Aditi Merchant
55 posts
@aditimerch
BioE PhD student @stanford in the Hie Lab // ML for SynBio
In new work, we lay out a vision for a high-level programming language for generative biology, called Proto. Proto composes generative and predictive models spanning DNA, RNA, proteins, ligands, and their interactions, which we use to design complex biological functions. 1/n
@aditimerch @BrianHie @euanashley @dan_guo_ @leba1127 @ev_hur @tinabmai @peteryin21 @samuelhking
Germinal is out today in Nature Biotechnology! Important additions to VHH design from the preprint: we demonstrate scFv design, evaluate binder polyreactivity, and characterise epitope specificity by alanine mutagenesis and a beautiful cryo-EM structure… nature.com/articles/s4158…
Biological engineering has long aimed to make biological systems designable, composable, and programmable across scales and modalities. However, existing biological AI models and tools are siloed and difficult to compose. Today, we’re proud to share our preprint for Proto, a high-level programming language and open infrastructure layer generative biology. *This thread is centered around the Proto Language. For the full paper thread, check out: x.com/aditimerch/sta…
Performing bioinformatics analysis and building biological design pipelines can mean a lot of infrastructure fighting: fragmented tools, idiosyncratic formats, and APIs that are hard to compose. That friction slows researchers down, and as this Anthropic blog post lays out, it's now a major bottleneck for modern agents as well. Today, we're releasing Proto, a design platform for generative biology. This thread is on the layer that makes it work: proto-tools, a universal open-source infrastructure layer for biological models and tools.
