Systems Engineer II

Job Title: Systems Engineer II
Location: Santa Clara, CA 95050 (Onsite)
Duration: 12 Months with strong possibility of extension
Job Description:
The Sequencing team is seeking a passionate Systems Engineer II to join the Systems Integration Group supporting Next Generation Sequencing (NGS) products. This is a hands-on role in which the Systems Engineer II will contribute to feasibility, development, and integration activities for end-to-end NGS solutions.
As a member of the Systems Integration team, this individual will work with a Single Molecule Sequencing platform to optimize operating protocols, design and perform wet-lab experiments, support integration of system subcomponents, and help improve the overall sequencing solution.
Key Responsibilities

• Design, execute, analyze, and document experiments to support feasibility, development, integration, verification, and validation of NGS workflows.
• Perform sample preparation, library preparation, sequencing-related experiments, and verification studies.
• Use the Single Molecule Sequencing platform to optimize final operating protocols and support system-level integration activities.
• Interpret experimental results using appropriate experimental design and statistical analysis methods.
• Troubleshoot instrument, workflow, or assay-related failures using standard root cause analysis methods.
• Collaborate with subject matter experts to understand failure modes and identify appropriate solutions.
• Develop, execute, and document test cases based on product requirements for verification and validation activities.
• Maintain accurate, well-organized, and concise laboratory records using best laboratory practices.
• Work cross-functionally with assay, instrumentation, software, bioinformatics, and systems teams to resolve integration challenges.
• Support continuous improvement of sequencing performance, including coverage, throughput, robustness, reproducibility, and overall system reliability.

Required Qualifications

• Bachelor's degree in chemistry, science, engineering, or a related field with 5 years of relevant experience, or a Master's degree in a related field with 1-3+ years of relevant experience.
• Demonstrated hands-on experience with PCR, DNA sequencing methods, raw sample preparation, nucleic acid extraction, library preparation, and/or NGS sequencing.
• At least 2 years of experience using MATLAB, Git, Python, or similar tools for data analysis and/or automation.
• Experience with statistical tools and methods, such as Python, JMP, regression analysis, and ANOVA.
• At least 2 years of experience with Design of Experiments methodology and application of statistical process control.
• Demonstrated ability to troubleshoot technical issues and identify root causes in laboratory, instrument, or workflow settings.
• Strong documentation skills and commitment to following best laboratory practices.

Preferred Qualifications

• Proven track record of performing in a fast-paced, matrixed environment.
• Ability to work independently while collaborating effectively across functions.
• Demonstrated ability to influence technical decisions and stakeholders without direct authority.
• Experience solving unique, ambiguous, or unpredictable problems that may impact project or organizational goals.
• Strong planning, prioritization, multitasking, and follow-through skills.
• Highly energetic, focused, and adaptable working style.
• Strong interpersonal, verbal communication, and relationship-building skills.
• Demonstrated ability to build and maintain effective relationships with key stakeholders.