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Bioinformatics Software Engineer Jobs in Boston, MA

Mass General Brigham

Bioinformatician I

Somerville, MA · On-site

$75K - $109K/yr

... tools and software analysis pipelines including secure dissemination of information generated. Qualifications Qualifications MS in Bioinformatics, Computer Science, or biological engineering;

Massgeneralbrigham

Bioinformatician I

Somerville, MA · On-site

$75K - $109K/yr

... tools and software analysis pipelines including secure dissemination of information generated. Qualifications Qualifications MS in Bioinformatics, Computer Science, or biological engineering;

Watershed Informatics

Infrastructure Engineer

Cambridge, MA · On-site

$117K - $154K/yr

Watershed enables scientists to conduct all essential analysis - from lab data to plot - with a single software platform. We have attracted some of the best bioinformatics, engineering, and ...

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All JobsBioinformatics Software Engineer JobsBioinformatics Software Engineer Jobs in Boston, MA

Bioinformatics Software Engineer information

See Boston, MA salary details

$46.7K

$142.4K

$259.1K

How much do bioinformatics software engineer jobs pay per year?

As of Jun 27, 2026, the average yearly pay for bioinformatics software engineer in Boston, MA is $142,369.00, according to ZipRecruiter salary data. Most workers in this role earn between $104,300.00 and $170,600.00 per year, depending on experience, location, and employer.

What is a Bioinformatics Software Engineer job?

A Bioinformatics Software Engineer develops and maintains software tools, algorithms, and databases for analyzing biological data, such as genomic sequences and protein structures. They work at the intersection of computer science and biology, using programming languages like Python, Java, or R to process and interpret large-scale biological datasets. Their role is crucial in fields like genomics, drug discovery, and personalized medicine, where computational solutions help researchers derive meaningful insights from complex biological information.

What are the typical daily responsibilities of a Bioinformatics Software Engineer?

As a Bioinformatics Software Engineer, your day-to-day responsibilities typically include designing, developing, and maintaining software tools or pipelines for analyzing biological data such as DNA, RNA, or protein sequences. You may collaborate closely with researchers and scientists to understand biological problems and translate them into computational solutions, reviewing and optimizing code for efficiency and scalability. Troubleshooting data processing issues, integrating new algorithms, and contributing to documentation are also common tasks. Additionally, you might participate in cross-functional meetings and keep up with emerging technologies and trends in the field.

What are the key skills and qualifications needed to thrive in the Bioinformatics Software Engineer position, and why are they important?

To thrive as a Bioinformatics Software Engineer, you need a strong background in software development (especially with Python, R, or C++), algorithm design, and biological data analysis, usually supported by a degree in bioinformatics, computer science, or a related field. Familiarity with bioinformatics tools, databases (like NCBI or Ensembl), version control systems (such as Git), and experience with cloud computing or high-performance computing environments is highly valued. Strong problem-solving skills, attention to detail, and the ability to collaborate effectively with biologists and data scientists set candidates apart. These competencies are crucial for efficiently developing reliable software solutions that support complex biological research and data-driven discoveries.

What are the most commonly searched types of Bioinformatics Software Engineer jobs in Boston, MA? The most popular types of Bioinformatics Software Engineer jobs in Boston, MA are:
What are popular job titles related to Bioinformatics Software Engineer jobs in Boston, MA? For Bioinformatics Software Engineer jobs in Boston, MA, the most frequently searched job titles are:
What job categories do people searching Bioinformatics Software Engineer jobs in Boston, MA look for? The top searched job categories for Bioinformatics Software Engineer jobs in Boston, MA are:
Bioinformatics Software Engineer jobs near you
Infographic showing various Bioinformatics Software Engineer job openings in Boston, MA as of June 2026, with employment types broken down into 50% Full Time, 25% Part Time, and 25% Contract. Highlights an 89% Physical, 4% Hybrid, and 7% Remote job distribution, with an average salary of $142,369 per year, or $68.4 per hour.
Software Engineer

Software Engineer

MIT Lincoln Laboratory

Lexington, MA

Other

Medical, Dental, Vision, Retirement, PTO

Posted 19 days ago

Job description

The Bioanalytics Systems & Technologies Group focuses on driving analytic and Al/ML solutions that leverage the vast and rapidly expanding biological datasets to address national security needs. The Group's efforts include developing software architectures and systems, bioinformatics tools, and AI algorithms to further the nation's efforts in biomedical, health, chemical and biological defense, biosecurity, public and global health and warfighter performance.

Job Description

The BioAnalytics Systems and Technologies Group is in search of an innovative and highly motivated software engineer to support several projects within our group, including development of software to support harmonization of medical and health data, web-based app development, modeling and simulation, and data streaming applications.               

This is an onsite position. 

Requirements
  • Master's degree in Computer Science or related discipline. In lieu of a master's degree, a bachelor's degree with 3 to 5 years of experience
  • Software Design and Development Life-cycle knowledge.
  • Strong proficiency in Python and related frameworks
  • Proficiency with relational databases (PostgreSQL, MySQL) and SQL
  • Understanding of software development lifecycle and agile methodologies
  • Strong problem-solving skills and attention to detail
  • Excellent written and verbal communication skills
  • Good interpersonal skills and ability to work collaboratively with a team

Desired Requirements:

  • Experience in AI/ML or data science a plus
  • Experience with biological and medical data a plus

Recent Graduate Hiring Range:$116,400 - $140,000 

Experienced Hiring Range: $116,400 - $182,200 

Disclaimer: MIT Lincoln Laboratory provides a typical hiring range as a good faith estimate of what we reasonably expect to offer for this position at the time of posting. The final salary offered to a selected candidate will depend on various factors, including-but not limited to-the scope and responsibilities of the role, the candidate's experience, skills and education/training, internal equity considerations and applicable legal requirements. This range reflects base salary only and does not include additional forms of compensation or benefits. 

At MIT Lincoln Laboratory, our exceptional career opportunities include many outstanding benefits to help you stay healthy, feel supported, and enjoy a fulfilling work-life balance. Benefits offered to employees include: 

  • Comprehensive health, dental, and vision plans 

  • MIT-funded pension 

  • Matching 401K 

  • Paid leave (including vacation, sick, parental, military, etc.) 

  • Tuition reimbursement and continuing education programs 

  • Mentorship programs 

  • A range of work-life balance options 

  • ... and much more! 

Please visit our Benefits page for more information. As an employee of MIT, you can also take advantage ofother voluntary benefits, discounts and perks. 

Selected candidate will be subject to a pre-employment background investigation and must be able to obtain and maintain a Secret level DoD security clearance. 

MIT Lincoln Laboratory is an Equal Employment Opportunity (EEO) employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, veteran status, disability status, or genetic information; U.S. citizenship is required. 

Requisition ID: 42291 

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