Jeff Ruffolo

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@jeffruffolo

Protein Design / ML @ProfluentBio | Molecular Biophysics PhD @JohnsHopkins

San Francisco, CA jeffreyruffolo.github.io Joined November 2014

188 Following 2.6K Followers 143 Posts

Latest posts 5

Jeff Ruffolo @jeffruffolo Jul 2

I’m heading to ICML in Seoul with the @ProfluentBio team. If you want to talk protein design, generative models, or anything BioML, come find me!

And if you want to meet the Profluent team, we're hosting dinners and doing coffee chats throughout the week. Sign up below.

Profluent Verified account @ProfluentBio Jul 2

The Profluent team will be at ICML in Seoul next week. Find us to chat, grab a coffee, or join us for dinner!

We’d love to talk shop (protein language models, protein optimization, sequence-first methods vs structure-first). Basically, anything at the intersection of AI and biology.

Want to grab coffee? Let us know here: forms.gle/yWQpAvLiQ1KfM8…

Or want to hang out and chat over dinner? Reserve a spot at our table: luma.com/qpc1mfw9
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Jeff Ruffolo @jeffruffolo Jun 30

Check out @park_jungy's work on discovering symmetry groups with flow matching at ICML on Wednesday!

Jung Yeon Park @park_jungy Jun 29

(1/8) Happy to share that our paper LieFlow has been accepted to #ICML2026.

Symmetry is a strong inductive bias in ML, but you have to know the symmetry in advance. Can a model discover it directly from data, for both discrete and continuous groups? 🧵

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Jeff Ruffolo @jeffruffolo Apr 28

Excited to share that we’ll be working with @EliLillyandCo to develop AI-designed recombinases for genetic medicine.

Profluent Verified account @ProfluentBio Apr 28

Today we announced a landmark partnership with @EliLillyandCo to use our AI models to design recombinases for genetic medicine—a collaboration valued at up to $2.25 billion before royalties.

The goal: use Profluent's AI models to design recombinase editors capable of inserting long stretches of DNA at precise locations in the genome.

Read the press release for more: businesswire.com/news/home/2026…

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Jeff Ruffolo @jeffruffolo Apr 24

We're hiring on my team at @ProfluentBio: Protein Design Scientist, Agentic Workflows.

Protein language models learn the evolutionary rules of natural sequences, but turning that into a design pipeline that works end-to-end is a different problem.

job-boards.greenhouse.io/profluent/jobs…

job-boards.greenhouse.io Profluent Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in...

Jeff Ruffolo @jeffruffolo Nov 14, 2025

I’m excited to share Profluent-E1, our internal encoder model for protein sequences, with the protein-ML community! The E1 series of models can be used as a drop-in replacement to upgrade a broad range protein modeling and design of workflows.

biorxiv.org/content/10.110…

www.biorxiv.org E1: Retrieval-Augmented Protein Encoder Models Large language models trained on natural proteins learn powerful representations of protein sequences that are useful for downstream understanding and prediction tasks. Because they are only exposed...