Bioinformatics Engineer Jobs

As a Bioinformatics Engineer, you will play a crucial role in the field of genomics and biotechnology. You will analyze large datasets to extract meaningful biological insights, leverage computational tools and algorithms to study genetic variations, and contribute to groundbreaking research in the field of medicine. The job market for Bioinformatics Engineers is rapidly growing, with ample opportunities in pharmaceutical companies, research institutions, and government agencies. The average annual salary for Bioinformatics Engineers is around $90,000 to $120,000, depending on experience and location. Key skills and tools needed for this role include proficiency in Python, R, machine learning, and statistical analysis. With a focus on precision medicine and personalized healthcare, Bioinformatics Engineers are at the forefront of revolutionizing the healthcare industry. Embrace the exciting challenges and rewarding opportunities in this dynamic field!

About this role

(ID: 2026-2391)

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) supporting the Rockville, MD.

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)

Axle is seeking a skilled Bioinformatics Engineer to join our team supporting major pharmaceutical clients. 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

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: [email protected]

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

$125,000—$150,000 USD

About Axle

Boost your fitness studio and stay engaged with existing clients. Our suite of products is designed to elevate your brand, increase your operational efficiency,

Team

Richard Geisler

Nolen Young