Principal Process Engineer

Department: Process Engineering | Employment Type: Full Time | Location: Redwood City, CA | Workplace type: Onsite

About the role

We are seeking a highly experienced and innovative Process Engineer to support process development activities for Codexis’ Enzyme Catalyzed Oligonucleotide (ECO) Synthesis® manufacturing platform. This role is pivotal in advancing sustainable oligonucleotide manufacturing technologies that disrupt traditional chemical synthesis methods and meet stringent quality and regulatory standards.

Ideal candidates possess a passion for being part of the therapeutic community, helping bring cutting-edge treatments to patients in need. They enjoy collaboration across different functional groups to gain a holistic understanding of process development and align data with internal stakeholders. Problem-solving through engineering and analytical solutions is a key aspect of this role.

Responsibilities

• Provide technical leadership in hands-on process development, applying advanced engineering principles to drive the design, build-out, and maturation of the ECO Synthesis® platform in close partnership with cross-functional development teams.
• Lead the scale-up strategy for the ECO Synthesis® platform, ensuring the process is robust, well-characterized, and ready for transition into a cGMP manufacturing environment.
• Champion laboratory safety, maintain a clean and compliant workspace, conduct process hazard analyses and risk assessments, and ensure a safe working environment for all team members.
• Oversee documentation quality, ensuring batch records, SOPs, and development reports meet GDP standards; provide mentorship and guidance to early-career engineers and scientists on documentation and experimental/statistical rigor.
• Lead the development and delivery of key technical work, including internal and external presentations, detailed technical reports, and comprehensive technology transfer packages for siRNA manufacturing processes.
• Own the creation of engineering design tools, including mass and energy balances, process flow diagrams (PFDs), equipment specifications, and cost models to support scale-up, facility integration, and long-term platform deployment.
• Serve as primary technical liaison with external vendors, driving equipment selection, qualification, and support activities essential for effective process development and scale-up.

Requirements

• Bachelor’s degree in Chemical Engineering, Biochemical Engineering, or related field with 10+ years of relevant industrial experience, or M.S. with 8+ years.
• Expertise in flow chemistry, biocatalysis, or oligonucleotide synthesis technologies (e.g., SPOS, enzymatic platforms).
• Demonstrated leadership in scale-up activities, including tech transfer of biocatalytic or nucleic acid–based processes from laboratory to pilot or commercial manufacturing environments.
• Proficiency in process modeling and simulation tools such as Aspen Plus, SuperPro Designer, COMSOL, or DynoChem; and proficient with data analytics or scripting tools (e.g., R, JMP, Python).
• Strong leadership and communication skills, with the ability to collaborate effectively across cross-functional teams including R&D, Operations, Quality, and Engineering.

Preferred Qualifications

• Prior experience managing early-career engineers, scientists, or research associates.
• Expertise in purification technologies, such as chromatography, filtration, or enzyme/oligonucleotide purification workflows.
• Experience with facility design or equipment specification for nucleic acid manufacturing.
• Deep understanding of quality systems and regulatory expectations, including ISO-based quality frameworks and GMP principles.

Pay

$165,000 - $185,000 / year

Benefits

• Medical, Dental, and Vision Insurance
• Basic Life, AD&D, Short- and Long-Term Disability Insurance
• 401k with Company Match up to 4%
• Company Equity
• Generous Paid Time Off including 18 Company Holidays (with a summer and winter shutdown), Vacation, and Wellness Time
• Annual Lifestyle Account for reimbursement of fitness programs, equipment, and more
• Employee Stock Purchase Program (ESPP)
• Flexible Spending Accounts (Commuter/Parking, Dependent Care & Healthcare)
• Student Debt Program (Company Contribution to Loans)
• Mental Health Wellness Program
• Subsidized onsite lunch program
• Onsite Gym Facilities
• Paid Parental Leave

About Codexis Inc

At Codexis, we offer a very competitive compensation package and excellent benefits. We foster career growth, continued education, and upskilling through our mentorship program and learning and development opportunities. You will learn and work alongside inspirational leaders and colleagues who are equally passionate about our mission and committed to fostering an inclusive, growth-centered, and rewarding culture. Diversity is valued, and mutual trust is of paramount importance to the ethos at Codexis.