Principal Process Engineer

Codexis, Inc.; Redwood City (CA); On-site; USD 165,000 - 185,000; Full time

Benefits offered by this job

401k with Company Match up to 4%

Company Equity

Generous Paid Time Off

ESPP

Onsite Gym Facilities

Onsite lunch program

Job summary

Codexis, Inc. in Redwood City, CA seeks a Principal Process Engineer to lead hands‑on process development for the ECO Synthesis platform, driving scale‑up and mature processes ready for cGMP manufacturing. You will mentor engineers and collaborate with cross‑functional teams across R&D, Operations, Quality, and Engineering.

The role emphasizes leadership in process modeling, data analytics, and risk assessment to ensure safety, compliance, and robust process transfer from bench to production.

Qualifications

• Extensive experience scaling up biocatalytic or nucleic acid processes.
• Strong leadership and cross‑functional collaboration across R&D, Operations, Quality, and Engineering.
• Proficiency with process modeling and data analytics tools.

Responsibilities

• Provide technical leadership in hands‑on process development for ECO Synthesis platform.
• Lead scale‑up strategy ensuring robust, well‑characterized processes for cGMP.
• Ensure safe, compliant lab operations with GDP‑standard documentation.
• Develop engineering design tools: mass and energy balances, PFDs, equipment specs, cost models.
• Serve as liaison with external vendors for equipment selection and qualification.
• Prepare technical reports and technology transfer packages for siRNA manufacturing.

Skills

Leadership

Collaboration

Problem Solving

Flow Chemistry

Biocatalysis

Oligonucleotide Synthesis

Process Modeling

Data Analytics

Communication

Education

Bachelor’s degree in Chemical Engineering

Bachelor’s degree in Biochemical Engineering

MS in related field

Tools

Aspen Plus

SuperPro Designer

COMSOL

DynoChem

R

JMP

Python

Job description

Principal Process Engineer

Department: 46 - Process Engineering

Employment Type: Full Time

Location: Redwood City, CA

Compensation: $165,000 - $185,000 / year

Description

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 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
• Leading the scale‑up strategy for the ECO Synthesis® platform, ensuring process is robust, well‑characterized, 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 early‑career 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 scale‑up, facility integration, and long‑term platform deployment.
• Serving as primary technical liaison with external vendors, driving equipment selection, qualification, and support activities essential for effective process development and scale‑up.

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 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, 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!