Director, Protein Engineering

SystImmune, Inc.; Bothell (WA); On-site; USD 180,000 - 240,000; Full time

Benefits offered by this job

100% paid employee premiums for health

401(k) with 50% company match up to 3%

15 PTO days per year

11 paid holidays

Job summary

SystImmune seeks a Director of Protein Engineering in Bothell, WA to lead the FUSE team, drive platform ownership, and guide program-level decisions across bi-specific/multi-specific antibodies and ADCs. The role combines hands-on leadership with strategic direction and cross-functional collaboration.

The successful candidate will own the next-generation yeast display platform, oversee library design, selection workflows, and integration with automation, while mentoring scientists and advancing

Qualifications

• PhD in protein engineering, biochemistry, structural biology, molecular biology, bioengineering, or related field.
• Minimum 10 years of industry experience in biologics drug discovery and development.
• Minimum 8 years of hands-on experience with yeast display, including library design and construction, FACS-based selection and sorting, deep sequencing, and downstream characterization.
• Demonstrated experience building or substantially advancing a yeast display platform with integration to automation.
• Track record leading a team of scientists and research associates with hiring, mentoring and performance management.
• Delivery of engineered binders or therapeutic leads into a biologics pipeline, ideally including bi-specific or multi-specific formats.
• Strong knowledge of antibody formats and engineering strategies (IgG, Fab, scFv, VHH).
• Experience leading display campaigns alongside discovery modalities (phage display, AI-based design) preferred.
• Excellent scientific judgment and decisive campaign strategy, hit triage and resource allocation.
• Strong written and verbal communication skills for senior leadership and external partners.

Responsibilities

• Lead and mentor a team of scientists and research associates with clear direction and career development.
• Own and advance the next-generation yeast display platform and integrate with FUSE automation.
• Direct display-based discovery and engineering campaigns for bi-specific and multi-specific antibodies and ADC binders.
• Represent FUSE in project teams and portfolio reviews; translate program needs into platform deliverables and timelines.
• Ensure data quality, reproducibility, and SOP/LIMS compliance across the team.
• Stay current on innovations in protein engineering, display tech, and lab automation.

Skills

Leadership

Team management

Communication

Protein engineering

Project planning

Decision making

Data interpretation

Education

PhD in protein engineering or related field

Tools

Yeast display platform

FACS-based selection

Laboratory automation

NGS

Job description

SystImmune is a leading and well-funded clinical-stage biopharmaceutical company located in Bothell, WA and Princeton, NJ. It specializes in developing innovative cancer treatments using its established drug development platforms, focusing on bi-specific, multi-specific antibodies, and antibody-drug conjugates (ADCs). SystImmune has multiple assets in various stages of clinical trials for solid tumor and hematologic indications. Alongside ongoing clinical trials. SystImmune has a robust preclinical pipeline of potential cancer therapeutics in the discover and IND-enabling stages, representing cutting-edge biologics development.

SystImmune is seeking a Director of Protein Engineering to lead the FUSE team. This is a hands-on scientific leadership role that combines team management, platform ownership, and program-level decision making across the company’s bi-specific, multi-specific antibody, and ADC pipeline. The Director will own and continue evolving the next-generation yeast display platform built to integrate directly with the FUSE automation wet lab, lead a team of scientists and research associates executing display-based discovery and engineering campaigns, and partner closely with discovery biology, antibody discovery, CMC, and computational teams to deliver optimized lead molecules into the pipeline.

This is a full-time onsite position in Bothell, WA.

Key Responsibilities

Leadership and team management

Lead, mentor, and develop a team of scientists and research associates, setting clear technical direction, performance expectations, and career development paths. Build team structure, hiring plans, and resource allocation to match pipeline demand; partner with HR on recruiting, onboarding, and retention. Establish team operating rhythms, including project reviews, technical reviews, and platform roadmap planning.

Platform ownership: next-generation yeast display

Own and advance the next-generation yeast display platform, including library design, surface display formats, selection workflows, and downstream characterization. Drive integration of the yeast display platform with the FUSE automation wet lab, including liquid handling, automated sorting workflows, cell-free expression, and LIMS/data infrastructure. Define platform performance metrics (throughput, diversity, hit rate, developability) and lead continuous improvement against those metrics. Evaluate and onboard new technologies, instrumentation, and methodologies; build the case and budget for capital investments where warranted.

Program and pipeline impact

Direct display-based discovery and engineering campaigns for bi-specific and multi-specific antibodies, ADC binder components, and effector molecules across oncology programs. Lead engineering strategy for affinity modulation, stability and developability optimization, epitope masking, conditional activation (pH, protease, etc.), and other novel binder properties. Represent FUSE on project teams and at portfolio reviews; translate program needs into platform deliverables and timelines.

Scientific rigor and operations

Ensure data quality, reproducibility, and integrity across the team; oversee SOPs, LIMS usage, and documentation standards. Use NGS, flow cytometry, and computational tools to inform iterative protein design and lead selection. Stay current on the protein engineering, display technology, and lab automation landscape; bring relevant advances into the platform.

Qualifications

• PhD in protein engineering, biochemistry, structural biology, molecular biology, bioengineering, or a related field.
• Minimum 10 years of industry experience in biologics drug discovery and development.
• Minimum 8 years of hands-on experience with yeast display, including library design and construction, FACS-based selection and sorting, deep sequencing analysis, and downstream characterization of selected binders.
• Demonstrated experience building or substantially advancing a yeast display platform, including integration with laboratory automation (liquid handlers, automated cell sorters, LIMS, or equivalent).
• Track record leading and developing a team of scientists and research associates, with clear examples of hiring, mentoring, performance management, and career progression.
• Demonstrated delivery of engineered binders or therapeutic leads into a biologics pipeline, ideally including bi-specific or multi-specific formats.
• Strong working knowledge of antibody and binder formats (IgG, Fab, scFv, VHH) and engineering strategies including affinity maturation, stability and developability optimization, and conditional activation.
• Experience leading display campaigns alongside complementary discovery modalities (phage display, immunization-derived repertoires, in silico/AI-based design) is strongly preferred.
• Excellent scientific judgment and the ability to make timely, decisive calls on campaign strategy, hit triage, and resource allocation.
• Strong written and verbal communication skills, with the ability to represent the function to senior leadership and external partners.

Preferred Qualifications

• Experience in oncology biologics, ADCs, or T cell engagers.
• Familiarity with computational and machine learning approaches to library design and binder optimization.
• Experience presenting at scientific conferences, contributing to patents, and publishing in peer-reviewed journals.

Compensation and Benefits:

The expected base salary range for this position is $180,000 - $240,000 annually. Actual compensation will be based on a variety of factors, including but not limited to a candidate’s level qualifications, experience, and skills.

SystImmune is a leading and well-funded biotech company with a bright future. We offer an opportunity for you to learn and grow while making significant contributions to the company’s success. SystImmune offers a comprehensive benefits package including: 100% paid employee premiums for medical/dental/vision, also STD, LTD, a 401(k) plan with a 50% company match of up to 3% and a vesting schedule of only 5 years, 15 PTO days per year, sick leave, plus 11 paid holidays and MORE.

We offer an opportunity for you to learn and grow while making significant contributions to the company’s success.

SystImmune is an Equal Opportunity Employer. We welcome diverse talent and encourage all qualified applicants to apply.