Automation Engineer

Yoh is seeking a Laboratory Automation Engineer – NGS & Molecular Diagnostics to support a client in the South Bay Area, CA. This is a hands‑on technical opportunity focused on developing, implementing, and optimizing automated laboratory workflows for cell‑free DNA (cfDNA), low‑input DNA, and next‑generation sequencing applications.

The successful candidate will combine strong robotic liquid‑handler programming skills with practical molecular biology and NGS experience. You will translate complex laboratory protocols into reliable automated methods, integrate laboratory instruments and software, troubleshoot workflow performance, and help establish scalable automation processes suitable for molecular diagnostic development.

This role is well suited for an automation specialist who can independently own projects from early method development through qualification, documentation, and transfer into routine laboratory operations.

Department: Assay Development / Research & Development

Location: Sunnyvale, CA

Salary: $103,000-$165,000 (DOE)

Employment Type: Full‑time

Responsibilities:

Development

• Evaluate, configure, and implement laboratory automation platforms such as Hamilton Microlab STAR, Agilent Bravo, Beckman Coulter Biomek , or comparable liquid‑handling systems.
• Assess automation platform capabilities against assay requirements, throughput needs, workflow complexity, and future scalability.
• Design robotic deck layouts, labware configurations, liquid classes, transfer parameters, and integrated workflows.
• Coordinate instrument setup, commissioning, vendor support, and operational readiness.
• Develop automation strategies that improve throughput, reproducibility, reagent utilization, and hands‑on time.

Robotic Programming and Instrument Integration

• Independently develop, debug, optimize, and maintain custom robotic methods using software such as Hamilton VENUS, Agilent VWorks, Beckman Biomek software , or equivalent programming environments.
• Translate manual molecular biology protocols into reliable and executable automated workflows.
• Develop custom routines for liquid transfers, reagent dispensing, magnetic‑bead handling, incubation, thermal cycling, plate movement, and workflow‑control logic.
• Implement barcode‑based sample identification, reagent tracking, operator alerts, error detection, and safe recovery procedures.
• Integrate liquid handlers with supporting laboratory systems, including thermal cyclers, plate readers, barcode scanners, and laboratory information management systems.
• Maintain version‑controlled scripts, technical documentation, method specifications, and change histories.
• Work with equipment vendors and internal technical teams to resolve complex automation, programming, and integration issues.

cfDNA and NGS Workflow Automation

• Automate and optimize cfDNA, low‑input DNA, and NGS library‑preparation workflows.
• Develop automated methods for processes such as magnetic‑bead purification, DNA cleanup, end repair, adapter ligation, unique molecular identifier incorporation, amplification, target enrichment, and library normalization, as applicable.
• Optimize liquid handling to minimize sample loss, improve transfer consistency, and control contamination and carryover.
• Support samples with variable DNA concentrations and fragment‑size distributions.
• Work closely with assay development scientists and other technical partners to assess library quality, sequencing metrics, and overall workflow performance.
• Investigate workflow failures and implement corrective actions that improve assay robustness, recovery, and reproducibility.

Method Development, Qualification, and Validation

• Design and execute experiments comparing automated workflows with established manual or reference methods.
• Establish and evaluate acceptance criteria for pipetting accuracy and precision, sample recovery, library yield, fragment‑size distribution, contamination, carryover, and reproducibility.
• Develop and execute instrument qualification, method verification, and performance‑testing protocols.
• Support analytical validation, method transfer, and process scale‑up in collaboration with assay development, quality, laboratory operations, and other cross‑functional teams.
• Maintain clear records of development experiments, deviations, corrective actions, and method changes.
• Develop and maintain automation workflows in alignment with applicable laboratory quality systems and regulatory requirements.

Troubleshooting and Operational Support

• Perform root‑cause analysis of robotic errors, liquid‑handling failures, assay variability, and instrument‑integration issues.
• Optimize liquid classes, mixing parameters, aspiration and dispense settings, deck configurations, and error‑handling logic.
• Develop operating, preventive‑maintenance, and troubleshooting procedures in partnership with equipment vendors.
• Train laboratory personnel on routine operation, workflow execution, and error recovery.
• Prepare technical documentation and provide ongoing support during transfer into routine laboratory use.

Requirments:

• Bachelor’s or master’s degree in automation engineering, robotics, biomedical engineering, bioengineering, mechanical engineering, biotechnology, molecular biology, or a related discipline.
• At least 3–5 years of hands‑on experience developing and implementing laboratory automation workflows.
• Demonstrated experience programming and debugging liquid‑handling robots, preferably using Hamilton, Agilent Bravo, Beckman Coulter Biomek, or comparable platforms.
• Proven ability to write custom automation scripts and translate laboratory protocols into automated methods.
• Experience with NGS library preparation, molecular biology workflows, DNA purification, or related sample‑preparation processes.
• Strong understanding of liquid handling, magnetic‑bead purification, reaction setup, thermal cycling, and multistep plate‑based workflows.
• Experience troubleshooting automation methods, liquid transfers, laboratory instruments, and integrated workflows.
• Ability to independently drive automation projects from development through implementation.
• Strong technical documentation, experimental‑design, and problem‑solving skills.
• Ability to collaborate effectively with scientists, engineers, laboratory operations personnel, quality teams, software or LIMS partners, and equipment vendors.

Preferred Qualifications:

• Experience with cfDNA, circulating tumor DNA, liquid biopsy, or other low‑input DNA workflows .
• Experience with targeted sequencing panels, hybrid‑capture methods, UMI‑based sequencing, or other highly sensitive molecular diagnostic applications.
• Familiarity with Illumina‑compatible library‑preparation chemistry and sequencing workflows.
• Experience with automation in clinical diagnostics, regulated laboratories, assay validation, or design‑control environments.
• Programming experience with Python, SQL, APIs , or related tools used for instrument integration, data processing, and LIMS connectivity.
• Experience with low‑volume liquid handling, liquid‑class optimization, automated sample tracking, and contamination control.
• Experience integrating laboratory automation with thermal cyclers, plate readers, barcode systems, robotic plate movement, or other supporting instrumentation.

Estimated Min Rate : $103000.00

Estimated Max Rate : $165000.00

What’s In It for You?

• Medical, Prescription, Dental & Vision Benefits (for employees working 20+ hours per week)
• Health Savings Account (HSA) (for employees working 20+ hours per week)
• Life & Disability Insurance (for employees working 20+ hours per week)
• MetLife Voluntary Benefits
• Employee Assistance Program (EAP)
• 401K Retirement Savings Plan
• Direct Deposit & weekly epayroll
• Referral Bonus Programs
• Certification and training opportunities

Note: Any pay ranges displayed are estimations. Actual pay is determined by an applicant's experience, technical expertise, and other qualifications as listed in the job description. All qualified applicants are welcome to apply.

Yoh, a Day & Zimmermann company, is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or status as a protected veteran.

Visit to contact us if you are an individual with a disability and require accommodation in the application process.

For California applicants, qualified applicants with arrest or conviction records will be considered for employment in accordance with the Los Angeles County Fair Chance Ordinance for Employers and the California Fair Chance Act. All of the material job duties described in this posting are job duties for which a criminal history may have a direct, adverse, and negative relationship potentially resulting in the withdrawal of a conditional offer of employment.

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