Stephen Nayfach, our Head of Bioinformatics and Platform R&D, is at @CSHL this week for the Genome Engineering: CRISPR Frontiers event. Find him and say hi if you're there! 👋 He's giving a talk on using our AI models to design CRISPR-Cas9 variants for base editing ("Programming PAM Specificity for Mutation-Specific Base Editor Design") and also chairing the session "CRISPR Technologies I"

The Profluent team is heading to Summer RosettaCon next week! Find @jeffruffolo, @richardwshuai, @ShiakiMinami, and Alex Hoffnagle and say hi 👋 You can hear Richard talk about E1, our encoder model, on Thur at 1:30pm (“E1: Retrieval-Augmented Protein Encoders for Fitness and Structure Prediction”) and Alex share his work on our AI-designed base editors on Mon at 7:30pm (“Design of Programmable Base Editors with Protein Language Models”).

A suite of AI-designed base editors, all from one scaffold. The only piece unique to each patient is the guide RNA. That's the shift AI unlocks: rare disease moves from 'one drug at a time' to a platform, built to bring cost down and reach more patients. More on our work with GEMMABio, now backed by @ARPA_H's THRIVE program, below.

We're still in the GPT 1.5 era of AI × biology The early models already work (signal: our $2.25B Lilly partnership) but we're nowhere near the ceiling We're speedrunning to GPT 5 as fast as we can @thisismadani with @nathanbenaich @airstreet

Biology is no less complex than text and (in our biased opinion) way more impactful. Yet a fraction of the world's AI talent and compute is pointed at it. The field is wildly undersaturated. Watch @thisismadani chat with @nathanbenaich @airstreetcapital about the opportunity.

OpenCRISPR was the first demonstration that AI could design a genome editor from scratch. We used our AI model to build a protein that doesn't exist in nature for a specific function and it worked. Watch @thisismadani chat with @nathanbenaich @airstreetcapital about where we’ve gone from there (and where we’re going)

Our partnership with Eli Lilly carries up to $2.25B in milestones. The bigger story is the unlock behind it: large gene insertion, a problem AI makes solvable for the first time. Watch @thisismadani in conversation with @nathanbenaich @airstreet.

At PEGS Boston? Don't miss our Lead Protein Design Scientist Jeliazko Jeliazkov presenting "Designing Optimal Proteins at Scale" Generating proteins that are simultaneously optimal across many properties (affinity, stability, developability, and beyond) is a hard problem. Jeli's sharing our work on alignment of our foundational AI models as a path to multi-parameter protein optimization, with applications from gene editors to antibodies. Interested in learning more about our multi-parameter optimization work? Shoot us a DM.

We're at @ASGCTherapy today sharing something we've been heads down building: using our AI models to scale base editing for personalized medicine. The gap between what's theoretically correctable and what we can actually fix today is huge. We think AI can close that gap. Not there? Peter Cameron, our SVP of Gene Editing, breaks it down here. Interested in learning more? Shoot us a DM.

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/2…

We’re excited to share our latest work published today in @NatureBiotech: Protein2PAM, an AI model that enables the rapid design of CRISPR editors with new PAM recognition And we’re making the model freely available for research and commercial use: protein2pam.profluent.bio

Our BD team just wrapped a fun year-end off-site (spoiler: we did an escape room!) Now we’re gearing up for the annual trek to JPM next month. If you’d like to connect and learn more about the intersection of AI and protein design—gene editing, antibodies, and beyond—reach out, our DMs are open.

Today we’re excited to announce a new strategic collaboration with @EnsomaBio to advance AI-designed base editors for hematopoietic stem cell (HSC) therapies. The goal: durable, one-time treatments that target the root causes of hematologic and immune diseases. businesswire.com/news/home/2…

📅  Thu 4 Dec 4:30 - 7:30 PM PST 📍Exhibit Hall C,D,E #1702 🔗 neurips.cc/virtual/2025/loc/… 👀 Look for Aadyot, lead ML scientist at Profluent!

#NeurIPS2025 friends! Meet the Profluent team *today* to talk about ProGen3, our generative protein language model that’s solving problems in medicine and agriculture. We're sharing how we built ProGen3 and how we validated it with real wet-lab data.

Excited for #NeurIPS2025! Join us to discuss language models for protein design ranging from ProGen3 (NeurIPS spotlight), E1 (our open-source encoder model), and more!

