Bioinformatics Scientist - Pipeline Development

Key Skills

AWS, Azure, Bash scripting, Bioinformatics, C Programming, C++, Data science techniques, Django, Docker, Flask, Google Cloud Platform (GCP), Python Programming, R Programming, R-Shiny, React.js

Job Description

Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).

Axle is seeking a highly ambitious, adaptable, structured, and detail-oriented Bioinformatics Scientist-Pipeline Development to join our vibrant team at the National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID), Division of Intramural Research (DIR), Research Technologies Branch (RTB), Integrated Data Sciences Section (IDSS) in Bethesda, MD. *Work remote*

Benefits We Offer:

• 100% Medical, Dental & Vision Coverage for Employees
• Paid Time Off and Paid Holidays
• 401K match up to 5%
• Educational Benefits for Career Growth
• Employee Referral Bonus

Flexible Spending Accounts:

• Healthcare (FSA)
• Parking Reimbursement Account (PRK)
• Dependent Care Assistant Program (DCAP)
• Transportation Reimbursement Account (TRN)

Responsibilities:

• Address bioinformatics, scientific computing, and data analysis needs of users within the Division of Intramural Research (DIR) at NIAID and their collaborators by lending expertise in the proper statistical design of biological experiments involving high-throughput genome-scale technologies, data mining and knowledge discovery techniques, automated workflow development, statistical and scientific experimental design consulting. Provide bioinformatics support to include somatic and germline variant calling and analysis, single-cell and bulk gene expression analysis, de novo assembly of genomes and transcriptomes, comparative genomics of model and non-model organisms, proteomics, ChIP-seq, ATAC-seq, and the development of high-throughput pipelines for the analysis of the above data modalities.
• Provide programming and troubleshooting support to the Research Technologies Branch (RTB) of the National Institute of Allergy and Infectious Diseases (NIAID) and collaborating Institutes in the dissemination of research data. Perform computational data analysis on genomic and clinical research data. Work with staff on scientific programming and experimental design. Provide statistical support/analysis on research data. Contribute to and co-author scientific publications in leading peer-reviewed journals.
• Contribute to the development of a scalable and flexible resource to provide NGS bioinformatics, structural biological and computational, machine learning data support to NIAID scientists and investigators. It is expected that the bioinformatics scientist will need strong skills in the following:
• NGS analysis (whole-exome, whole-genome, RNA-seq, ChIP-Seq, both long- and short-read technologies, etc.)

• Statistical modeling
• Scripting
• Biological interpretation

Specific Qualifications:

• Ability to obtain and maintain a Public Trust Security clearance
• Minimum Bachelor’s degree in related field, Master’s or Ph.D. preferred
• 4+ years of experience in bioinformatics
• 2+ years of experience developing and maintaining production bioinformatics pipelines
• Expert in two (2) of the following languages: Python, R, C/C++, sh/bash
• Experience building images using one (1) of the following: Docker, Podman, Singularity/Apptainer
• Expert in one (1) pipeline framework: Snakemake, Nextflow, CWL/WDL
• Expertise building technical and user documentation for tools, pipelines, and applications
• Experience building pipelines locally on-premise using available HPC infrastructure
• Experience building pipelines/applications in the Cloud with AWS/GCP/Azure is a plus
• Experience building applications using one (1) of the following frameworks is a plus: Django, Flask, RShiny, Electron, Flutter, React
• Experience working in a laboratory setting is a plus but not required

Disclaimer:The above description is meant to illustrate the general nature of work and level of effort being performed by individuals assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.