Bioinformatics Scientist - HIV-SOMAL

Axle; Oregon; Hybrid; USD 105,000 - 130,000; Full time

Benefits offered by this job

Medical coverage for employees

Paid time off and holidays

401K match up to 5%

Educational benefits

Referral bonus

Flexible Spending Accounts

Job summary

Axle, a bioscience and information technology company, is seeking a Bioinformatics Scientist to support HIV research within the NIAID DIR/IDSS. You will analyze genomic and clinical data, develop production pipelines, and contribute to scalable tools that empower NIH investigators.

You should have strong skills in sequencing analysis, scripting, and data interpretation, with 4+ years in bioinformatics. A bachelor’s degree is required; advanced degrees are preferred.

Qualifications

• Bachelor's degree in a related field; master's or PhD preferred.
• 4+ years of experience in bioinformatics and production pipelines.
• Expert-level proficiency in Python or R and at least one of C/C++, sh/bash.
• Experience with NGS data analyses (RNA-seq, WGS, ChIP-seq) and single-cell data.
• Ability to obtain a Public Trust clearance.

Responsibilities

• Provide bioinformatics analysis for HIV-related datasets.
• Develop and maintain high-throughput data pipelines.
• Offer programming support to disseminate research data.
• Collaborate with researchers and publication teams.
• Contribute to scalable resources for NIH investigators.

Skills

Statistical modeling

Scripting

Biological interpretation

Pipeline development

Collaboration

Education

Bachelor's degree in related field

Master's or PhD preferred

Tools

Docker

Nextflow

Snakemake

CWL/WDL

AWS / Cloud

Job description

(ID: 2026-3884) 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).

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)

Position Overview

The Bioinformatics Scientist will address the bioinformatics, scientific computing, and data analysis needs of investigators within the NIAID Division of Intramural Research (DIR) and their collaborators, as part of the Integrated Data Sciences Section (IDSS) within the Research Technologies Branch (RTB), with particular emphasis on HIV research. The incumbent will provide analysis support across genomic and clinical research data — including viral sequence, host-pathogen, and immunologic datasets generated by HIV studies — develop and maintain production pipelines, and contribute to a scalable resource supporting NIAID scientists. A substantial portion of the work will directly support HIV investigators and their laboratory and clinical research teams. The successful candidate will be highly motivated, adaptable, structured, and detail-oriented.

Key Responsibilities

• Scientific consultation. Address the bioinformatics, scientific computing, and data analysis needs of users within the NIAID Division of Intramural Research and their collaborators, providing expertise in the statistical design of biological experiments involving high-throughput genome-scale technologies, data mining and knowledge discovery techniques, automated workflow development, and experimental design consultation.
• Bioinformatics support. Provide support spanning 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, and ATAC‑seq, including development of high-throughput pipelines for these data modalities.
• Programming support. Provide programming and troubleshooting support to the Research Technologies Branch and collaborating Institutes in the dissemination of research data.
• Data analysis. Perform computational data analysis on genomic and clinical research data, and provide statistical support and analysis on research data.
• Collaboration. Work with staff on scientific programming and experimental design.
• Publication. Contribute to and co-author scientific publications in leading peer-reviewed journals.
• Resource development. Contribute to the development of a scalable and flexible resource providing next‑generation sequencing bioinformatics, structural and computational biology, and machine learning data support to NIAID scientists and investigators.

The Bioinformatics Scientist is expected to bring strong skills in the following areas:

• Next‑generation sequencing analysis (whole‑exome, whole‑genome, RNA‑seq, ChIP‑seq, using both long- and short-read technologies)
• Statistical modeling
• Scripting
• Biological interpretation

Required Qualifications

• Clearance. Ability to obtain and maintain a Public Trust security clearance.
• Education. Minimum of a bachelor's degree in a related field; master's degree or doctorate preferred.
• Experience. Four or more years of experience in bioinformatics, including two or more years developing and maintaining production bioinformatics pipelines.
• Programming languages. Expert-level proficiency in two of the following: Python, R, C/C++, sh/bash.
• Containerization. Experience building images using one of the following: Docker, Podman, Singularity/Apptainer.
• Pipeline frameworks. Expert-level proficiency in one pipeline framework: Snakemake, Nextflow, or CWL/WDL.
• Documentation. Demonstrated expertise building technical and user documentation for tools, pipelines, and applications.
• Infrastructure. Experience building pipelines on‑premises using available high‑performance computing infrastructure.

Preferred Qualifications

• Experience supporting HIV research, including the analysis of HIV sequence data — for example viral genome assembly, phylogenetic and quasi‑species analysis, drug‑resistance profiling, or characterization of the latent reservoir.
• Familiarity with HIV and infectious disease data resources and host‑pathogen study designs, including integration of viral sequence data with host genomic, transcriptomic, or immunologic datasets.
• Experience building pipelines or applications in the cloud using AWS, GCP, or Azure.
• Experience building applications using one of the following frameworks: Django, Flask, RShiny, Electron, Flutter, or React.
• Experience working in a laboratory setting.

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.The diversity of Axle's employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.Accessibility: If you need an accommodation as part of the employment process please contact:This role has a market-competitive salary with an anticipated base compensation range listed below. Actual salaries will vary depending on a candidate's experience, qualifications, skills, and location.Salary Range$105,000—$130,000 USD