Automation Engineer, NGS & cfDNA

Yoh, A Day & Zimmermann Company

Sunnyvale (CA)

On-site

USD 103,000 - 165,000

Full time

39 hours ago

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Benefits offered by this job

Medical, Prescription, Dental & Vision

Health Savings Account (HSA)

Life & Disability Insurance

401K Retirement Savings Plan

Employee Assistance Program (EAP)

Job summary

Yoh, a Day & Zimmermann company, seeks a Laboratory Automation Engineer – NGS & Molecular Diagnostics in Sunnyvale, CA to design, implement, and optimize automated cfDNA and NGS workflows. The role combines robotics programming with molecular biology expertise to translate complex protocols into scalable automation while maintaining documentation and transfer to routine operations.

The successful candidate will own projects from development through qualification, working with Hamilton, Agilent,

Qualifications

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.

Responsibilities

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.
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.
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.
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.
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.