Bioinformatics Engineer

(ID: 2026-1586) 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)

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. #IND Apply tot his job Apply To this Job