmatched benefits such as: o a premium-free health insurance plan that saves employees over $10K annually, per a 2024 assessment. o additional health, fitness, and financial benefits may be available based on the position's associated union/benefit fund. o a public sector defined benefit pension plan with steady monthly payments in retirement. o a tax-deferred savings program and o 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. CITY RESEARCH SCIENTIST - 21744 Qualifications 1. 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; or 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; or 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. NOTE: Probationary Period Appointments to this position are subject to a minimum probationary period of one year.