GDIT is seeking a Senior Bioinformatics Scientist and Bioinformatics Team Lead to join our team in Atlanta of highly skilled engineers, bioinformaticians (Ph.D.; M.S.), software engineers and operations staff supporting the Centers for Disease Control and Prevention (CDC), Office of Advanced Molecular Detection (OAMD).
This individual and the bioinformatics team broadly support the CDC scientific community and provide subject matter expertise pertaining to genomic analysis, comparative genomics, and next generation sequencing (NGS) analysis of known and unknown bacterial and viral pathogens impacting human health.
This role requires direct interaction with expert CDC scientists from various scientific and technical backgrounds therefore strong interpersonal and communication skills are crucial. To succeed in this role, you must maintain awareness of current technical trends that pertain to NGS technologies and analytical methods and be able to translate them into solutions for CDC stakeholders and the broader national public health community.
The ideal candidate will be a highly skilled bioinformatics scientist with broad knowledge of NGS platforms and data analysis approaches, including the development of scalable and maintainable solutions. Experience leading multidisciplinary initiatives, including project management experience, is preferred. Familiarity with major bioinformatics file formats, analytical tools, comparative genomics, high throughput genomic data analysis using command line tools, and developing standards-based workflows using scripting languages (Python, R/Bioconductor, BASH, etc.) are required. Previous experience in biosurveillance and laboratory diagnostic tool development, open source software development, and data visualization is a plus. Working as part of diverse team of bioinformaticians and IT professionals, the candidate is expected to lead the development standards-based algorithms and analysis pipelines/workflows; the application of those tools to emerging needs of the CDC; and integration of those capabilities into broader bioinformatics activities and software development efforts. The incumbent must possess strong interpersonal, organizational, and communication (verbal and written) skills. This is an industrial bioinformatics group and although there will be elements of research to this position, the incumbent is expected to maintain a focus on product delivery.
Key responsibilities will involve being hands on to perform and to direct a small team in the following:
- Building and supporting cutting-edge workflows for the analysis and interpretation of NGS data from sequence production to variant calling and interpretation.
- Participation in the technical development process of an emerging NGS surveillance platform.
- Implementation of state-of-the-art computational methods, and developing innovative approaches to software challenges that touch all aspects of NGS data analysis.
- Conduct programming and/or scripting using languages such as Python, R/Bioconductor, JavaScript, and Java
- Provide expertise in algorithm generation and statistical and computational methods for the analysis of complex, high-throughput biological data.
- Analysis of large-scale genomic datasets acquired internally and through collaboration with others using R/Bioconductor or BioPython, BioJava.
- Ensure software adheres to appropriate government and regulatory compliance requirements.
- Maintain expertise in the science and application of genomic technologies.
- Provide professional grade reports on ongoing sequencing, analysis, and surveillance activities.
- Work with software development team members to mature and integrate analytical tools/pipelines into user accessible tools/interfaces in UNIX/Linux and high performance computing environments.
- Serve as a subject matter expert to guide complex software development activities.
- Perform project and staff management for the bioinformatics team including scheduling and reporting to GDIT and CDC leadership
Required Qualifications and Skills:
- Ph.D. in bioinformatics, biostatistics, computational biology or related
- 8+ years’ experience or equivalent combination of education and experience
- 2+ years’ hands on experience in bioinformatics and NGS data analysis, including the development of multistep analysis pipelines/workflows using scripting languages
- Prior Project management experience
- Demonstrated fluency in Linux and high performance computing environments
- Demonstrated programming/scripting ability in languages such as Python, R, JavaScript, or Java
- Familiarity with principles of object oriented programming
- Demonstrated experience in developing software in the Linux environment
- Experience in algorithm generation as well as pipeline generation and/or computational methods implementation
- Familiarity with statistical/mathematical packages, such as R/MATLAB
- Must have good understanding of the theory of major NGS platforms
- Prior experience in using software revision control systems (e.g. GIT)
Desired Qualifications and Skills:
- Prior Team management experience
- Experience performing complex bioinformatics analyses using High Performance Computing environments
- Strong background in statistical/mathematical analytical methods and tools such as R/Bioconductor
- Familiarity with workflow orchestration tools/standards such as Common Workflow Language (CWL) or Workflow Description Language (WDL)
- Expertise in phylogenetic analysis
- Expertise with multiple Next Generation Sequencing (NGS) technologies
- Experience developing production quality bioinformatics tools, workflows, and applications
- Experience developing portable bioinformatics tools using contemporary container technologies such as Docker or Singularity
- Experience with full software development life cycle and software development best practices
- Familiarity with service-oriented architectures (SOA); experience developing within such architectures
- Experience using collaboration and tracking tools such as JIRA and Confluence
- Experience working as part of Agile software development team