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Bioinformatic Data Engineer Jobs (NOW HIRING)

Caris MPI, Inc.

Scientist - Bioinformatics

Phoenix, AZ · On-site

Knowledge and analytic skills managing bioinformatics data including FASTQ, BAM, and VCF.Programming experience with Python, bash, SQL, GIT.Experience with AWS services (e.g., Lambda, Step Functions ...

Ambry Genetics

Bioinformatics Engineer II

$90K - $140K/yr

Act as a role model for the team, settings standards for excellence and mentoring junior engineers ... Knowledge of next-generation sequencing technologies and standard bioinformatics data formats (e.g ...

Earli, Inc.

Senior Scientist, Bio AI

Redwood City, CA · On-site

$205K - $235K/yr

Leverage cutting-edge ML, bioinformatics, and high-throughput assay data to design cancer-specific ... GCP) with appropriate engineering adaptations as needed. Help develop and work within budgets for ...

Flagship Pioneering, Inc.

Lead Data Engineer

Cambridge, MA

$112K - $147K/yr

Collaborate across I&O, Lab IT, PI Tech, data science, and bioinformatics teams to ensure ... Mentor junior engineers and establish engineering standards that drive excellence, reproducibility ...

Flagship Pioneering, Inc.

Lead Data Engineer

Cambridge, MA · On-site

$112K - $147K/yr

Collaborate across I&O, Lab IT, PI Tech, data science, and bioinformatics teams to ensure ... Mentor junior engineers and establish engineering standards that drive excellence, reproducibility ...

ROSALIND

Bioinformatics Engineer

San Diego, CA · On-site

... data • Experience with building / supporting / using bioinformatic pipelines • Work collaboratively with other bioinformatics and research scientists and engineers for various projects as ...

Tempus

Bioinformatics Engineer II

$90K - $140K/yr

Act as a role model for the team, settings standards for excellence and mentoring junior engineers ... Knowledge of next-generation sequencing technologies and standard bioinformatics data formats (e.g ...

Aequor

Skills: • Programming experience with Python and R for bioinformatic data analysis in unix-like systems. • Proficiency in working with bulk and single cell NGS data • Experience with any of ...

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Bioinformatic Data Engineer information

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$44.5K

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$177.5K

How much do bioinformatic data engineer jobs pay per year?

As of Sep 10, 2026, the average yearly pay for bioinformatic data engineer in the United States is $129,716.00, according to ZipRecruiter salary data. Most workers in this role earn between $114,500.00 and $137,500.00 per year, depending on experience, location, and employer.

What is a bioinformatic data engineer?

Bioinformatic Data Engineers are professionals who design, build, and maintain data pipelines and infrastructure for storing, processing, and analyzing large-scale biological and genomic data. They work at the intersection of biology, computer science, and data engineering to ensure that complex datasets from experiments, sequencing platforms, or clinical studies can be efficiently managed and analyzed. Their responsibilities often include developing software tools, optimizing data workflows, and collaborating with bioinformaticians and researchers to enable scientific discovery. This role requires expertise in programming, database systems, and understanding of biological data formats and standards.

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

To thrive as a Bioinformatic Data Engineer, you need strong programming skills (such as Python, R, or Java), a solid background in computational biology, and experience with large-scale data analysis, typically supported by a degree in bioinformatics, computer science, or a related field. Familiarity with bioinformatics tools, pipeline development, cloud platforms, and data management systems is commonly required, and certifications in cloud technologies or data engineering are advantageous. Strong problem-solving, critical thinking, and collaboration skills help bridge the gap between biological research and data infrastructure needs. These competencies ensure accurate analysis, scalable solutions, and effective communication within multidisciplinary teams, driving scientific discovery and innovation.

What are some common challenges faced by bioinformatic data engineers when integrating diverse biological datasets?

Bioinformatic Data Engineers often encounter challenges when integrating datasets from various sources due to differences in data formats, quality, and annotation standards. Ensuring data compatibility and consistency requires a strong understanding of both computational methods and biological context. Additionally, they must address issues like missing values, large-scale data storage, and efficient data retrieval to support downstream analyses. Collaboration with biologists, software engineers, and data scientists is key to successfully overcoming these challenges and delivering valuable insights.

What is the difference between Bioinformatic Data Engineer vs Bioinformatics Analyst?

AspectBioinformatic Data 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 EnvironmentData pipelines, database management, software development in research or biotech companiesData analysis, interpretation, and reporting in research labs or healthcare settings
Employer & Industry UsageTech-driven biotech firms, research institutions, pharma companiesAcademic institutions, healthcare providers, research organizations

While both roles require a background in bioinformatics and data handling, the Bioinformatic Data Engineer focuses on building and maintaining data infrastructure and pipelines, whereas the Bioinformatics Analyst emphasizes analyzing and interpreting biological data to generate insights.

What cities are hiring for Bioinformatic Data Engineer jobs?

Cities with the most Bioinformatic Data Engineer job openings:

What states have the most Bioinformatic Data Engineer jobs?

States with the most job openings for Bioinformatic Data Engineer jobs include:

What are popular job titles related to Bioinformatic Data Engineer jobs?

