Case Study: Anagenex, a drug discovery company, accelerates next-gen drug discovery and unites bench and ML with Benchling

Teaming up with a trailblazer to develop next-gen drug discovery

Anagenex is a Bay Area drug-discovery startup combining DNA-encoded libraries (DELs) with machine learning to accelerate small-molecule discovery. Their challenge was managing highly complex DEL workflows and next‑gen sequencing readouts while avoiding machine‑learning traps like batch effects—requiring complete, standardized experimental metadata and a scalable, data‑first infrastructure from day one.

They implemented Benchling with a custom relational schema and templatized registration to link DEL constructs, DNA tags, and NGS results and to capture rich, consistent metadata. The platform let them decode sequencing readouts reliably, reduce data entry and cleanup time by 50%, better separate biological signal from artifacts, and is estimated to have doubled their discovery speed—while 100% of scientists agree Benchling helped connect bench and ML work.

Anagenex

Nicolas Tilmans

Chief Executive Officer