Protein Scientist, Assistant Director or Associate Director

Ionis•Carlsbad, CA

11d•Onsite

About The Position

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 will focus on adapting ligands emerging from primary screens into robust, scalable protein fusion formats suitable for downstream characterization, development, and larger-scale production. The successful candidate will bring deep expertise in protein engineering, molecular design, and recombinant protein production across both microbial and mammalian expression systems. They will be expected to drive the progression of candidate ligands from early discovery into manufacturable protein fusion constructs for conjugation to oligonucleotides, while partnering closely with discovery, chemistry, analytical, and development teams. The ideal candidate is a creative and rigorous scientist who combines strong hands-on technical depth with strategic thinking. They are comfortable moving between molecular design, experimental execution, and program-level decision-making, and they thrive in collaborative environments where protein science must integrate tightly with chemistry and therapeutic platform goals. This role will be central to building a bridge between early ligand discovery and scalable production of protein fusion molecules suitable for protein-oligonucleotide conjugate applications. The individual in this position will help define candidate quality, establish developable construct formats, and enable the progression of promising ligands into broader therapeutic evaluation. The final title, Assistant Director or Associate Director, will be determined based on the candidate’s depth of experience, scientific leadership, and demonstrated track record in protein engineering and recombinant protein production.

Requirements

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

Nice To Haves

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

Responsibilities

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 as appropriate 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