Bioinformatics Scientist Bureau of the Public Health Laboratory

Division/Program Summary Description:

The Division of Disease Controls 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.

The Public Health Laboratory (PHL) seeks a qualified candidate to serve as a Bioinformatics Scientist. This position will work primarily in PHLs Bioinformatics Unit. This position will develop and maintain analysis pipelines as well as perform bioinformatics analyses for high throughput sequencing (HTS) data. It will play an integral role in genomics analysis aimed at responding to public health threats including but not limited to COVID19 vaccine preventable diseases HIV Legionella as well as respiratory foodborne and waterborne disease outbreaks. This is an excellent opportunity to join our multidisciplinary team and collaborate with local state federal and academic partners.

Job Duties and Responsibilities:
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 crosstraining 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. Dockerbased pipelines) to improve accessibility of bioinformatics analyses to nonbioinformaticians (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 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 multicore server resources automating processes containerization and workflow languages.
Experience with common tools for Next Generation Sequencing Analysis (NGSA) including referencebased 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.

An 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: 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 Educations website ()
Benefits: City employees are entitled to unmatched benefits such as:
oa premiumfree health insurance plan that saves employees over $10K annually per a 2024 assessment.
oadditional health fitness and financial benefits may be available based on the positions associated union/benefit fund.
oa public sector defined benefit pension plan with steady monthly payments in retirement.
oa taxdeferred savings program and
oa 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.

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 antitobacco 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 COVID19 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!

Commitment to Equity:

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 individuals 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 SyeEun Ahn Director of the Office of Equal Employment Opportunity at or.

Qualifications :

1. For Assignment Level I (only physical biological and environmental sciences and public health) A masters 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 fulltime experience in a responsible supervisory administrative or research capacity in the appropriate field of specialization; or
2. A masters 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 fulltime 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 masters 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.

Additional Information :

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 individuals sex race color ethnicity national origin age religion disability sexual orientation veteran status gender identity or pregnancy.

Remote Work :

No

Employment Type :

Fulltime