The Alaka`ina Foundation Family of Companies (FOCs) has a need for a Bioinformatician Level III to support our government customer located in Silver Spring, MD, with the potential need to travel to remote sites CONUS and OCONUS.

DESCRIPTION OF RESPONSIBILITIES:

• Maintain and Modify Multiple Sequencing Pipeline.
• Design and deploy an ad hoc bioinformatics sequencing pipeline (for all targeted organisms: including but not restricted to the multidrug resistant ESKAPE+ pathogens).
• Provide bioinformatics support to perform knowledge engineering functions between the IT staff and the medical research staff.
• Management of information management programs, projects, and systems; designing, developing, testing, and documenting software, hardware, and interface requirements; enhancing existing systems used for genotypic, phenotypic, epidemiological, and demographic data; and attending seminars, scientific conferences, and meetings relevant to the MRSN, among other duties.
• Collaborate with IT staff and other MRSN personnel to accomplish assignments as needed and as determined by the developmental stages of each pipeline.
• Perform Retrospective Sequencing and Genomic Analysis of Historical Isolates.
• Work collaboratively within MRSN laboratories to sequence and analyze (assemblies, typing, comparative genomics, resistance gene predictions, etc.) the isolates in the MRSN repository as requested/prioritized by MRSN leadership.
• Perform Prospective Sequencing and Real-time Genomic Analysis.
• Utilize long and short sequencing technologies for high-throughput bacterial genome sequencing and support in the near real-time sequencing and genomic analysis of contemporary isolates received on a weekly, monthly, and quarterly basis at the MRSN.
• Troubleshoot existing technologies and validate and implement new sequencing technologies as required.
• Provide sequencing and analysis for collaborative projects.
• Perform sequencing and/or genomic analysis of isolates as part of collaborative projects initiated by the MRSN leadership.
• Participate in the development and automation of bioinformatic workflows.
• Assist the development of the MRSN Integrated Genome Handling Tool (MIGHT), a single software package custom-designed to handle the automated, a la carte execution of several of the CARB-MRSN bioinformatic core analysis tools.
• Assist the development of custom Python scripts for the rapid analysis of tens to thousands bacterial genomes to include QC thresholds, species identification, typing, cluster detection, prediction of resistance and virulence genes, annotation, variant analysis, and the implementation of NextFlow or similar workflow management system.
• Assist the development of Long-read Sequencing.
• Establish a reliable, efficient, and economic Oxford Nanopore MinION long-read sequencing analysis pipeline to include developing SOPs for long-read whole genome sequencing, bioinformatic analyses, and data storage.
• Conduct presentations and publications of genomic epidemiology data.
• Present data to colleagues and collaborators at conferences and meetings and travel to collaborating facilities to provide bioinformatics support. The Contractor shall participate in the design, analysis, and writing of scientific projects and/or publications as determined by MRSN leadership and mission directives.
• Assist in the instruction and execution of Next-Generation Sequencing teaching courses offered by the MRSN that involve whole genome sequencing assembly and analysis using a variety of software tools to better understand bacterial epidemiology and antibiotic resistance.
• Provide bioinformatician support and work collaboratively, as determined by mission directives, with MRSN clinical and molecular laboratories to validate in vitro hypotheses derived from in silico genomic analyses. This includes, but is not limited to, targeted gene deletion/expression, quantitative gene expression, ad hoc antibiotic susceptibility testing using microdilution approach, and experimental evolution of bacterial isolates.

REQUIRED DEGREE/EDUCATION/CERTIFICATION:

• BS or MS level in Bioinformatics or equivalent with an emphasis on bacterial genomics.
• Programming abilities in other languages such as HTML, Java, JavaScript, PHP, PERL, Rust, SQL will be required.

REQUIRED SKILLS AND EXPERIENCE:

• Ability to serve as the primary POC for technical expertise regarding bioinformatics tools and MIGHT (MRSN Integrated Genome Handling Tool) workflow.
• Comprehensive knowledge and experience with scripting languages, NoSQL databases, HPC computing environments, secure cloud infrastructure, and open-source bioinformatics tools.
• Comprehensive knowledge of current long- and short-read NGS platforms

DESIRED SKILLS AND EXPERIENCE:

• 5 years of experience in the development, deployment, and maintenance of software and pipelines for the analysis of bacterial genomic data.

REQUIRED CITIZENSHIP AND CLEARANCE:

• Must be a U.S. Citizen
• Must have completed NACI with ability to obtain Secret Clearance.
• Must have valid U.S. Passport.
  

The Alaka`ina Foundation Family of Companies (FOCs) is a fast-growing government service provider. Employees enjoy competitive salaries. Eligible full-time employees enjoy a 401K plan with company match; medical, dental, disability, and life insurance coverage; tuition reimbursement; paid time off; and 11 paid holidays.

We are an Equal Opportunity/Affirmative Action Employer. We are proud to state that we do not discriminate in employment decisions on the basis of race, color, religion, sex, pregnancy, sexual orientation, gender identity, national origin, age, protected veteran status, or disability status. If you are a person with a disability and you need an accommodation during the application process, please clickhereto request accommodation. We E-Verify all employees.

The Alaka`ina Foundation Family of Companies (FOCs) is comprised of industry-recognized government service firms designated as Native Hawaiian Organization (NHO)-owned and 8(a) certified businesses. The Family of Companies (FOCs) includes Ke`aki Technologies, Laulima Government Solutions, Kpono Government Services, and Kpili Services, Po`okela Solutions, Kkaha Solutions, LLC, and Pololei Solutions, LLC. Alaka`ina Foundation activities principally benefit the youth of Hawaii through charitable efforts which includes providing innovative educational programs that combine leadership, science & technology, and environmental stewardship.

For additional information, please visit www.alakainafoundation.com.

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