Protein Scientist, Assistant Director or Associate Director
Ionis Pharmaceuticals, Inc.
July 02, 2026
On-site
Carlsbad, CA
Clinical Research and Development
Protein Scientist, Assistant Director or Associate Director
Summary:
Lead and advance protein discovery and production efforts supporting protein-oligonucleotide conjugate programs. Adapt ligands from primary screens into robust, scalable protein fusion formats for downstream characterization, development, and larger-scale production.
Key Responsibilities:
- Lead design, engineering, expression, purification, and characterization of protein ligands and protein fusion constructs for protein-oligonucleotide conjugates
- Translate primary-screen hits into optimized lead molecules with improved expression, stability, manufacturability, and functional performance
- Develop and execute protein production strategies and select fit-for-purpose platforms
- Design fusion proteins/engineered constructs for scale-up and conjugation workflows
- Oversee purification and analytical characterization (integrity, aggregation, binding, stability)
- Partner with oligonucleotide chemistry and conjugation teams to ensure compatibility with conjugation and downstream process needs
- Drive experimental strategy, data interpretation, and decision-making across multiple programs
- Mentor scientists/research associates; present results and recommendations to cross-functional teams and senior leadership
- Hands-on laboratory based effort expected
Requirements:
- PhD in protein science/biochemistry/molecular biology/chemical biology/bioengineering or related field, with relevant industry experience
- Assistant Director: at least 5 years relevant industry experience; Associate Director: at least 8
- Significant hands-on recombinant protein expression and purification in microbial and mammalian systems
- Protein engineering/design expertise; construct optimization for expression, stability, and function
- Track record advancing from discovery/screening through lead optimization and scale-up
- Experience with protein fusions/complex engineered formats and protein characterization analytical methods
- Strong judgment, rigor, problem-solving, communication, publications, and ability to manage multiple assignments
Preferred Qualifications:
- Experience supporting protein-based ligand discovery and bioconjugation/oligonucleotide-conjugation constructs
- Structure-guided/computational design or directed evolution experience
- Scaling protein production for preclinical/development studies
- Prior cross-functional leadership; interface experience across protein engineering, conjugation chemistry, and therapeutic platform development
Application Instructions:
Apply via http://www.ionis.com; reference requisition #IONIS004044
Benefits/Pay Scale:
- Pay scale: $144,200–$196,444
- Assistant Director: $144,200–$176,800
- Associate Director: $165,597–$196,444
Summary:
Lead and advance protein discovery and production efforts supporting protein-oligonucleotide conjugate programs. Adapt ligands from primary screens into robust, scalable protein fusion formats for downstream characterization, development, and larger-scale production.
Key Responsibilities:
- Lead design, engineering, expression, purification, and characterization of protein ligands and protein fusion constructs for protein-oligonucleotide conjugates
- Translate primary-screen hits into optimized lead molecules with improved expression, stability, manufacturability, and functional performance
- Develop and execute protein production strategies and select fit-for-purpose platforms
- Design fusion proteins/engineered constructs for scale-up and conjugation workflows
- Oversee purification and analytical characterization (integrity, aggregation, binding, stability)
- Partner with oligonucleotide chemistry and conjugation teams to ensure compatibility with conjugation and downstream process needs
- Drive experimental strategy, data interpretation, and decision-making across multiple programs
- Mentor scientists/research associates; present results and recommendations to cross-functional teams and senior leadership
- Hands-on laboratory based effort expected
Requirements:
- PhD in protein science/biochemistry/molecular biology/chemical biology/bioengineering or related field, with relevant industry experience
- Assistant Director: at least 5 years relevant industry experience; Associate Director: at least 8
- Significant hands-on recombinant protein expression and purification in microbial and mammalian systems
- Protein engineering/design expertise; construct optimization for expression, stability, and function
- Track record advancing from discovery/screening through lead optimization and scale-up
- Experience with protein fusions/complex engineered formats and protein characterization analytical methods
- Strong judgment, rigor, problem-solving, communication, publications, and ability to manage multiple assignments
Preferred Qualifications:
- Experience supporting protein-based ligand discovery and bioconjugation/oligonucleotide-conjugation constructs
- Structure-guided/computational design or directed evolution experience
- Scaling protein production for preclinical/development studies
- Prior cross-functional leadership; interface experience across protein engineering, conjugation chemistry, and therapeutic platform development
Application Instructions:
Apply via http://www.ionis.com; reference requisition #IONIS004044
Benefits/Pay Scale:
- Pay scale: $144,200–$196,444
- Assistant Director: $144,200–$176,800
- Associate Director: $165,597–$196,444