City of New York
Bioinformatics Scientist, Bureau of the Public Health Laboratory
City of New York - New York, New York, United States, 10001
Work at City of New York
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Overview
Bioinformatics Scientist, Bureau of the Public Health Laboratory
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. The Public Health Laboratory (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 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 COVID-19, 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 include: 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 fellows, 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 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. 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; 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. 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 individual's sex, race, color, ethnicity, national origin, age, religion, disability, sexual orientation, veteran status, gender identity, or pregnancy.
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. The Public Health Laboratory (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 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 COVID-19, 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 include: 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 fellows, 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 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. 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; 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. 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 individual's sex, race, color, ethnicity, national origin, age, religion, disability, sexual orientation, veteran status, gender identity, or pregnancy.