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Biotech Software Engineer Jobs in Washington, DC

Axle

Bioinformatics Engineer

Rockville, MD · On-site

With experts in biomedical science, software engineering, and program management, we focus on ... Experience in pharmaceutical, biotech, or regulated research environments * Familiarity with FAIR ...

Black Canyon Consulting

Engineering Team Leader

Bethesda, MD · On-site

$109K - $144K/yr

... Biotechnology Information (NCBI) at the National Library of Medicine (NLM), an institute of the ... The TPM reports to the IEB Software Development Section Head. The position is essential to ensuring ...

Black Canyon Consulting

Engineering Team Leader

Bethesda, MD · On-site +1

$109K - $144K/yr

... Biotechnology Information (NCBI) at the National Library of Medicine (NLM), an institute of the ... The TPM reports to the IEB Software Development Section Head. The position is essential to ensuring ...

Black Canyon Consulting

Platform DevEx Engineer

Bethesda, MD · On-site +1

$56.50 - $77.25/hr

... Biotechnology Information (NCBI) at the National Library of Medicine (NLM), an institute of the ... The Platform Services team builds and maintains the systems that software developers across NCBI ...

Black Canyon Consulting

Platform DevEx Engineer

Bethesda, MD · On-site

$56.50 - $77.25/hr

... Biotechnology Information (NCBI) at the National Library of Medicine (NLM), an institute of the ... The Platform Services team builds and maintains the systems that software developers across NCBI ...

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All JobsBiotech Software Engineer JobsBiotech Software Engineer Jobs in Washington, DC

Biotech Software Engineer information

See Washington, DC salary details

$72.5K

$168.3K

$234.5K

How much do biotech software engineer jobs pay per year?

As of Aug 13, 2026, the average yearly pay for biotech software engineer in Washington, DC is $168,345.00, according to ZipRecruiter salary data. Most workers in this role earn between $136,900.00 and $197,400.00 per year, depending on experience, location, and employer.

What are the key skills and qualifications needed to thrive as a biotech software engineer?

To thrive as a Biotech Software Engineer, you need a solid background in computer science or software engineering, coupled with an understanding of biology, genetics, or related life sciences. Familiarity with programming languages such as Python or Java, experience using bioinformatics tools (like BLAST or Bioconductor), and, in some settings, knowledge of regulatory standards are highly valuable. Strong problem-solving abilities, effective communication, and the ability to work well in interdisciplinary teams distinguish top performers in this field. These skills are crucial for building reliable software solutions that support scientific discovery and innovation in biotechnology organizations.

What does a biotech software engineer do?

As a Biotech Software Engineer, you'll often develop and maintain software tools for analyzing biological data, automate laboratory workflows, or create user-friendly interfaces for scientific researchers. Your daily tasks might include writing code, troubleshooting algorithms, reviewing scientific data, and collaborating closely with biologists, data scientists, and laboratory technicians. Depending on the company, you may be involved in developing cloud-based platforms, integrating new laboratory hardware, or ensuring software compliance with industry regulations. This dynamic and collaborative environment means your work directly impacts ongoing research and helps accelerate scientific discoveries in the biotech sector.

What is a biotech software engineer?

A Biotech Software Engineer develops software solutions for the biotechnology industry, enabling research, data analysis, and automation in fields like genomics, bioinformatics, and drug discovery. They work with scientists to design algorithms, manage biological data, and create applications that support experiments and workflows. This role requires expertise in programming, cloud computing, and biological sciences to bridge the gap between technology and life sciences.

What are the most commonly searched types of Biotech Software Engineer jobs in Washington, DC?

The most popular types of Biotech Software Engineer jobs in Washington, DC are:

What are popular job titles related to Biotech Software Engineer jobs in Washington, DC?

For Biotech Software Engineer jobs in Washington, DC, the most frequently searched job titles are:

What job categories do people searching Biotech Software Engineer jobs in Washington, DC look for?

The top searched job categories for Biotech Software Engineer jobs in Washington, DC are:

Biotech Software Engineer jobs near you
Infographic showing various Biotech Software Engineer job openings in Washington, DC as of August 2026, with employment types broken down into 94% Full Time, and 6% Part Time. Highlights an 88% In-person, 6% Hybrid, and 6% Remote job distribution, with an average salary of $168,345 per year, or $80.9 per hour.

Bioinformatics Engineer

Axle

Rockville, MD • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 22 days ago

Job description

(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: careers@axleinfo.com


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.

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