Scientist II, Bioinformatics (Applications Lab)

Pacific Biosciences • Menlo Park, CA

6d • $112,000 - $168,000 • Hybrid

About The Position

PacBio is seeking a Scientist II, Bioinformatics to join its Applications Lab, an internal customer and services laboratory supporting product development, customer evaluations, and commercial opportunities. The role supports production and proof-of-concept sequencing projects by developing and maintaining computational infrastructure, automating data-processing workflows, and delivering high-quality bioinformatics analyses for internal and customer projects.

The Scientist II performs analyses of PacBio sequencing data and collaborates with laboratory scientists, Product Management, Marketing, and Sales to communicate results demonstrating PacBio technology. The role also maintains computational tools and infrastructure for laboratory operations, including sample and project tracking, data organization, and automated analysis workflows. It is a hands-on position requiring strong programming and scientific skills and the ability to independently troubleshoot complex technical problems.

Non-Field Based Employees are required to work onsite Monday through Thursday, with Friday work from home. Depending on the role, some employees may be required to work 100% onsite. The employee may also be required to visit and work at PacBio locations as necessary. The salary range is $112,000 to $168,000.

Requirements

• PhD in Bioinformatics, Computational Biology, Computer Science, Life Sciences, or a related field, plus 0–2 years of related experience (which may include postdoctoral experience); alternatively, a master's degree plus 3–5 years of relevant experience, or a bachelor's degree plus 5–7 years of related experience.
• Proficiency in Python programming, including data processing.
• Strong working knowledge of Linux, including command-line tools, shell scripting, and file-system organization.
• Experience with high-performance computing environments, including job schedulers, computational resource allocation, and pipeline execution.
• Familiarity with scientific development practices, including testing, version control, code review, workflow management frameworks, reproducible computational environments such as containers, and code documentation.
• Experience with next-generation sequencing data analysis and bioinformatics pipelines.
• Strong analytical, troubleshooting, and organizational skills, including the ability to independently solve technical problems and manage multiple priorities.
• Excellent written and verbal communication skills, including documenting workflows and explaining complex technical concepts to diverse audiences.
• Current authorization to work in the United States without the need for present or future sponsorship.

Nice To Haves

• Experience working in a sequencing facility, genomics core laboratory, or commercial sequencing service provider.
• Experience with laboratory operations, including sample tracking, metadata management, and project coordination.
• Experience analyzing PacBio HiFi or other long-read sequencing data.
• Experience with cloud-based data storage and analysis, particularly AWS.
• Experience with SQL and relational databases for managing and querying scientific data.
• Familiarity with AI agentic software development tools such as Claude Code or Codex.
• Experience in a customer-facing role.
• Experience communicating scientific results through conference presentations or peer-reviewed publications.

Responsibilities

• Collaborate with laboratory scientists to support sequencing projects, ensuring reliable data processing, execution of analyses, and timely delivery of results.
• Analyze PacBio sequencing data for internal projects, customer evaluations, and proof-of-concept studies; deliver results, visualizations, and summaries to scientific and commercial stakeholders.
• Maintain tools and computational infrastructure supporting laboratory operations, including sample and project tracking and data organization.
• Develop, maintain, and troubleshoot bioinformatics pipelines and automated workflows using Python, Linux, and high-performance computing environments, reducing manual intervention and improving processing reliability.
• Evaluate emerging bioinformatics methods and sequencing applications with academic and commercial collaborators.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: Ph.D. or professional degree