Principal Process Engineer

Sacbar; Redwood City (CA); On-site; USD 180,000 - 240,000; Full time

Benefits offered by this job

Medical Insurance

401k with company match

Company equity

Generous PTO

Job summary

Codexis Inc. is seeking a Principal Process Engineer to drive process development for the ECO Synthesis platform, leading scale-up activities and ensuring readiness for cGMP production.

You will collaborate across R&D, Operations, Quality, and Engineering to advance sustainable oligonucleotide manufacturing technologies. The role emphasizes hands-on engineering leadership, safety, and rigorous documentation, with opportunities to mentor scientists and engineers and to contribute to technology

Qualifications

• Bachelor's degree in Chemical Engineering or Biochemical Engineering with 10+ years of industrial experience or MS with 8+ years.
• Experience in flow chemistry, biocatalysis, or oligonucleotide synthesis technologies (SPOS, enzymatic platforms).
• Demonstrated leadership in scaleup activities and tech transfer from lab to pilot or commercial manufacturing.
• Proficiency with process modeling and data analytics tools and scripting.

Responsibilities

• Provide technical leadership in hands-on process development to mature the ECO Synthesis platform.
• Lead scaleup strategy to ensure robust, well-characterized processes ready for cGMP manufacturing.
• Champion laboratory safety and maintain compliant workflows and documentation.
• Oversee batch records, SOPs, and development reports ensuring GDP standards; mentor junior staff.
• Develop and deliver technical work including reports and technology transfer packages for siRNA processes.
• Create engineering design tools (mass/energy balances, PFDs, equipment specs, cost models) to support scaleup and facility integration.
• Serve as primary liaison with external vendors for equipment selection, qualification, and support.

Skills

Flow chemistry

Biocatalysis

Oligonucleotide synthesis

Process modeling

Data analytics

Leadership

Education

Bachelor's degree in Chemical Engineering

M.S. in Chemical Engineering

Tools

Aspen Plus

SuperPro Designer

COMSOL

DynoChem

R

JMP

Python

Job description

Principal Process Engineer

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

If any of the below describes you, we would love to meet you!

• Possess a passion for being part of the therapeutic community helping bring cutting edge treatments to patients in need.
• Enjoys collaboration across different functional groups to get a holistic understanding of process development along with aligning data with internal stakeholders.
• Enjoys problem solving by implementing engineering and analytical solutions.

Key Responsibilities

• Providing technical leadership in handson process development, applying advanced engineering principles to drive the design, buildout, and maturation of the ECO Synthesis® platform in close partnership with crossfunctional development teams
• Leading the scaleup strategy for the ECO Synthesis® platform, ensuring process is robust, wellcharacterized, and ready for transition into a cGMP manufacturing environment.
• Championing laboratory safety, maintaining a clean and compliant workspace, conducting process hazard analyses and risk assessments, and ensuring safe working environment for all team members.
• Overseeing documentation quality, ensuring batch records, SOPs, and development reports meet GDP standards; providing mentorship and guidance to earlycareer engineers and scientists on documentation and experimental/statistical rigor.
• Leading 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.
• Owning the creation of engineering design tools, including mass and energy balances, process flow diagrams (PFDs), equipment specifications, and cost models to support scaleup, facility integration, and longterm platform deployment.
• Serving as primary technical liaison with external vendors, driving equipment selection, qualification, and support activities essential for effective process development and scaleup.

Skills, Knowledge & Expertise

• 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 scaleup 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, communication skills, with the ability to collaborate effectively across cross-functional teams including R&D, Operations, Quality, and Engineering.

Additional experience that would be valuable for this role includes:

• Prior experience managing early career engineers, scientist, 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.

Job 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
• And More!

About Codexis Inc

At Codexis we offer a very competitive compensation package and beyond 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. The people, the culture and working with others with a common goal is what makes Codexis a great place to work.

Why join Codexis?

For more information, visit www.codexis.com.

Codexis is an equal opportunity employer & prohibits unlawful discrimination based on race, color, religion, gender, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, marital & veteran status.