Associate Director Engineering Jobs in California

Summary: We are seeking a highly motivated protein scientist for an Assistant Director or Associate Director role to lead and advance protein discovery and production efforts supporting protein-oligonucleotide conjugate programs. This role focuses on adapting ligands emerging from primary screens into robust, scalable protein fusion formats for downstream characterization, development, and larger-scale production.

Locations: Carlsbad, CA (onsite with potential for hybrid/work arrangements as applicable).

• Lead design, engineering, expression, purification, and characterization of protein ligands and protein fusion constructs intended for protein-oligonucleotide conjugates
• Translate hits from primary screening campaigns into optimized lead molecules with improved expression, stability, manufacturability, and functional performance
• Develop and execute protein production strategies, selecting fit-for-purpose platforms based on construct requirements and downstream use
• Design fusion proteins and other engineered constructs suitable for scale-up and conjugation workflows
• Oversee purification and analytical characterization of recombinant proteins, including assessment of integrity, aggregation, binding, and stability
• Work closely with oligonucleotide chemistry and conjugation teams to ensure protein constructs are compatible with conjugation requirements and downstream process needs
• Drive experimental strategy, data interpretation, and decision-making across multiple programs
• Mentor scientists and research associates and contribute to building scientific capability in protein engineering and production
• Present results and recommendations clearly to cross-functional teams and senior leadership
• Hands-on laboratory based effort will be expected

• PhD in protein science, biochemistry, molecular biology, chemical biology, bioengineering, or related discipline, with relevant industry experience
• For the Assistant Director position, at least 5 years of relevant industry experience
• For the Associate Director position, at least 8 years of relevant experience
• Significant hands-on experience in recombinant protein expression and purification in both microbial and mammalian systems
• Demonstrated expertise in protein engineering and design, including construct optimization for expression, stability, and function
• Strong track record of advancing protein molecules from early discovery or screening through lead optimization and scale-up
• Experience generating and evaluating protein fusions or other complex engineered protein formats
• Experience with analytical methods used for protein characterization
• Strong scientific judgment, experimental rigor, and problem-solving ability in a fast-moving research environment
• Excellent written and verbal communication skills and ability to work effectively across disciplines
• Excellent track record of publications
• Ability to manage multiple assignments effectively in a quickly evolving environment
• An entrepreneurial spirit; enthusiasm and vision for converting cutting-edge science into commercial applications

• Experience supporting protein-based ligand discovery programs
• Experience with protein constructs intended for bioconjugation or oligonucleotide conjugation
• Familiarity with protein structure-guided design, computational design tools, or directed evolution approaches
• Experience scaling protein production to support preclinical or development-stage studies
• Prior leadership experience in matrixed, cross-functional research teams
• Experience working at the interface of protein engineering, conjugation chemistry, and therapeutic platform development

For more information and to apply, please visit Ionis website and reference requisition # IONIS004044.

Ionis offers an excellent benefits package. The pay scale for this position is $144,200 to $196,444. The pay scale for the Assistant Director position is $144,200 to $176,800. The pay scale for the Associate Director position is $165,597 to $196,444.

Equal Opportunity Employer
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