Bioinformatician I

JOB TITLE: Bioinformatician I

POSITION NUMBER: 2408-17961-BIO-001

POSITION LOCATION: Atlanta, GA, USA

ANTICIPATED START DATE: Four-six weeks after candidate identification

TRAVEL: As required to fulfill the responsibilities of the position

ASRT, Inc. provides scientific, information management, management consulting, bioinformatics, and administrative program support to the Centers for Disease Control and Prevention (CDC) and other Federal and private sector clients. The successful candidate will be a full-time employee of ASRT, Inc. and will be assigned to the Mycotic Diseases Branch (MDB), Division of Foodborne, Waterborne, and Environmental Diseases (DFWED), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), at the CDC, 1600 Clifton Road, Atlanta, GA, to provide bioinformatics support for the branch.

SCOPE OF WORK

The Bioinformatician I will provide technical and intellectual support towards the development of new rapid methods to detect and characterize fungi based on whole genome sequence and metagenomic analysis.

MAJOR DUTIES AND RESPONSIBILITIES

• Design and manage large-scale sequence databases to enable the rapid integration, querying, and selective enrichment or depletion of large sequence datasets. In this capacity, the contractor is expected to draw on the following disciplines and skills:
  • Database design, management, and tuning.
  • Scripting and programming.
  • Statistical analysis.
  • Algorithmic selection and optimization.
  • Visualization of complex datasets:
    • These efforts include design and customization of small-scale, local applications for data access, analysis, and visualization; the development and administration of database systems; and the identification and implementation of new techniques and technologies for advanced analysis of complex biological data.
• Design, program, test, modify, enhance, maintain, and support novel and existing bioinformatics applications and pipelines for genomic analysis, pathogen identification and characterization, using both open source (ex: GATK, MEGAN, MetaGeneMark, kraken, CLARK, etc.) and commercial off-the-shelf software applications, as appropriate. This will include data from short-read sequencing (Illumina) and long-read sequencing (PacBio and Oxford Nanopore Technologies).
• In consultation with the CDC project team representatives, develop standardized pipelines or toolchains for metagenomic analysis of different sample types, configure and deploy them into the CDC Bioinformatics computing environment, and use these for standardized benchmarking of laboratory extraction and sample preparation methods.
• In consultation with the CDC project team representatives, develop standardized pipelines or toolchains for characterization of specific genes and identification of specific mutations/genetic elements from WGS data of different sample types, configure and deploy them into the CDC Bioinformatics computing environment, and use these for standardized benchmarking of laboratory extraction and sample preparation methods.
• In consultation with the CDC project team representatives, design and maintain comprehensive and highly-curated genomic sequence databases, including microbial and fungal genomic sequences for inclusion or exclusion of known pathogens; plant and animal genomic sequences for exclusion of host DNA; signature databases for known virulence and antimicrobial resistance markers; and databases of known strain type or pathotype-specific markers. This task requires the design and implementation of gigabase-scale, high-performance databases of genomic and/or signature sequences drawn from public and limited-access sequencing activities.
• Develop scripts and software to automate scientific data analysis using Python, Perl/BioPerl, Ruby and Java. Documented authoritative source code to all software and scripts developed during the period of performance will be maintained in a managed GitLab source code repository in CDC's bioinformatics computing environment. Any software tools developed during the course of this work will be published as open source software on approved public source code repositories (e.g.: http://www.github.com/CDCgov).
• Receive next generation sequencing data from both internal and external collaborators. Contractor shall then perform standardized quality assurance and control procedures on the raw sequence reads and analyze them using established pipelines and methods. Sequence data shall be derived from isolates biological and environmental samples, with multiple replicates, representing different specimen processing and extraction techniques, and different platforms.
• Develop and refine quantitative methods to compare multiple datasets to advise the project team on optimal parameters for sample processing, extraction, and sequencing. Consult with internal and external partners on strategies and solutions for data retention, storage, and management.

MINIMUM QUALIFICATIONS

Education and Experience:

• Master of Science degree in bioinformatics, genetics, biology, microbiology, biochemistry, computational biology, or other area related to the responsibilities of the position.

Required:

• Experience with whole genomic sequencing, and genome-based typing systems.
• Experience performing quality control, assembly, annotation, and analysis of pathogen genome sequences.
• Proficiency with open source and commercially available software for bioinformatics analysis of next generation sequencing data.
• Proficiency with Microsoft Word, Excel, and PowerPoint.
• Excellent attention to detail and the ability to efficiently organize multiple priorities.
• Documentation of daily work with good laboratory practice compliance.
• Ability to work and build coalitions with partners involved and develop strategies for effectively conveying information to partners.
• Ability to work independently and maintain the flexibility to respond to the needs of Mycotic Diseases Branch.
• Skills and experience writing project reports, research protocols, and manuscripts.
• Knowledge of CDC policy, quality, and regulatory training.
• Ability to independently resolve conflicts.
• Working knowledge of CDC applications.

Desirable:

• Experience with standard molecular methods including, but not limited to, ELISA, PCR, qPCR, DNA/RNA isolation, and cloning.
• Proficiency with computer software such as Microsoft Access, DNA star, Minitab, MathCAD, BioNumerics, and statistical software.
• Experience with bioinformatics analysis of genomic data generated by PacBio and Illumina sequencing platforms, especially in relation to genomic typing systems.
• Experience with the design and implementation of genomic typing systems and novel bioinformatics tools.
• Experience with Unix/Linux, Perl, Python, Java, and R.
• Experience with comparative genomics/metagenomics analysis.
• Experience with de novo genome assembly and genomic annotation programs.
• Experience with data management.
• Experience working with open source repositories such as GitHub.

Language Skills:

• The candidate must possess excellent oral and written communication skills in English.

REQUIREMENT: Must be a United States citizen or permanent resident or have authorization for employment in the United States.

SALARY: Commensurate with qualifications and experience.

To apply for this position:

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• If you are viewing this position on a site other than the ASRT Career page, you may use the "click to apply" link, or you may apply by visiting our Career page and searching for the job title and position number listed at the top of this job posting.
• To view all of our open positions and to apply to job openings in which you may be interested, please visit our Career page at https://www.asrtinc.com/careers.

ASRT, INC. IS AN EQUAL OPPORTUNITY AND AFFIRMATIVE ACTION EMPLOYER. It is the policy of ASRT, Inc. to provide equal employment opportunities without regard to race, color, religion, citizenship, age, sex, sexual orientation, gender identity, national origin, ancestry, genetic information, veteran or disability status, or any other characteristic protected by applicable federal, state or local law, and to take affirmative action in accordance with applicable laws and Executive Orders.