Bioinformatics Specialist III

About the Role

We are seeking a Bioinformatics Specialist III to support wastewater surveillance for the Division of Healthcare Quality Promotion (DHQP) at the Centers for Disease Control and Prevention (CDC).

Responsibilities

• Maintain sequencing data inventory for the laboratory.
• Monitor SciComp and High-Performance Computing Cluster functioning daily or as frequently as appropriate for problems, issues, updates.
• Track sequencing requests for projects.
• Coordinate sequence data sharing with requestors and collaborating laboratories.
• Manage incoming sequence data for processing, documentation, tracking, and inventory as needed.
• Maintain files in accordance with records management policies and procedures.
• Review incoming and outgoing correspondence and distribute to the appropriate person.
• Manage daily activities, procedures and processes related to molecular characterization and classification of emerging antimicrobial resistance in healthcare-associated and emerging pathogens.
• Analyze data from scientific projects and programs using appropriate programs and bioinformatics tools.
• Develop appropriate analytic plans for bioinformatic/sequence data analyses to address the project goals and objectives.
• Run in-house bioinformatics pipelines (e.g., QuAISAR-H) to perform quality checks and preliminary analyses of whole genome sequencing data.
• Generate appropriate data files from QuAISAR-H, format, and send to sequencing coordinator for data summaries.
• Perform quality assessment of next generation sequence data using appropriate tools and pipelines, (e.g., tools for quality assessment of amplicon and/or shotgun metagenomic sequencing).
• Perform bioinformatics analyses for the identification and subtyping of healthcare-associated and emerging pathogens.
• Perform protocols and incorporate into analyses epidemiologic data, and data generated from conventional and real-time PCR, next-generation sequencing, and/or metagenomic analysis of samples related to healthcare-associated infection and other emerging pathogen studies.
• Develop, validate, and implement methods and procedures to analyze laboratory data, including methods for characterization and phylogenetic analyses of next-generation sequencing data, making adjustments in methods and procedures as appropriate.
• Perform bioinformatics analysis of complex samples, including characterizing and visualizing the microbial communities, quantifying diversity, identifying antimicrobial resistance genes, virulence factors, and other functions using appropriate bioinformatics tools and databases (e.g., KRAKEN2, MetaPhlAn3, database-independent kmer approaches to community characterization, GROOT, SRST2, ARIBA, DESeq2).
• Analyze, visualize and summarize data from scientific projects and programs using appropriate programs, tools and pipelines (e.g., R, python, bath, LefSe, GROOT, ARIBA, DESeq2).
• Develop, revise and review project protocols and documents according to QMS guidelines.
• Coordinate and participate in regular meetings relating to assigned projects.
• Upload sequence data (raw reads and/or assemblies as appropriate) to public databases (e.g., NCBI) under timelines established by the SME/project leads or Team Leads.
• Meet with SME/project leads at least monthly to discuss project work plans, project updates, test results, and testing plans.
• Assist staff with preparation of presentation materials for meetings and conferences by drafting, editing, and/or reviewing.
• Effectively interpret analyses and assist with preparation of and independently prepare written documents, reports, and analyses or various scientific projects and programs.
• Provide a written weekly progress update to SME/project and team leads.
• Using appropriate programs, tools, and methods, generate project reports, which may be presented to others internal and external to CDC.
• Assist in training of various analytical methodologies employed in Division projects by instructing, teaching, and/or observing as determined by quality management procedures.
• Develop new and improved concepts, principles, and techniques that will advance the body of knowledge of information management and apply advanced bioinformatic or computer science methods and techniques to solve complex computer processing requirements for data analysis, inventory management and clinical system interface.
• Enhance existing systems used for genotypic, phenotypic, epidemiological and demographic data.
• Apply theoretical expertise and innovation to create or apply new technology.
• Consult with users, management, vendors, and technicians to determine computing needs and system requirements.
• Coordinate core activities of bioinformatics staff and fellows.
• Lead tool development for AR lab Network state public health laboratories.
• Oversee strategy for development and implementation of in-house bioinformatics pipelines.
• Complete custom bioinformatics analyses for molecular epidemiology products or metagenomic projects, that require going above and beyond the standard in-house pipelines.
• Provide subject matter expertise for troubleshooting in-house pipelines.

Required Experience and Skills

• Minimum 5 years of experience in the capacity of bioinformatician.
• Experience running in-house bioinformatics pipelines (e.g., QuAISAR-H) to perform quality checks and preliminary analyses of whole genome sequencing data.
• Experience performing bioinformatics analysis of complex samples, including characterizing and visualizing the microbial communities, quantifying diversity, identifying antimicrobial resistance genes, virulence factors, and other functions using appropriate bioinformatics tools and databases (e.g., KRAKEN2, MetaPhlAn3, database-independent kmer approaches to community characterization, GROOT, SRST2, ARIBA, DESeq2).
• Experience analyzing, visualizing and summarizing data from scientific projects and programs using appropriate programs, tools and pipelines (e.g., R, python, bath, LefSe, GROOT, ARIBA, DESeq2).
• Experience performing quality assessment of NGS data using appropriate tools and pipelines, (e.g., tools for quality assessment of amplicon and/or shotgun metagenomic sequencing).
• Experience developing appropriate analytic plans for bioinformatic/sequence data analyses to address project goals and objectives.
• Experience maintaining sequencing data inventory for a laboratory.
• Experience monitoring SciComp and High-Performance Computing Cluster functioning daily or as frequently as appropriate for problems, issues, updates.
• Experience working at CDC or in a public health setting preferred.
• Strong attention to detail.
• Ability to work independently and as part of a team in a fast-paced setting.
• Ability to work with a diverse interdisciplinary team.
• Excellent written and verbal communication skills.
• Effective organization skills.
• Ability to obtain a government clearance.

Education and Training

• Master’s degree in Bioinformatics, Computational Biology, Computer Science, Microbiology, Biology or closely related field plus minimum 6+ years of experience in the capacity of bioinformatician, or
• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Microbiology, Biology or closely related field plus minimum 4-5 years of experience in the capacity of bioinformatician.

As a federal contractor and consistent with CDC guidance, we strongly encourage all employees working on a covered contract or in support of a covered contract to be fully vaccinated against COVID-19 by or before their start date and to submit their vaccination documents. Federal guidance allows for disability/medical and religious accommodations with respect to the vaccine. Any requested accommodations must be reviewed and approved (if applicable) in advance of your start date. If the Executive Order 14042 suspension is lifted, we will inform you of the vaccination requirements for continued employment and the applicable deadlines, which may have a short turnaround time. We will abide by what the government requires of us as a federal contractor.

Physical Requirements

• Prolonged periods of sitting at a desk and working on a computer. May need to lift 25 pounds regularly.