Bioinformatics Engineer

Axle • Rockville, MD

3h • $125,000 - $150,000 • Onsite

About The Position

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.

Requirements

• 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)

Nice To Haves

• 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

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

Benefits

• 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)

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level