Protein Scientist, Assistant Director or Associate Director

Ionis Pharmaceuticals, Inc.; Carlsbad (CA); Hybrid; USD 144,200 - 196,444; Full time

Benefits offered by this job

Excellent benefits package

Job summary

Ionis Pharmaceuticals, Inc. is seeking a highly motivated Protein Scientist for an Assistant Director or Associate Director role to lead protein discovery efforts. Based in Carlsbad, CA, this position focuses on scalable protein fusion formats supporting protein-oligonucleotide conjugates.

The ideal candidate holds a PhD in protein science with extensive industry experience in protein engineering and production. The role includes hands-on lab work and significant responsibility in mentoring scientists while driving experimental strategies across multiple programs.

Qualifications

• At least 5 years of relevant industry experience for the Assistant Director position.
• At least 8 years for the Associate Director position.
• Demonstrated expertise in protein engineering and construct optimization.

Responsibilities

• Lead design and engineering of protein constructs.
• Develop protein production strategies based on construct requirements.
• Mentor scientists and oversee laboratory efforts.

Skills

Recombinant protein expression and purification

Protein engineering and design

Analytical methods for protein characterization

Excellent written and verbal communication skills

Education

PhD in protein science or related discipline

Job description

Protein Scientist, Assistant Director or Associate Director

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).

Key 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 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

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

Preferred Qualifications

• 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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