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Bioinformatics Engineer Jobs in Boston, MA (NOW HIRING)

Watershed Informatics

Infrastructure Engineer

Cambridge, MA

$117K - $154K/yr

We have attracted some of the best bioinformatics, engineering, and commercial talent, and we are growing! Join a team that's intellectually curious with a bias for action, headquartered in Cambridge ...

Prime Medicine

Informatics Engineer

Cambridge, MA · On-site

Your engineering judgment about what to build and how to build it will shape how Prime Medicine works with scientific data day-to-day. What you'll do * Design and build the data platform connecting ...

Watershed Informatics

Site Reliability Engineer

Cambridge, MA · On-site

$62.25 - $82.75/hr

We have attracted some of the best bioinformatics, engineering, and commercial talent, and we are growing! Join a team that's intellectually curious with a bias for action, headquartered in Cambridge ...

Watershed Informatics

Site Reliability Engineer

Cambridge, MA · On-site

$62.25 - $82.75/hr

We have attracted some of the best bioinformatics, engineering, and commercial talent, and we are growing! Join a team that's intellectually curious with a bias for action, headquartered in Cambridge ...

Watershed Informatics

Software Engineer, UI

Boston, MA

$113K - $151K/yr

We have attracted some of the best bioinformatics, engineering, and commercial talent, and we are growing! Join a team that's intellectually curious with a bias for action, headquartered in Cambridge ...

micro1 AI

AI Training Specialist - Life Sciences

Lynn, MA · Remote

$90 - $120/hr

Familiarity with software tools, databases, and programming languages commonly used in bioinformatics (e.g., Python, R, RDKit, KNIME). * Strong scientific communication skills, with the ability to ...

Massgeneralbrigham

Bioinformatician I

Somerville, MA · On-site

$75K - $109K/yr

Qualifications Qualifications MS in Bioinformatics, Computer Science, or biological engineering; Applicants will have understanding programming with agile development methods SKILLS/ ABILITIES ...

Winaxis

Cloud Infrastructure/AI/ML Engineer

Boston, MA · On-site

$116K - $153K/yr

Cloud Infrastructure/AI/ML Engineer (Contract, 12+ months, Hybrid) - Location : Waltham, MA (Hybrid ... Must have strong experience in bioinformatics, including pipeline execution and workflow management ...

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All JobsBioinformatics Engineer JobsBioinformatics Engineer Jobs in Boston, MA

Bioinformatics Engineer information

See Boston, MA salary details

$46.7K

$142.4K

$259.1K

How much do bioinformatics engineer jobs pay per year?

As of Aug 18, 2026, the average yearly pay for bioinformatics engineer in Boston, MA is $142,374.00, 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 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.

What does a bioinformatics engineer do?

A bioinformatics engineer develops and applies computational tools and algorithms to analyze biological data, such as genetic sequences and molecular structures. They often work with programming languages like Python or R, utilize databases, and collaborate with biologists to interpret data for research or medical purposes.
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For Bioinformatics Engineer jobs in Boston, MA, the most frequently searched job titles are:

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Cities near Boston, MA with the most Bioinformatics Engineer job openings:

Bioinformatics Engineer jobs near you
Infographic showing various Bioinformatics Engineer job openings in Boston, MA as of August 2026, with employment types broken down into 90% Full Time, 5% Part Time, and 5% Contract. Highlights an 86% Physical, 6% Hybrid, and 8% Remote job distribution, with an average salary of $142,374 per year, or $68.4 per hour.

Infrastructure Engineer

Watershed Informatics

Cambridge, MA

$117K - $154K/yr

Full-time

Re-posted 2 days ago

Job description

About Watershed

Our vision is to become the leading biocomputing platform. The future of biology is in big data analysis, and we are on a mission to accelerate digital drug discovery with the Watershed platform. 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 commercial talent, and we are growing! Join a team that's intellectually curious with a bias for action, headquartered in Cambridge, Massachusetts, composed of people who have come together to enable outcomes while empowering the research of all those committed to changing lives - all while bringing transformational change to a $40 billion industry.

Role

Infrastructure Engineers at Watershed engineer infrastructure to meet the high-performance computing needs of modern biology. Designing systems that keep pace with the explosive growth in the kinds and size of biological data, you will work in a containerized environment where our biocomputing platform and analyses run at scale. You will be tasked with engineering a new cloud experience while enabling our technology evolution in a disciplined way.

Responsibilities
  • Build, manage, and deploy an enterprise infrastructure. 
  • Research new technologies and solutions, implement them or build better
  • Be the connection between systems and software
  • Monitor system performance and manage capacity.
  • Fix and analyze technical incidents, solve ad hoc technical problems.

Qualifications

  • Experience composing infrastructure-as-code for a modern environment
  • Demonstrate a software developer mindset, building tools when necessary
  • Knowledge of virtualization, networking, and Linux internals
  • Ability to clearly communicate your thoughts, ask the right questions, and defend your views
  • Responsibility and ownership over your domain

Apply