Optics / Microscopy Principal Scientist

Job Description

Vertex Pharmaceuticals is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases. At our San Diego site, the Engineering & Applied Physics group is a dynamic, fast-paced team of 20 applied physicists and mechanical, electrical, and automation engineers.  Together, we design and develop custom instruments that integrate cutting-edge technology and full automation to accelerate Vertex’s internal drug discovery pipeline. These instruments are tailored to specific project needs, enabling capabilities that are not commercially available.

We are seeking an experienced and innovative Principal Scientist with expertise in optical design, microscopy, and functional imaging to join our team. This role bridges the disciplines of science and engineering, requiring a deep understanding of disease biology and assays, as well as the ability to design and develop advanced optical instruments. While working directly in a multi-disciplinary team comprised of physicists, biologists, chemists, engineers and software specialists, the Principal Scientist will collaborate closely with drug discovery teams to ensure utility and integration of new approaches into therapeutic projects. This position offers exciting opportunities for career growth, with potential pathways to either a scientific leadership role driving cross-functional projects or a managerial role with increasing supervisory responsibilities within the group.

Key duties and responsibilities:

• Collaborate with cross-disciplinary teams to understand project needs and identify opportunities where custom instrumentation can have a transformative impact.
• Align stakeholders and propose new projects to senior leaders.
• Design and build prototype optical instruments.
• Conduct proof-of-concept experiments and optimize assays in partnership with biologists and chemists.
• Work closely with engineers to specify, design, and build robust, production-ready instruments for deployment in automated drug discovery applications.
• Communicate findings and progress effectively through written reports, presentations, and discussions.

Knowledge and Skills:

• Knowledge of formal optical design principles, including ray tracing, ABCD matrices, Gaussian beams, and optical aberrations.
• Familiarity with formal engineering design processes, including developing quantitative instrument specifications.
• Familiarity with automation and high-throughput screening technologies.
• Understanding of the pharmaceutical research and drug discovery process.
• Strong written and verbal communication skills.
• Experience supervising and mentoring junior researchers or staff.
• Demonstrated ability to deliver innovative solutions to complex scientific and technical challenges.

Education & Experience:

• Ph.D. in Physics, Physical Chemistry, Bioengineering, or a related discipline and 8+ years of relevant experience.
• Proven hands-on experience applying optical techniques in the design and development of novel imaging platforms or technologies (e.g., optical table setups), in biological research.
• Proficiency in programming for data analysis and instrument control.
• Experience with functional measurements in cells, such as voltage or calcium imaging.
• Expertise in multiple biological imaging modalities, such as widefield fluorescence, confocal, light sheet, super-resolution, or two-photon microscopy.

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At Vertex, we embrace continuous learning and encourage employees to stay informed on advances in AI, technology, automation, and industry trends. We seek talent who bring an external perspective, demonstrate curiosity and sound judgment, and thoughtfully adopt new capabilities that improve decision-making, drive innovation, increase efficiency, and help deliver better outcomes for patients.

Pay Range:

$144,400 - $216,600

Disclosure Statement:

Flex Designation:

On-Site Designated

Flex Eligibility Status:

In this On-Site designated role, you will work five days per week on-site with ad hoc flexibility.  

Note: The Flex status for this position is subject to Vertex’s Policy on Flex @ Vertex Program and may be changed at any time.

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Company Information

Vertex is a global biotechnology company that invests in scientific innovation.

Vertex is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E-Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law.

Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at ApplicationAssistance@vrtx.com