Scientist II, Upstream Development for Protein Development and Manufacturing

Summary

Vaxcyte is seeking a curious and scientifically rigorous Scientist II to join the Upstream Process Development group within the Protein Development and CMC organization. The successful candidate's primary responsibility will be to design and execute experimental programs that build a deeper mechanistic understanding of bacterial fermentation for the production of critical raw materials that support production of Vaxcyte's novel carrier proteins - how host physiology, media composition, feeding strategy, and bioreactor conditions together govern cell growth, protein expression, and product quality.

This is a role for a scientist who is not satisfied with a process that works, but wants to understand why it works and where its limits are. The candidate will frame questions, design studies to answer them, analyze the resulting data with statistical rigor, and translate findings into process knowledge that supports scalability, robustness, and technical readiness for clinical and commercial manufacturing.

Work spans the current pneumococcal conjugate vaccine program and earlier pipeline programs, and requires close intellectual partnership with Downstream Process Development, Analytical Development, MSAT, and Pilot Plant colleagues.

Essential Functions

• Design and execute hypothesis-driven fermentation studies to establish how critical process parameters influence cell growth kinetics, protein expression, and product quality attributes.
• Apply Design of Experiments and statistical analysis to characterize the process, identify critical and key process parameters, define proven acceptable ranges, and support establishment of the process design space.
• Investigate unexpected or anomalous results - variability in growth, titer, or quality - through structured, root-cause experimentation.
• Develop, qualify, and challenge scale-down models; assess their representativeness against pilot- and manufacturing-scale data and use them to predict performance at scale.
• Design feeding strategies and control approaches for fed-batch fermentation, including recipe scripting on Ambr® 250 and benchtop systems, as a means of testing metabolic hypotheses and improving process robustness.
• Evaluate and implement new experimental approaches, at-line or online monitoring, and analytical or data-analysis tools that increase the resolution with which the team can observe and interpret the process. Develop workflows beyond established procedures where existing methods are insufficient.
• Integrate and interpret data across upstream, downstream, and analytical functions to connect upstream conditions to downstream performance and final product quality.
• Author study protocols, development reports, and technical memoranda; contribute technical content to tech transfer packages and regulatory filings. Present and defend conclusions at internal project meetings.
• Advise colleagues on experimental design, data interpretation, and troubleshooting; mentor junior team members in scientific rigor, documentation practices, and reproducibility.
• Maintain highly organized records in electronic notebooks and upstream data systems to enable reproducibility, retrospective analysis, and knowledge transfer.

Requirements

• PhD with 2-5 years, MS with a minimum of 7 years, or BA/BS with a minimum of 10 years of relevant Pharma/Biotech industry experience in a relevant discipline. Other combinations of education and/or experience may be considered.
• Strong scientific grounding in microbial physiology and metabolism, with the ability to reason from first principles about how process conditions drive cell behavior and protein quality.
• Hands-on experience designing and executing laboratory-scale bacterial fermentation studies; high-throughput systems such as Ambr® 250 preferred but not required.
• Familiarity with Design of Experiments and statistical analysis software (e.g., JMP); comfort analyzing and drawing defensible conclusions from large, multivariate process datasets.
• Working understanding of bioreactor design, operation, and control, including mixing, mass transfer, and oxygen transfer fundamentals, as they inform experimental design and scale translation.
• Strong aseptic technique.
• Understanding of how primary recovery operations - homogenization, centrifugation, depth filtration - influence product quality and constrain upstream design choices, is a plus.
• Strong scientific writing skills and a track record of authoring protocols, development reports, or peer-reviewed publications.
• Familiarity with regulatory expectations for process characterization and validation of biotherapeutics. Late-stage process characterization experience is a plus.
• Intellectual curiosity and independence: willingness to question assumptions, pursue explanations for unexpected observations, and learn new techniques outside the current area of expertise.
• An exceptional collaborator who speaks up, engages in vigorous technical debate, and stays focused on the best outcome for the program.

Reports to: Senior Scientist, Upstream Development and Manufacturing

Location: San Carlos, CA

Work Arrangement (may be adjusted based on business needs, job responsibilities, or changes to company policy):

Onsite (5 days per week onsite)

Compensation

The compensation package will be competitive and includes comprehensive benefits and an equity component.