Protein Scientist, Assistant Director or Associate Director (Protein Engineering)

Location: Onsite; company offices are located in Carlsbad, California, Boston, Massachusetts, and Dublin, Ireland.

Salary: $144,200–$196,444 annually. Assistant Director: $144,200–$176,800; Associate Director: $165,597–$196,444.

Company

Ionis is a biotechnology company developing RNA-targeted medicines, gene-editing approaches, and therapeutic programs for serious diseases.

What you will do

• Lead the design, engineering, expression, purification, and characterization of protein ligands and fusion constructs for protein-oligonucleotide conjugates.
• Translate primary-screening hits into optimized lead molecules with improved expression, stability, manufacturability, and functional performance.
• Develop protein production strategies across microbial and mammalian expression systems and support scale-up.
• Oversee analytical characterization, including protein integrity, aggregation, binding, and stability assessments.
• Partner with oligonucleotide chemistry, conjugation, analytical, discovery, and development teams.
• Drive experimental strategy and program decisions, mentor scientists and research associates, and present recommendations to senior leadership.

Requirements

• PhD in protein science, biochemistry, molecular biology, chemical biology, bioengineering, or a related discipline, plus relevant industry experience.
• At least 5 years of relevant industry experience for Assistant Director or 8 years for Associate Director.
• Significant hands-on experience with recombinant protein expression and purification in both microbial and mammalian systems.
• Expertise in protein engineering and construct optimization for expression, stability, and function.
• Experience advancing protein molecules from discovery or screening through lead optimization and scale-up, including protein fusions or other complex engineered formats.
• Strong scientific judgment, experimental rigor, communication skills, and ability to work across disciplines.

Nice to have

• Experience supporting protein-based ligand discovery or protein constructs for bioconjugation and oligonucleotide conjugation.
• Familiarity with structure-guided design, computational design tools, or directed evolution.
• Experience scaling protein production for preclinical or development-stage studies.
• Leadership experience in matrixed, cross-functional research teams.

Culture & Benefits

• Onsite laboratory-based work is expected.
• Collaborative environment integrating protein science, chemistry, and therapeutic platform development.
• Opportunity to contribute to RNA therapies and gene-editing programs addressing unmet medical needs.
• Benefits package is offered.