Senior Protein Scientist — Engineering Fusion Conjugates

Ionis Brand; Carlsbad (CA); On-site; USD 144,000 - 196,000; Full time

Benefits offered by this job

Ionis Benefits

Job summary

Ionis Pharmaceuticals, Inc. in Carlsbad, CA, seeks a Protein Scientist at Assistant Director or Associate Director level to lead protein discovery and production for conjugates with oligonucleotides.

You will design, optimize, and produce protein fusion constructs, collaborating across discovery, chemistry, and development teams. The role focuses on translating ligands into manufacturable formats, driving progression from early discovery to broader evaluation, and mentoring researchers in a

Qualifications

• PhD in protein science or related field with relevant industry experience.
• For the Assistant Director position: at least 5 years of industry experience.
• For the Associate Director position: at least 8 years of industry experience.
• Hands-on experience in recombinant protein expression and purification in microbial and mammalian systems.
• Expertise in protein engineering and construct optimization for expression, stability, and function.
• Strong track record of advancing protein molecules from discovery to scale-up.
• Experience generating and evaluating protein fusions or complex engineered formats.
• Experience with analytical methods used for protein characterization.
• Strong scientific judgment, experimental rigor, and problem-solving in fast-moving environments.
• Excellent written and verbal communication skills; publications.
• Ability to manage multiple assignments in a dynamic setting.
• Entrepreneurial spirit; translating cutting-edge science to applications.

Responsibilities

• Lead design, engineering, expression, purification, and characterization of protein ligands and fusion constructs for protein‑oligonucleotide conjugates.
• Translate hits into optimized lead molecules with better expression, stability, and manufacturability.
• Develop and execute protein production strategies selecting suitable platforms.
• Design fusion proteins and constructs for scale-up and conjugation workflows.
• Oversee purification and analytical characterization of recombinant proteins.
• Collaborate with oligonucleotide chemistry and conjugation teams for compatibility.
• Drive strategy, data interpretation, and decisions across programs.
• Mentor scientists and build capability in protein engineering and production.
• Present results and recommendations to cross-functional teams and leadership.
• Hands-on laboratory work will be expected.

Skills

Protein engineering

Molecular design

Recombinant protein production

Team mentorship

Experimental rigor

Data interpretation

Education

PhD in protein science

PhD in biochemistry/related

Tools

Analytical methods

Protein purification methods

Mammalian expression systems

Job description

Ionis Pharmaceuticals, Inc. in Carlsbad, CA, seeks a Protein Scientist at Assistant Director or Associate Director level to lead protein discovery and production for conjugates with oligonucleotides.

You will design, optimize, and produce protein fusion constructs, collaborating across discovery, chemistry, and development teams. The role focuses on translating ligands into manufacturable formats, driving progression from early discovery to broader evaluation, and mentoring researchers in a