For Bioinformatic Data Engineer jobs, the most frequently searched job titles are:

Scientific Data Engineer

Berkeley, CA • On-site

Lawrence Berkeley National Laboratory
5 - 10K employees
Learn more about Lawrence Berkeley National Laboratoryexternal

$140K - $168K/yr

Full-time

Medical, Retirement, PTO

Posted 18 days ago

Lawrence Berkeley National Laboratory rating

9.5

Company rating: 9.5 out of 10

Based on 5 frontline employees who took The Breakroom Quiz

Job description

Lawrence Berkeley National Laboratory is hiring a Scientific Data Engineer within the Scientific Data Division.
The Computational Biosciences Group has an immediate opening for a software and data engineer in the area of multi-modal data modeling and analysis with applications to bioscience research. You will develop new methods and software tools that enable scientific knowledge discovery using modern data management and machine learning technologies and advance the state-of-the-art in data-intensive analysis. Your projects will focus on the domains of omics/structural biology data and neurophysiology data. Under limited instruction, you will be part of an experienced team conducting R&D in the areas of FAIR data science, AI, and modern methods for data understanding. You will be working as part of a multi-disciplinary team composed of computer scientists, data scientists, and bioinformaticians. Please note this is a scientific software/data engineering position- it is not a pure machine learning or AI research position, and it is not a pure data science or analytics position.
You will:
  • Design and develop user-friendly software packages for scientific data management and analysis
  • Work with domain experts to develop FAIR data models (i.e., models of the structure organization of the data) and management solutions for bioscience applications
  • Support machine learning and AI use of biological data by making it well-structured, documented, and efficiently accessible
  • Work closely with the community of developers of the Neurodata Without Borders and LinkML open source data ecosystems, as well as the Joint Genome Institute.
  • Maintain and manage open source software products, including managing development priorities, software releases, continuous integration, and testing
  • Design, implement and maintain high performance computing and cloud solutions for visualization and analysis of complex biological data
  • Develop machine learning and AI solutions for analysis of biological data in close collaboration with diverse teams of scientists
  • Train scientists and research software engineers in the use of the developed software products at workshops and conferences
  • Demonstrate good judgment in selecting methods and techniques for obtaining solutions.
  • Network with senior internal and external personnel in their own area of expertise.

We are looking for:
  • Typically requires a minimum of 5 years of related experience with a Bachelor's degree in computer science, data science, machine learning, bioinformatics, or equivalent; or 3 years and a Master's degree; or equivalent work experience designing and developing software for data modeling or analysis; or a PhD in a relevant STEM field
  • Demonstrated experience developing software in a scientific or research context, such as in a research group, a scientific user facility, or on a scientific software project
  • Demonstrated hands-on experience in a production environment, developing scientific software, scientific data models, or scientific data pipelines
  • Strong programming experience in Python. Working proficiency in C++ or Javascript is a plus.
  • Experience testing large code bases
  • Experience contributing to community-driven open source software
  • Demonstrated experience in one or more of the following areas: data management, scientific data analysis, machine learning
  • Works well in a collaborative team environment
  • Demonstrated capability with the Git version control and continuous integration systems, such as GitHub or GitLab
  • Ability to work effectively with domain scientists whose expertise is outside computing, and to translate their requirements into technical designs.
  • Excellent oral and written communication skills.
  • Demonstrated ability to work effectively as part of a cross-disciplinary team.

Desired skills/knowledge:
  • Master's or PhD in Computer Science or related field, with 5 or more years of professional experience designing and developing scientific data modeling or analysis software
  • Experience working with modern scientific data formats and database systems, such as HDF5, Zarr, MongoDB, PostgreSQL, MySQL, and Redis
  • Experience with Neurodata Without Borders, LinkML, or similar software ecosystems
  • Experience working with large biological data, such as in the areas of neurophysiology, microbiology, genomics, or protein design
  • Experience designing or working with structured data models, schemas, ontologies, or data standards
  • Familiarity with FAIR data principles, persistent identifiers, provenance, and controlled vocabularies and ontologies
  • Experience preparing scientific datasets for use by machine learning pipelines or LLM-based agents
  • Experience working with cloud object storage, cloud computing, High-Performance Computing, data lakehouse architecture, or containerization.
  • Experience developing web-based graphical user interfaces (GUIs) or application programming interfaces (APIs) for scientific data analysis and management

How to apply:
In addition to your resume, please include a brief cover letter (max 300 words) that describes one scientific software project you have contributed to, or one scientific data model, schema, standard, or pipeline you have helped design or implement. Describe your specific role and what the technical challenge was. Thesis, internship, research lab, and personal projects count. If the code is public, include a link.
We're here for the same mission, to bring science solutions to the world. Join our team and YOU will play a supporting role in our goal to address global challenges! Have a high level of impact and work for an organization associated with 17 Nobel Prizes!
Why join Berkeley Lab?
We invest in our employees by offering a total rewards package you can count on:
  • Exceptional health and retirement benefits, including pension or 401K-style plans
  • A culture where you'll belong - we are invested in our teams!
  • In addition to accruing vacation and sick time, we also have a Winter Holiday Shutdown every year.
  • Parental bonding leave (for both mothers and fathers)
  • Pet insurance

Additional information:
  • Appointment type: This is a full-time, 2 years, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
  • Salary range: The expected salary for this position is $131,760 - $161,064, which fits into the full salary of $117,132 - $197,676 depending upon the candidate's skills, knowledge, and abilities. This includes education, certifications, and years of experience.
  • Background check: This position is subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
  • Work modality: Work may be performed on-site, or hybrid. The primary location for this role is Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA. Work must be performed within the United States. A REAL ID or other acceptable form of identification is required to access Berkeley Lab sites (for more information click here).

Want to learn more about working at Berkeley Lab? Please visit: careers.lbl.gov
Equal Employment Opportunity Employer: The foundation of Berkeley Lab is our Stewardship Values: Team Science, Service, Trust, Innovation, and Respect; and we strive to build community with these shared values and commitments. Berkeley Lab is an Equal Opportunity Employer. We heartily welcome applications from all who could contribute to the Lab's mission of leading scientific discovery, excellence, and professionalism. In support of our rich global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories under State and Federal law.
Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts an offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; or have filed an appeal of a finding of substantiated misconduct with a previous employer. For additional information, click here.

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