Bioinformatics Software Engineer Jobs in New York

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 ensurere producibility and accuracy of down stream 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. 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.
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.
Established in 1805, the New York City Department of Health and Mental Hygiene (NYC Health Department) is the oldest and largest health department in the U.S., dedicated to protecting and improving the health of NYC. Our mission is to safeguard the health of every resident and cultivate a city where everyone, regardless of age, background, or location, can achieve their optimal health. We provide a wide array of programs and services focused on food and nutrition, anti-tobacco support, chronic disease prevention, HIV/AIDS treatment, family and child health, environmental health, mental health, and social justice initiatives. As the primary population health strategist and policy authority for NYC, with a rich history of public health initiatives and scientific advancements, from addressing the 1822 yellow fever outbreak to the COVID-19 pandemic, we serve as a global leader in public health innovation and expertise.
Come join us and help to continue our efforts in making a difference in the lives of all New Yorkers!
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.
The NYC Health Department is an inclusive equal opportunity employer committed to providing access and reasonable accommodation to all individuals. To request reasonable accommodation to participate in the job application or interview process, contact Sye-Eun Ahn, Director of the Office of Equal Employment Opportunity, at [email protected] or 347-396-6549.
CITY RESEARCH SCIENTIST - 21744

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.

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.