Today we’re announcing $106M in new funding led by Altimeter Capital and Bezos Expeditions. This brings our total to $150M to scale our frontier AI models which make biology programmable. Our frontier models have generated functional proteins (Nature Biotech, 2023), created the first CRISPR system designed from scratch (Nature, 2025), and showed clear scaling behavior (NeurIPS spotlight, 2025). The opportunities ahead are unimaginable. If you’re excited by shaping the future of biology – join us in pushing the science forward. Forbes: forbes.com/sites/amyfeldman/… Press Release: businesswire.com/news/home/2… -- Nature Biotech, 2023: nature.com/articles/s41587-0… NeurIPS spotlight, 2025: biorxiv.org/content/10.1101/… Nature, 2025: nature.com/articles/s41586-0…

There’s always been a tension between addressing rare diseases and making the economics work. At Profluent, we believe that AI can be the equalizer, making it possible to design personalized genomic medicines and democratize the field of gene editing. Learn more about our partnership with the Rett Syndrome Research Trust:

AI can bring high quality genetic tools within reach for rare diseases. Today, Profluent is partnering with the Rett Syndrome Research Trust (RSRT) to design personalized genomic medicines for Rett syndrome. Our aim is to engineer compact editors that can fit into a single AAV delivery capsid, a key step toward reaching the central nervous system. Once there, our editors will need to precisely correct recurrent MECP2 hotspot mutations that drive Rett syndrome pathology. Rare disease used to mean rare attention. Specialized genetic tools were reserved only for the most common conditions. AI is changing that, bringing state-of-the-art biotechnology to a rare neurodevelopmental disorder that touches families every day. Profluent and RSRT are excited to bring the ProGen3 model and the full strength of our platform to bear on Rett syndrome. We’re working relentlessly toward a future when AI helps to make the best science accessible to all patients. 🔗 reverserett.org/news/article…

For both zero-shot fitness and unsupervised contact map prediction, E1 sets a new bar and unanimously beats baselines like ESM-2/C, PoET-1, and MSA-Pairformer. Feel free to use it as a drop-in replacement for these models.

E1 can take in homologous sequence in addition to an input query sequence. The homologous sequences are prepended to the input query sequence to construct a multi-sequence input to the model. E1 alternates between intra-sequence and block-causal attention, enabling it to build internal representations based on residues within the same protein sequence and those in preceding homologous sequences within the concatenated multi-sequence input.

Protein language models just got an upgrade. Meet Profluent-E1: a free, flexible, frontier protein sequence encoder. E1 is built with retrieval augmentation to learn from multiple sequences. Models trained over 4T tokens with only 150M-600M params, E1 is SOTA for zero-shot functional and unsupervised structural tasks. It raises the bar for protein representation learning and is freely available today.

Language models learn powerful representations of protein biology. At @CHI_Healthtech's PEGS Europe 2025 @thisismadani will introduce new foundation models that directly investigate scaling laws. This has relevant implications for antibody optimization and broader protein generation. Don't miss it. 🔗 pegsummiteurope.com/machine-…

"We're making biology programmable with AI" -- what does that even mean? Catch @thisismadani speaking at @WebSummit on the Profluent mission and why now? 🔗 websummit.com/attendees/lis2…

🔬 🤝📈 AI designed editors meets rare diseases. @HilaryEaton14 presents on democratizing OpenCRISPR-1 and the future of personalized medicine. Catch it all at GATC2025. 🔗 dynotx.com/gatc2025

We’re excited to announce our new partnership with @idtdna! Combining our AI with IDT’s world-class enzymology and manufacturing, this collaboration reflects our belief that AI-designed proteins can unlock step-changes in enzyme efficiency, precision, and manufacturability, without being constrained by what evolution has already tried. 🔗 idtdna.com/pages/about/news/…

We’re excited to announce a multi-year partnership between Profluent Bio and @Corteva Agriscience to accelerate sustainable, AI-powered crop innovation. 🌱🤝 Together, we aim to unlock new possibilities for developing resilient crops, improving resource efficiency, and advancing global sustainability goals. This partnership reflects the transformative potential of AI in biology—delivering real-world solutions for farmers and communities worldwide. 🔗 businesswire.com/news/home/2… #AI #Agriculture #Sustainability #GeneEditing

👋🇪🇸 Hola, #ESGCT Let’s talk next-gen genome editing. Our foundational ai models (e.g., ProGen3*) can generate editors such as OpenCRISPR-1† and novel enzymes‡ that companies and labs can use today. Message our CBO, @HilaryEaton14, to explore collaborations. * profluent.bio/showcase/proge… † profluent.bio/modality/openc… ‡ news.revvity.com/press-annou… #GeneTherapy #CellTherapy #AIinBiology

🌵🧬 We’re headed to Phoenix for the Alliance for Regenerative Medicine’s Cell & Gene Meeting on the Mesa, Oct 6–8. If you’re attending, let’s connect! @HilaryEaton14 and Jim Knabb will be on-site and would love to talk before or during the conference. Don’t miss our presentation on Monday the 6th. #CGMesa25 #CellandGeneTherapy #CellTherapy #GeneTherapy #AIinBiology #OpenCRISPR

We are excited to announce that our work on ProGen3 has been accepted as a Spotlight paper at NeurIPS 2025 – the premier AI research conference. This year NeurIPS received 21,575 valid submissions, of which only 3.2% earned a Spotlight distinction. We’re thrilled that ProGen3 is among them. 🎉 ProGen3 is a family of generative protein language models, scaled up to 46B parameters, trained on our curated Profluent Protein Atlas which continues to grow as the largest protein sequence data resource in the world. It brings compute-optimal scaling, sparse architectures, and alignment with experimental data into the domain of protein generation.

