Manager Downstream Engineer Jobs in California (NOW HIRING)

Job Title: Associate Director/Director, Formulation & Downstream Process Development

Location:San Diego

Job Type:Full-Time

About Us:A new stealth-mode biotech focused on in vivo gene editing.

Job Summary:We are seeking an Associate Director/Director to lead downstream process development for our targeted lipid nanoparticle (tLNP) platform. This is a hands-on, lab-based role focused on the purification, concentration, and buffer exchange of tLNP drug product using size exclusion chromatography (SEC), tangential flow filtration (TFF), and complementary downstream unit operations. The successful candidate will be a technical expert in nanoparticle purification, responsible for developing robust, scalable downstream processes that deliver high-purity tLNP product while preserving particle integrity, targeting functionality, and cargo activity. This individual will also contribute to formulation development, stability assessment, and technology transfer to CDMOs. Title and salary commensurate with experience.

The Director will provide scientific and technical leadership for downstream process development activities, partnering cross-functionally to establish strategy, and support advancement of the company's tLNP platform while remaining an active technical contributor.

Key Responsibilities:

• Design, optimize, and execute downstream purification processes for targeted LNPs, with emphasis on SEC (gravity flow and column chromatography, including CIMmultus monolithic columns) and TFF (hollow fiber and flat sheet cassettes) at research and pilot scale.
• Develop and optimize TFF operating parameters including transmembrane pressure, cross-flow rate, membrane molecular weight cutoff selection, diafiltration volumes, and flux decay management to maximize product recovery and minimize particle stress.
• Establish SEC-based purification methods to separate assembled tLNP product from free protein, unincorporated lipid components, and process-related impurities; optimize resin selection, column loading, and elution conditions.
• Characterize downstream process intermediates and final drug product using DLS, zeta potential, nanoparticle tracking analysis (NTA), cryo-TEM, encapsulation efficiency assays, and protein/lipid quantitation methods.
• Evaluate and benchmark alternative and emerging purification modalities (e.g., bind-elute chromatography, membrane chromatography, depth filtration) for tLNP applications.
• Develop and optimize final formulation and buffer exchange conditions to ensure tLNP stability, including excipient screening, cryoprotectant selection, and lyophilization feasibility assessment.
• Lead process characterization studies to define critical process parameters (CPPs) and critical quality attributes (CQAs) for downstream unit operations.
• Support technology transfer of downstream processes to CDMOs, including process documentation (batch records, SOPs, technical reports), on-site support, and process troubleshooting.
• Collaborate with formulation scientists, analytical scientists, and biology teams to ensure downstream processes preserve LNP integrity, targeting ligand functionality, and cargo bioactivity.
• Design and execute process development studies using DOE approaches to systematically optimize purification and formulation parameters.
• Maintain detailed electronic laboratory notebooks and contribute to regulatory filings (IND/CTA) for downstream process and drug product CMC sections.
• Stay current with advances in nanoparticle purification, LNP downstream processing, and scalable manufacturing technologies.

• Provide scientific leadership for downstream process development strategy.
• Establish technical priorities across multiple programs.
• Partner cross-functionally with Formulation, Biology, Analytical, CMC, Manufacturing, and Regulatory.
• Represent downstream process development in technical and strategic discussions.

Qualifications:

• PhD. in Chemical Engineering, Biomedical Engineering, Pharmaceutics, Chemistry, Biochemistry, or a related field with 5+ years of industry experience; or M.S. with 8+ years of relevant industry experience, or B.S. with 10+ years of relevant experience.
• Demonstrated hands-on expertise in TFF process development for nanoparticle or biopharmaceutical applications, including membrane selection, process optimization, and scale-up.
• Direct experience with SEC or chromatographic purification of lipid nanoparticles, liposomes, or related colloidal drug delivery systems.
• Strong understanding of LNP formulation and characterization, including DLS, zeta potential, cryo-TEM, encapsulation efficiency, and particle stability assessment.
• Experience defining CPPs and CQAs for downstream processes and contributing to process characterization and validation.
• Proficiency with DOE-based experimental design and statistical analysis of process development data.
• Excellent scientific communication skills, including technical report writing, SOPs, and presentation of data to cross-functional teams.
• Ability to work independently in the lab, manage multiple projects, and mentor junior scientists.

• Demonstrated experience leading scientific programs and influencing cross-functional teams.
• Experience mentoring and developing scientists.
• Ability to establish technical strategy while remaining an active scientific contributor.

Preferred Qualifications:

• Direct experience with targeted or functionalized nanoparticle purification, including separation of decorated particles from free targeting ligands (e.g., antibodies, peptides, aptamers).
• Experience with monolithic column chromatography (e.g., CIMmultus) or membrane chromatography for nanoparticle purification.
• GMP manufacturing experience for LNP or liposomal drug products, including process validation, batch record authoring, and deviation investigation.
• Experience with AAV or viral particle purification and characterization.
• Experience with lyophilization process development for nanoparticle formulations.
• Familiarity with regulatory requirements for CMC sections of gene therapy INDs (ICH Q8-Q12) and experience supporting technology transfer to CDMOs.
• Track record of scientific publications and/or patents in LNP purification, downstream processing, or nanoparticle formulation.

Benefits:

• Competitive salary, equity, and benefits package. Salary Range $120,000 - $220,000 per year
• Opportunities for professional growth and development.
• Fast-paced collaborative and innovative work environment.

How to Apply:Interested candidates should submit their resume and a cover letter detailing their relevant experience. To be considered for the role, applicants must be:

1. Eligible to work in the United States for any employer without sponsorship.
2. Able to work onsite in the lab located in San Diego.
3. A direct candidate and not from a third party, i.e. staffing agency.