Bioinformatics Engineer

Axle; Rockville (MD); On-site; USD 125,000 - 150,000; Full time

Benefits offered by this job

Paid Time Off and Paid Holidays

401K match up to 5%

Educational Benefits for Career Growth

Employee Referral Bonus

Flexible Spending Accounts (Healthcare, Parking, Dependent Care, Transportation)

Job summary

Axle is seeking a Bioinformatics Engineer to enhance and optimize bioinformatics workflows at the National Institutes of Health in Rockville, MD. This role demands expertise in genomics analysis and software engineering practices.

Responsibilities include developing Nextflow workflows for RNA-seq, optimizing data operations, and collaborating with experts across various disciplines. A competitive salary range of $125,000 – $150,000 is offered, along with a range of benefits.

Qualifications

• Master's or equivalent experience in bioinformatics, computational biology, computer science.
• 3+ years in developing and maintaining bioinformatics pipelines.
• Strong experience with RNA-seq and DNA sequencing analysis.

Responsibilities

• Evaluate and optimize bioinformatics workflows for high-throughput sequencing.
• Develop and maintain Nextflow workflows for RNA-seq and other assays.
• Architect scalable solutions on Google Cloud Platform.

Skills

Nextflow (DSL2)

RNA-seq analysis

DNA sequencing workflows

Python/R scripting

Google Cloud Platform

Containerization (Docker, Singularity)

Version control (Git)

Education

Master's degree in bioinformatics or related field

Tools

Google Cloud Platform services

Common bioinformatics tools (STAR, Salmon, BWA)

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 Bioinformatics Engineer to join our vibrant team at the National Institutes of Health (NIH) in Rockville, MD.

Benefits We Offer

• 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)

In this role, you will review, assess, optimize, integrate, and extend production‑grade bioinformatics workflows for high‑throughput sequencing analysis. The ideal candidate combines deep expertise in genomics analysis methods with strong software engineering practices and cloud computing experience.

Key Responsibilities

• Evaluate existing bioinformatics pipelines for performance, accuracy, and maintainability, identifying opportunities for optimization and enhancement.
• Develop, extend, and maintain Nextflow workflows for bulk RNA‑seq, single‑cell RNA‑seq, DNA variant calling, methylation analysis, and emerging assay types.
• Architect scalable solutions capable of processing thousands of samples efficiently on Google Cloud Platform.
• Optimize data input/output operations across pipeline modules to minimize bottlenecks and reduce computational costs.
• Prepare and structure analysis outputs for visualization platforms and downstream statistical or machine learning applications.
• Implement best practices for workflow versioning, containerization, testing, and documentation.
• Collaborate with computational biologists, data scientists, and software engineers to integrate pipelines into broader analytical ecosystems.
• Stay current with advances in sequencing technologies and analytical methods, evaluating and incorporating new tools as appropriate.

Required Qualifications

• Master's degree in bioinformatics, computational biology, computer science, or a related field (or equivalent experience).
• 3+ years of hands‑on experience developing and maintaining bioinformatics pipelines in a production environment.
• Proficiency with Nextflow (DSL2) and familiarity with workflow management concepts.
• Strong experience with RNA‑seq analysis (both bulk and single‑cell) and DNA sequencing workflows (variant calling, methylation).
• Working knowledge of Google Cloud Platform services (Compute Engine, Cloud Storage, Batch, Life Sciences API, or similar).
• Proficiency in Python and/or R for scripting, data manipulation, and tool development.
• Experience with containerization technologies (Docker, Singularity).
• Familiarity with version control systems (Git) and CI/CD practices.
• Strong understanding of genomic file formats (FASTQ, BAM, VCF, BED) and common bioinformatics tools (STAR, Salmon, BWA, GATK, Bismark, Cell Ranger, Seurat, Scanpy).

Preferred Qualifications

• PhD in a relevant field.
• Experience with nf‑core pipelines and community standards.
• Familiarity with workflow orchestration at scale (Cromwell, AWS Batch, or similar platforms).
• Experience optimizing cloud costs and resource utilization for large‑scale genomics workloads.
• Knowledge of data visualization tools and frameworks (e.g., R Shiny, Plotly, custom dashboards).
• Experience in pharmaceutical, biotech, or regulated research environments.
• Familiarity with FAIR data principles and metadata standards.

What We Offer

• Opportunity to work on cutting‑edge genomics projects with industry‑leading pharmaceutical partners.
• Collaborative environment with experts in bioinformatics, data science, and software engineering.
• Professional development and growth opportunities.
• Competitive salary and benefits package.

Salary Range: $125,000 – $150,000 USD.

Equal Employment Opportunity Statement

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.