We’re proud to announce a new partnership between Profluent Bio and @RevvityInc 🤝 that represents an important step forward in base editing. By combining Profluent’s AI-engineered adenine deaminases 🧬 with Revvity’s Pin-point™ base editing platform 🎯, we are delivering AI-enhanced base editing systems designed for therapeutic applications where precision, safety and reproducibility are paramount. This collaboration opens the door to: - Unmatched precision—the power to base edit at the single-nucleotide level, eliminating bystander activity - Tailored versatility—a handpicked portfolio of AI-crafted enzymes broadens the scope of treatable mutations - Effortless access—bundled licensing from Revvity speeds up adoption for therapeutic innovators

In a conversation with Nicole Raleigh of @pharmaphorum, our CBO @HilaryEaton14 discusses how AI is reshaping the drug development paradigm, promising applications in gene editing, and the potential to speed new treatment options for people living with rare diseases. Listen here: pharmaphorum.com/rd/changing…

Profluent has been named to @mariogabriele’s Future 50, featuring some of the world’s highest-potential companies! We were recognized for our moonshot achievements in AI-first protein design, including successfully editing human DNA with an AI-created gene editor and validating the existence of AI scaling laws in biology. This is just the beginning as we revolutionize biological design from discovery to invention.

Heading to Summer #RosettaCon 2025 hosted by @RosettaCommons? Our Head of Protein Design @jeffruffolo is chairing the panel Protein Language Models: Power and Limitations of Scaling for Structure, Function, and Design at 8:45am PT on Tues, Aug 5. You can also catch Jeff on the Chalk Talks: Careers in Industry panel at 2:40pm PT that day. Hope to see you there!

We’re excited to share new data published in @Nature detailing the impressive activity, specificity, and low immunogenicity of our AI-designed CRISPR-Cas proteins, including OpenCRISPR-1. The future of gene editing is here and we’re scaling our capabilities to tackle the hardest problems that will unlock new medicines.

Next week @thisismadani joins #AIxBio25, hosted by @ConnectingSci @eventsWCS, to explore scaling benefits in protein design in his talk, “Scaling Foundation Models for Protein Generation.” Learn more: bit.ly/4gh164E

We welcomed summer (a little early) with a picnic and a few rounds of Uno. Uno may be polarizing, but we think it brings out the best in us, with a bit of fun, fierce competition, and some lively debate about house rules. In fact, these are the values that fuel our work daily.

We're heading to #BIO2025 in Boston (June 16-19)! Our CEO @thisismadani and CBO @HilaryEaton14 will be representing Profluent onsite and are eager to connect with fellow industry leaders and discuss the future of this exciting field. Let’s collaborate!

On June 16, @HilaryEaton14 will join @jenasherphd of @1910Genetics and Martin Gomez, Sarah Solomon and Robert Carroll of @goodwinlaw on a “Diligence Considerations with Tech Acquirers and IP Risks from AI in Drug Discovery and Development” panel during #BIO2025.

Profluent will be at #TIDESUSA in San Diego next week! Join us on May 19-22, 2025 and drop us a line to connect. @HilaryEaton14 will be onsite to discuss how partners can license our molecules and models to tackle the most challenging protein design problems.

Make sure to catch @thisismadani at #PEGSSummit next week for a talk titled, “Scaling Foundation Models for Protein Generation,” on Thursday, May 15 at 4:30pm PT to investigate scaling effects and molecular design applications for our latest foundation model suite, ProGen3.

Attending the @ASGCTherapy’s #ASGCT2025 next week? Meet with our CBO @HilaryEaton14 to explore how we can build together.

At #SynBioBeta2025, @thisismadani will join a panel titled, "AI-Powered Biological Design: Breaking Barriers or Hitting Limits?", with @BrianHie, @julian_englert, and Esteban Toro to explore the evolving landscape of AI in biological design.

We’re opening early access to ProGen3 for select users. For your protein engineering needs, are you looking to generate a new starting point or optimize a given sequence? Check out our instructional video below. vimeo.com/1079479747/7ec755a…

ICYMI: Our platform enables generation of unique Cas-like systems that are less than 1/2-1/3 the size of legacy Cas9 proteins, with demonstrated functionality in the wet lab. These molecules (and more) are ready for licensing. Find out more below 👇