Associate Scientist, AAV Vector Production

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of living systems.

Using proprietary molecular barcoding technology, we screen hundreds of thousands of protein designs simultaneously in living systems, producing in vivo-validated datasets at a scale no one else can match. The datasets power our computational models, which leads to better drug designs, creating a flywheel that gets stronger with every campaign. Our team of protein engineers, biologists, and computational scientists works across this full stack to pursue programs both internally and with leading pharma companies.

Position

We are seeking an exceptional

Associate Scientist with hands-on expertise in adeno-associated virus (AAV) vector production, purification, and analytical characterization to join our team. In this role, you will contribute end-to-end to the generation of high-quality, well-characterized AAV lots that enable both rodent and non-human primate (NHP) in vivo studies.

You will scale transient transfection, optimize downstream purification processes (affinity chromatography, ion exchange, tangential-flow filtration), and perform key characterization assays (qPCR/ddPCR, ELISA, HPLC, SDS-PAGE, western blot, CGE, endotoxin, sterility). You will be responsible for processing ex-vivo tissues and preparing samples for NGS analysis. You will work closely with molecular biology, protein engineering, in vivo pharmacology to ensure timely delivery of qualified vector lots.

Responsibilities

• Produce, purify, and qualify AAV vector lots, from plasmid DNA to study-ready material.
• Maintain and troubleshoot cell-culture systems.
• Develop and execute QC assays; analyze, interpret, and report data.
• Drive process-optimization experiments to improve yield and quality.
• Process ex-vivo tissues for NGS analysis
• Communicate progress, timelines, and results to cross-functional teammates.
• Required Qualifications
• Education & Experience
• B.S. or M.S. in Biochemistry, Molecular Biology, Chemical Engineering, Virology, or a related field, with 2–5 years of relevant industry experience.
• Wet-Lab Expertise
• Hands-on experience producing AAV in HEK293 (triple transfection), from ≤1 L to ≥50 L scale.
• Proficiency with downstream purification techniques, including affinity and ion-exchange chromatography, or gradient ultracentrifugation.
• Analytical Expertise
• Experience with viral-genome titer assays (qPCR, ddPCR) and capsid quantification (ELISA, A260/280, western blot).
• Working knowledge of purity and impurity assays such as SEC-HPLC/UHPLC, capillary gel electrophoresis (CGE), LC-MS, SDS-PAGE.
• Ability to troubleshoot analytical methods and interpret data to drive process decisions.

Preferred Qualifications

• Prior experience leading or supporting ≥1 × 10¹⁵ vg-scale AAV campaigns for NHP studies.
• Protein purification experience (AKTA-FPLC, affinity chromatography, preparative SEC, ion-exchange chromatography
• Library-scale cloning (Golden Gate Assembly, Gibson Assembly)
• NGS library prep experience
• Experience with other viral vectors (e.g., lentivirus, adenovirus) or lipid-nanoparticle formulation.
• This Role Might Be Perfect For You If
• You take pride in meticulous lab work and hold yourself to high standards, including clear, thorough electronic lab-notebook documentation.
• You stay organized and communicate clearly while juggling multiple projects in a fast-paced environment.
• You thrive in collaborative, cross-functional teams and are excited about integrating experimental and computational approaches to solve complex problems.
• If you’re excited to build the high-quality AAV vectors that power large-scale in vivo screening of novel protein designs, and to contribute directly to our mission of advancing breakthrough treatments, please apply!
• Base Salary Range: $100,000-$115,000
• This reflects the typical offer range for this role, based on experience, role scope, and internal equity. Final compensation decisions are made using a consistent leveling framework and consider the candidate’s experience, interview performance, and expected impact.
• This role is eligible for: Annual performance-based target bonus
• Stock options
• Comprehensive medical, dental, and vision coverage
• 401(k) plan
• Flexible paid time off and holidays