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Every patient sample is a story.

That's why our Lab Ops team is focused on providing physicians with comprehensive genomic information about each person's cancer. Information that's as unique as the patients are. The insights discovered in our labs may help change their story.


Automation Engineer

  • Second Street, Cambridge, Massachusetts, United States
  • Full Time

About the Job

The Automation Engineer is responsible for automating and scaling workflows and implementing processes for deployment in clinical laboratories at multiple sites. This position is involved in all aspects of assay automation development and instrument integration from concept to requirements definition, method development, optimization, troubleshooting and validation. The Automation Engineer identifies problem areas and develops solutions to reduce Turn-Around-Time (TAT), increase sample processing capacity and reduce cost of goods sold.

The incumbent leverages knowledge and skills of automation to contribute to cross-functional teams on a variety of projects to explore, develop, optimize, test, and implement robust, scalable solutions for FMI’s sample processing workflows. Additionally, this position works with outside vendors to develop integrated robotic solutions and ensures all automated solutions fully address business and user requirements.

The Automation Engineer position requires working in a lab environment in the presence of chemicals and reagents.

This is a regulated position and additional information may be available from QA on the qualifications for this role pertaining to regulatory guidelines.

Regular onsite work at a designated FMI location is an essential function of this role.

Key Responsibilities

• Develop and improve robust automated solutions utilizing Hamilton liquid handlers and other laboratory automation equipment designed to remove bottlenecks, increase capacity and reduce TAT in FMI’s high throughput (24/7) Next Generation Sequencing laboratory.

• Program, optimize, verify and implement new and/or improved methods on Hamilton robotic liquid handling workstations and integrated robotic systems.

• Perform the exploration into workflows for process optimization.

• Analyze workflows, identify bottlenecks, develop solutions and lead teams in solution implementation that improves efficiency, throughput, cost, and quality.

• Maintain requirements and test plan documentation.

• Integrate instrument components and perform unit testing.

• Contribute to innovation of current and new assay workflows, technologies and processes.

• Execute guard-banding, response surface and optimization studies to optimize and characterize automated methods to improve robustness.

• Provide on-site technical support of automation platforms.

• Contribute to protocol generation, report writing, and presentation preparation related to automation as needed.

• Install, test and control new versions of automated protocols on applicable instrumentation across labs and possibly across sites.

• Provide training and documentation for new or modified workflows to end users.

• Other projects as periodically assigned.


Basic Qualifications

• Bachelor’s Degree in Bioengineering, Biotechnology or life sciences and 1+ year(s) of related experience with high-throughput laboratory instrumentation; OR,

• Master’s Degree in Bioengineering, Biotechnology or life sciences

• Experience with operating and programming liquid handling robotics platforms

Preferred Qualifications

• 2+ years of related experience with high-throughput laboratory instrumentation

• Experience with robotic liquid handlers from Hamilton, TECAN, Agilent Technologies, or Beckman Coulter

• Experience with developing and implementing integrated robotic systems for use in a high throughput environment

• Experience with agile project management

• Experience with FMEA, MTBF and test case development

• Experience with developing, optimizing, and validating assays for use in a high throughput environment

• Experience communicating and collaborating with internal and external colleagues and customers from diverse scientific, engineering, operational, and regulatory disciplines

• Experience with statistical data analysis using R or JMP, monitoring data quality and troubleshooting technical problems

• Experience with standard molecular biology techniques such as nucleic acid isolation, purification and quantitation, bioanalyzer, DNA/RNA quantitation, qPCR or Next Generation Sequencing

• Experience working in a regulated environment (e.g. CLIA, CAP, GxP, ISO)

• Previous experience working in a molecular diagnostics/clinical laboratory setting

• Previous teaching or technical training experience

• Knowledge of safety protocols in workshop, factory or laboratory setting

• Familiarity with streamlining workflows and developing automated laboratory processes and instrumentation systems, including collecting and documenting requirements, developing concepts, design, testing/validation, implementing, and training

• Familiarity with JIRA/Confluence, Solidworks, VBscript, Python, PERL and/or JavaScript, relational databases, SQL, LIMS or other relevant enterprise software packages

• Ability to document and report troubleshooting procedures and resolutions

• Ability to work as an individual as well as in a team environment

• Strong written and oral communication skills

• Detail oriented and well organized

• Understanding of HIPAA, and the importance of privacy of patient data

• Commitment to reflect FMI’s values: passion, patients, innovation, and collaboration


Please be aware that Foundation Medicine mandates COVID-19 vaccination of all employees regardless of work location. Accommodations may be made in accordance with applicable law.


About Foundation Medicine

Foundation Medicine, Inc. (FMI) began with an idea—to simplify the complex nature of cancer genomics, bringing cutting-edge science and technology to everyday cancer care. Our approach generates insights that help doctors match patients to more treatment options and helps accelerate the development of new therapies. Foundation Medicine is the culmination of talented people coming together to realize an important vision, and the work we do every day impacts real lives.

Confidence, or the belief that we need to check every box before applying for a job, can sometimes hold us back from going after a role that inspires us. At Foundation Medicine there's no such thing as the 'perfect' applicant, and our company is a place where every employee can make an impact and continue to grow whatever background they may have or path they may have taken. So, as long as you meet the basic qualifications for a role, please apply if you see a position that would make you excited to come into Foundation Medicine every day and help us transform cancer care.

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Internal applicants, please use your FMI email address.

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Foundation Medicine is proud to be an Equal Opportunity and Affirmative Action employer and considers all qualified applicants for employment without regard to race, color, religion, sex, gender, sexual orientation, gender identity, ancestry, age, or national origin. Further, qualified applicants will not be discriminated against on the basis of disability or protected veteran status. We also consider qualified applicants regardless of criminal histories, consistent with legal requirements. See also FMI’s EEO Statement and EEO is the Law and Supplement. If you have a disability or special need that requires accommodation, please let us know by completing this form.  (EOE/AAP Employer)

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