Automation Engineer I/II - Functional Genomics

Location:  San Rafael, California Category: Research


BioMarin is the world leader in delivering therapeutics that provide meaningful advances to patients who live with serious and life-threatening rare genetic diseases. We target diseases that lack effective therapies and affect relatively small numbers of patients, many of whom are children. These conditions are often inherited, difficult to diagnose, progressively debilitating and have few, if any, treatment options. BioMarin will continue to focus on advancing therapies that are the first or best of their kind.

BioMarin’s Research & Development group is responsible for everything from research and discovery to post-market clinical development. Research & Development involves all bench and clinical research and the associated groups that support those endeavors. Our teams work on developing first-in-class and best-in-class therapeutics that provide meaningful advances to patients who live with rare diseases. Come join our team and make a meaningful impact on patients’ lives.

We are seeking a highly motivated, innovative and team-oriented individual to join the Human Genetics research group. Within the Human Genetics group, the Functional Genomics group is expanding in order to carry out its mission of applying genetic screens and other functional genomic technologies to discover and validate novel therapeutic targets.  The successful candidate will work to design, develop, and implement automation solutions for high-throughput biology protocols and next generation sequencing workflows.  Expertise should include the integration of automated liquid handling systems for discovery and validation of novel therapeutic targets. The position requires adaptability, creativity, and a capacity for constant innovation in pursuit of company goals. 


  • Collaborate with scientists to develop, transfer and validate manual process steps to automated liquid handling (STAR, Biomek, OT-2) and integrated systems.
  • Work with equipment and system integrators on the design, implementation and support of high-throughput automated platforms.
  • Operate robotic platforms and laboratory automation to execute biological protocols and next generation sequencing workflows. Assess the efficiency and quality of operations to prioritize process improvements and optimizations.
  • Mentor lab users with the implementation of a wide range of technologies, experiment design and the use of systems engineering best practices.
  • Integrate laboratory equipment into laboratory information management systems (LIMS) and accurately document methods in SOPs and electronic lab notebook (ELN) system.


  • Significant experience in developing, optimizing and managing high-throughput integrated systems. Hands-on experience with a broad range of lab automation (4+ years preferred); some experience with Hamilton Venus software is required.  
  • Experience working with vendors to make modifications to existing software and hardware to enable expanded usage and new features for automated platforms.
  • Demonstrated track record integrating biological assays and/or NGS workflows to transition an assay from the bench to a high throughput screen using liquid handling automated workflows.
  • Familiarity with molecular biology and cell culture workflows and experience developing and optimizing new workflows in collaboration with scientists.
  • Competent using programming languages such as Python or R to perform modeling/analysis.
  • Working proficiency in UNIX and bash shell scripting highly preferred.
  • Experience automating NGS workflows, iPSC cell culture protocols, and standard in vitro biochemical and cell-based assays (e.g. luminescence-based assays, high content imaging, etc.) including assay development, execution and troubleshooting.


  • Bachelor’s or Master’s degree in Engineering, Computer Science, Molecular/Cell Biology, or related discipline with 2+ years of experience in either an academic or industry lab.
  • Strong analytical, written, and verbal communication skills.
  • Track record of productivity and effective projects.
  • Interested in learning new techniques and approaches. Attention to detail, time management, the ability to run multiple projects in parallel, and organization skills are critical.
We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, or any other characteristic protected by law.