Summary

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.

Job description

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.

Requirements

B.S. or M.S. in Biochemistry, Molecular Biology, Chemical Engineering, Virology, or a related field
2–5 years of relevant industry experience
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
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

Benefits

Annual performance-based bonus
Stock options
Medical, Dental & Vision
401(k) plan
Flexible PTO & holidays
On-site gym
Onsite lunch
Commuter support

Company overview

Manifold Bio is a pioneering platform therapeutics company founded in 2018 that is revolutionizing drug discovery through its AI-guided direct-to-vivo discovery platform. The company has developed the first high-throughput in vivo (HTV) discovery engine that combines massively multiplexed in vivo screening with AI-powered protein design to create targeted biologics. Based in Boston, Massachusetts, Manifold Bio's innovative approach enables the testing of thousands of molecules simultaneously in living systems, providing physiologically relevant data at unprecedented scale. This allows the company to overcome traditional translational barriers in drug development and create tissue-targeted medicines for neurodegenerative, metabolic, and other major diseases. The company's mDesign engine integrates AI-guided protein design with multiplexed in vivo data, creating a virtuous cycle of design and translation. Manifold Bio has raised over $78 million in funding and recently entered into a strategic collaboration with Roche worth up to $2 billion to develop next-generation brain shuttles for neurological diseases. With a team of 11-50 employees, the company is positioned to become a leader in tissue-specific medicines by unlocking AI's full potential with translationally relevant data generation.