Protein Scientist, Assistant Director or Associate Director

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

Headquartered in Carlsbad, California, and with offices in Boston, Massachusetts, and Dublin, Ireland, Ionis has been at work for more than three decades discovering medical breakthroughs that have redefined life for people with serious diseases. We’re pioneers in RNA-targeted medicines, and our platform continues to revolutionize drug discovery and transform lives for patients with unmet needs. With multiple marketed medicines and a leading pipeline in neurology, cardiology and select areas of high patient needs, we continue to drive innovation in RNA therapies in addition to advancing new approaches in gene editing to provide greater value to patients and are well positioned financially to deliver on our strategic goals.

At Ionis, we pride ourselves on cultivating a challenging, motivating and rewarding environment that fosters innovation and scientific excellence. We know that our success is a direct result of the exceptional talents and dedication of our employees.

With an unprecedented opportunity to change the course of human health, we look to add diverse individuals, skill sets and perspectives to our exceptional team. We continue to invest time, money and energy into making our onsite, hybrid and remote work environments a place where solid and lasting relationships are built and where our culture and employees can thrive.

We’re building on our rich history, and we believe our greatest achievements are ahead of us. If you’re passionate about the opportunity to have meaningful impact on patients in need, we invite you to apply and join us. Experience and contribute to our unique culture while you develop and expand your career!

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 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.

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 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

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

Ionis offers an excellent benefits package! Follow this link for more details: Ionis Benefits

Full Benefits Link: https://ionis.com/careers#:~:text=Highly competitive benefits

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

NO PHONE CALLS PLEASE. PRINCIPALS ONLY.

Ionis Pharmaceuticals, Inc. and all its subsidiaries are proud to be EEO employers.