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Bioinformatics Engineer Jobs in California (NOW HIRING)

Predicine, Inc

Bioinformatics Scientist

Hayward, CA · On-site

$149K/yr

This position requires Master's degree or foreign equivalent in Biology, Biomedical Engineering, Bioinformatics, or a related field plus 3 years of experience in the job offered or an R&D related ...

GATC Health

Bioinformatics Analyst - CA

Irvine, CA · On-site

... in programming in scripting (Python or similar) and interpreted languages (R, etc). • ... and bioinformatics innovation. Company : GATC Health uses AI to speed drug discovery, predict ...

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Bioinformatics Engineer information

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$42.4K

$129.3K

$235.4K

How much do bioinformatics engineer jobs pay per year?

As of Aug 1, 2026, the average yearly pay for bioinformatics engineer in California is $129,337.00, according to ZipRecruiter salary data. Most workers in this role earn between $94,700.00 and $154,900.00 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, and why are they important?

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 Is Bioinformatics Engineering?

A bioinformatics engineer uses various methods for the analysis of complex biological data such as gene sequence and protein absorption. In this career, your job duties include performing detailed data analysis, developing data queries, and presenting your results back to the research team. The qualifications needed for a career as a bioinformatics engineer include a bachelor’s degree in engineering, statistics, computer science, or mathematics. Some employers prefer a master’s degree as well. You also need strong analytical skills and a good understanding of the biosciences.

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 the most commonly searched types of Bioinformatics Engineer jobs in California? The most popular types of Bioinformatics Engineer jobs in California are:
What are popular job titles related to Bioinformatics Engineer jobs in California? For Bioinformatics Engineer jobs in California, the most frequently searched job titles are:
What job categories do people searching Bioinformatics Engineer jobs in California look for? The top searched job categories for Bioinformatics Engineer jobs in California are:
What cities in California are hiring for Bioinformatics Engineer jobs? Cities in California with the most Bioinformatics Engineer job openings:
What are popular job titles related to Bioinformatics Engineer jobs in CA? For Bioinformatics Engineer jobs in CA, the most frequently searched job titles are:
Bioinformatics Engineer jobs near you
Infographic showing various Bioinformatics Engineer job openings in California as of July 2026, with employment types broken down into 7% Internship, 3% As Needed, 62% Full Time, 13% Part Time, 2% Contract, and 13% Nights. Highlights an 79% Physical, 3% Hybrid, and 18% Remote job distribution, with an average salary of $129,337 per year, or $62.2 per hour.

Software Engineer - Bioinformatics /NGS Sequencing Systems

APN Software Services Inc

South San Francisco, CA • On-site

Contractor

Re-posted 23 days ago

Job description

Job title: Bioinformatics Software Engineer – NGS Sequencing Systems
Duration: till end of year

Location: South SFO, CA

Position Summary
We are seeking a highly motivated Bioinformatics Software Engineer to support software systems and data workflows within a Next Generation Sequencing (NGS) laboratory environment. The successful candidate will develop, maintain, and support applications and pipelines used for sequencing data processing, laboratory workflow management, and data analysis.
This role requires a strong background in software development, database management, and workflow automation, with experience supporting scientific data systems. The candidate will collaborate closely with bioinformaticians, scientists, and laboratory staff to ensure reliable data processing and scalable analysis pipelines.
Experience with NGS sequencing workflows and bioinformatics tools is highly desirable, but not required.
Key Responsibilities
Software Development
● Design, develop, test, and maintain Java and Java EE web applications used to support sequencing lab workflows and laboratory data systems.
● Develop software tools to support sequencing data processing, data tracking, and laboratory operations.
● Participate in software design discussions and contribute to scalable and maintainable system architecture.
Workflow & Pipeline Development
● Develop and maintain bioinformatics pipelines for processing NGS data.
● Implement workflow automation using WDL (Workflow Description Language).
● Manage and support workflow execution through the Cromwell workflow engine.
● Optimize pipeline performance and ensure efficient processing of large sequencing datasets.
Database & Data Management
● Develop and execute SQL and PL/SQL queries to support data retrieval, transformation, and system integration.
● Support Oracle database systems, including writing queries, performing updates, and maintaining database integrity.
● Ensure reliable data storage, accessibility, and traceability across sequencing workflows.
Data Processing & Automation
● Develop and maintain Python and Bash scripts to automate data processing, analysis workflows, and system integration tasks.
● Implement data validation and quality checks to ensure accuracy and consistency of sequencing data.
Systems Integration
● Integrate laboratory information systems such as LIMS with sequencing platforms and downstream analysis pipelines.
● Support data flow between laboratory instruments, analysis systems, and databases.
Infrastructure & Deployment
● Support deployment and execution of pipelines in High Performance Computing (HPC) environments.
● Assist with cloud-based workflow deployment using AWS services.
● Build and maintain containerized software environments (e.g., Docker) to ensure reproducibility of computational workflows.
Troubleshooting & Support
● Monitor and troubleshoot pipeline execution issues and system performance problems.
● Identify and resolve bottlenecks in data processing pipelines.
● Provide technical support to scientists and lab personnel using the software systems.
Collaboration
● Work closely with bioinformaticians, data scientists, software engineers, and laboratory staff to understand workflow requirements.
● Translate scientific and operational needs into scalable software solutions.
● Participate in cross-functional discussions to improve sequencing workflow efficiency.
Documentation & Best Practices
● Maintain clear documentation of pipelines, applications, and database structures.
● Use Git repositories and version control best practices to manage software development.
● Support testing, validation, and continuous improvement of systems.
Required Qualifications
● Bachelor’s or Master’s degree in Computer Science, Bioinformatics, Computational Biology, Software Engineering, or related field w/ MIN 3 years exp
● Strong experience with Oracle databases.
● Proficiency in SQL and PL/SQL.
● Experience with Java and Java EE web application development.
● Strong programming skills in Python.
● Experience with Bash scripting.
● Experience developing or supporting workflow pipelines using WDL.
● Familiarity with the Cromwell execution framework.
● Experience working with data processing pipelines or scientific data systems.
Preferred Qualifications
● Experience working in NGS sequencing or genomics environments.
● Familiarity with bioinformatics data processing workflows.
● Experience working in HPC computing environments.
● Experience with AWS cloud services.
● Experience with container technologies (Docker, Singularity, etc.).
● Experience using Git version control systems.
● Experience supporting LIMS systems or laboratory data platforms.
Skills & Competencies
● Strong problem-solving and troubleshooting skills.
● Ability to work independently in a fast-paced research environment.
● Strong communication skills and ability to collaborate with scientific teams.
● Ability to manage multiple priorities and support complex data workflows.
Interview process: 1. phone (15-20mins) 2. In-person (1 hr)
Hybrid- 2-3 days onsite
Function: gRED


APN Software services Inc. is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran or disability status.”