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Bioinformatics Engineer Jobs in Gaithersburg, MD

Axle

Bioinformatics Engineer

Rockville, MD

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 ...

Axle

Bioinformatics Engineer

Rockville, MD · On-site

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 ...

Axle

Bioinformatics Engineer

Rockville, MD · On-site

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 ...

Axle

Bioinformatics Engineer

Rockville, MD · On-site

They are seeking a Bioinformatics Engineer to join their team supporting major pharmaceutical clients, focusing on optimizing and integrating bioinformatics workflows for high-throughput sequencing ...

Axle

Bioinformatics Scientist

Bethesda, MD · On-site

With experts in biomedical science, software engineering, and program management, we focus on ... Bioinformatics Scientist To be considered for this position, please upload a document as your Cover ...

Axle

Bioinformatics Scientist

Bethesda, MD

With experts in biomedical science, software engineering, and program management, we focus on ... Bioinformatics Scientist To be considered for this position, please upload a document as your Cover ...

Axle

Bioinformatics Scientist

Bethesda, MD

With experts in biomedical science, software engineering, and program management, we focus on ... Bioinformatics Scientist To be considered for this position, please upload a document as your Cover ...

Guidehouse

Bioinformatics Scientist

Bethesda, MD

$65K - $108K/yr

Provide programming and troubleshooting support to the Federal Government in the dissemination of ... Evaluate and adapt bioinformatics techniques based on scientific literature, available resources ...

Guidehouse

Bioinformatics Scientist

Bethesda, MD · On-site

$65K - $108K/yr

Provide programming and troubleshooting support to the Federal Government in the dissemination of ... Evaluate and adapt bioinformatics techniques based on scientific literature, available resources ...

Axle

Data Engineer

Rockville, MD

$116K - $140K/yr

Bachelor's degree in Computer Science, Data Science, Bioinformatics, Biomedical Informatics, Information Systems, Engineering, or a related field, or equivalent practical experience. Proven ...

Axle

Data Engineer

Rockville, MD · On-site

$116K - $140K/yr

Bachelor's degree in Computer Science, Data Science, Bioinformatics, Biomedical Informatics, Information Systems, Engineering, or a related field, or equivalent practical experience. Proven ...

Axle

Data Engineer

Rockville, MD

$116K - $140K/yr

Bachelor's degree in Computer Science, Data Science, Bioinformatics, Biomedical Informatics, Information Systems, Engineering, or a related field, or equivalent practical experience. Proven ...

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All JobsBioinformatics Engineer JobsBioinformatics Engineer Jobs in Gaithersburg, MD

Bioinformatics Engineer information

See Gaithersburg, MD salary details

$46.5K

$141.6K

$257.7K

How much do bioinformatics engineer jobs pay per year?

As of Aug 9, 2026, the average yearly pay for bioinformatics engineer in Gaithersburg, MD is $141,596.00, according to ZipRecruiter salary data. Most workers in this role earn between $103,700.00 and $169,600.00 per year, depending on experience, location, and employer.

What is a bioinformatics engineer?

A Bioinformatics Engineer is a professional who combines expertise in computer science, statistics, and biology to develop software tools and algorithms for analyzing biological data. They often work with large datasets such as genomic sequences, protein structures, and clinical information to help scientists make sense of complex biological systems. Their work is essential in fields like genomics, personalized medicine, and drug discovery, where managing and interpreting vast amounts of data is crucial. Bioinformatics Engineers may also collaborate with researchers to design experiments and interpret results, bridging the gap between biology and technology.

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

To thrive as a Bioinformatics Engineer, you need a strong background in biology, computer science, and statistics, often supported by a degree in bioinformatics or a related field. Experience with programming languages such as Python or R, familiarity with databases, and knowledge of tools like BLAST, Bioconductor, or next-generation sequencing (NGS) analysis platforms are typically required. Strong problem-solving, analytical thinking, and effective communication skills help you collaborate with interdisciplinary teams and convey complex findings. These skills and qualifications are essential for efficiently analyzing biological data, developing robust computational tools, and advancing research in genomics and life sciences.

What are some common challenges faced by bioinformatics engineers when integrating new data sources into existing pipelines?

Bioinformatics Engineers often encounter challenges such as data format inconsistencies, varying quality of datasets, and the need to ensure compatibility with existing analysis pipelines. Integrating new data sources may require custom scripts or tools for parsing and preprocessing, as well as thorough validation to maintain reproducibility and reliability of results. Collaboration with wet-lab scientists and software engineers is essential to clarify data requirements and streamline the integration process.

What is the difference between Bioinformatics Engineer vs Bioinformatics Analyst?

AspectBioinformatics EngineerBioinformatics Analyst
Required CredentialsBachelor's or Master's in Bioinformatics, Computer Science, or related fields; programming skillsBachelor's or Master's in Bioinformatics, Biology, or related fields; data analysis skills
Work EnvironmentResearch labs, biotech companies, pharmaceutical firmsResearch institutions, healthcare organizations, biotech companies
Employer & Industry UsageDevelops tools, pipelines, and software for biological data analysisInterprets data, performs statistical analysis, and reports findings

While both roles require a background in bioinformatics and involve working with biological data, Bioinformatics Engineers focus on developing software and tools, whereas Bioinformatics Analysts primarily analyze and interpret data to support research and decision-making.

More about Bioinformatics Engineer jobs
What are popular job titles related to Bioinformatics Engineer jobs in Gaithersburg, MD? For Bioinformatics Engineer jobs in Gaithersburg, MD, the most frequently searched job titles are:
What job categories do people searching Bioinformatics Engineer jobs in Gaithersburg, MD look for? The top searched job categories for Bioinformatics Engineer jobs in Gaithersburg, MD are:
What cities near Gaithersburg, MD are hiring for Bioinformatics Engineer jobs? Cities near Gaithersburg, MD with the most Bioinformatics Engineer job openings:
Bioinformatics Engineer jobs near you
Infographic showing various Bioinformatics Engineer job openings in Gaithersburg, MD as of July 2026, with employment types broken down into 95% Full Time, 2% Part Time, and 3% Contract. Highlights an 88% Physical, 4% Hybrid, and 8% Remote job distribution, with an average salary of $141,596 per year, or $68.1 per hour.

Bioinformatics Engineer

Axle

Rockville, MD

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 17 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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