full stack AI x Bio engineer @romerolab1 | prev. @MSFTResearch

Durham, NC
Joined May 2024
Highly recommend applying for the opportunity to work with world-class researchers at the intersection of machine learning and biology, in the heart of Cambridge, MA. One of my favorite experiences of all time!
Are you a PhD student interested in the intersection of machine learning and biology or healthcare? Come do an internship with the BioML Group at MSR! Make sure you submit a research statement! apply.careers.microsoft.com/…
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plot twist: OpenAI retracts the result on the Hodge conjecture.
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Incredible. If the key argument for watermarking proteins is biosecurity, it is a weak argument in my opinion. If there is another argument for watermarking proteins outside of biosecurity, I'd love to hear it
Biosecurity is too important for security theater. In a quick test with Raygun, we found that DeepMind's SynthIDBio watermark signal could be washed out while preserving the predicted structure. We don’t think protein sequence watermarks buy much biosecurity.
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Today we are announcing Topos-2, our next-generation model for generating the full range of shapes a protein can take, across the order-disorder spectrum. We are also previewing Topos-Bind: to our knowledge, the first generative model to capture the range of shapes for disordered proteins bound to small molecules. Read the technical blog post here: toposbio.ai/topos-2-topos-bi… (1/7)
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Use your favorite LLM inside PyMol to manipulate molecules with a cool new tool from the Romero lab💻🧪 All you need is an API key!🔑 Check it out and send us feedback here! github.com/RomeroLab/pymol-c…
Have you ever wanted to talk to your molecules? Now you can with Chat with PyMOL! We built this in the Romero Lab to make PyMOL more accessible to our BME undergrads, but quickly found it’s simply a better way to interact with molecular structures. (1/2)
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Benjamin Perry retweeted
These guys find "by AI" a gene which perhaps may have a CRISPR-like function. The CEO hypes this on Twitter as if they did in fact cure all diseases in 5 years. No function. No mechanism. No peer review. Nothing besides something any undergrad could do. Sad.
Today we announced the Claude-led discovery of a molecular machine that we suspect could represent a new gene editing mechanism. Its precise function, biotechnological utility (if any), or level of significance is not yet clear, but at minimum it is work I would have been proud to do as a PhD student. The work was done mostly, though not entirely, by Claude: our life sciences team suggested a broad area of research, Claude read through the literature and a bunch of genome data and discovered something interesting, then Claude proposed experiments to verify the discovery and our team carried them out. It’s easy to dismiss this as a one-off or curiosity, but we’ve repeatedly seen a pattern where AI performance in new intellectual domains goes from weak to superhuman in a matter of a few years. In 2023 models struggled to do math at the level of an average high-school student. In 2024 they started to do well on math competitions for the best high-schoolers in the country, in 2025 they started to solve minor open problems, in early 2026 more significant open problems, and in late 2026 they are beginning to solve the top few open problems in all of mathematics. We believe AI for biology is on a similar exponential trend. The main difference between biology and mathematics, of course, is that math can be done purely theoretically, while biology requires experimentation. Some have used this to draw the conclusion that AI’s utility in biology will be limited. We think this is wrong. As we’ve demonstrated today, humans can collaborate with AI to perform the experiments, validate key results in a few weeks and, if necessary, work with the AI to iterate on what they find. Eventually it may even be possible for Claude itself to safely perform the experiments by autonomously controlling lab equipment, with appropriate safeguards in place, but we aren’t doing that today (our lab is also a BSL1/BSL2 facility that doesn't handle materials dangerous to humans). More broadly, biomedical advancement has many stages — from fundamental biology discoveries, to translational research, to drug discovery, clinical trials, and finally the actual delivery of medicines and health care to patients. We are also interested in these later stages, but even simply accelerating the first stage of fundamental biological discoveries has the potential to speed up and broaden the entire pipeline. Improving our understanding of biology and sharpening biologists’ tools can drive forward all of the later stages, for example by identifying new drug targets, finding new therapeutic modalities, allowing for more precise measurement, and speeding up the experimental loop which itself further accelerates our understanding of biology. This will not in itself speed up clinical trial times, but if it succeeds it could greatly increase the number of promising candidates that go into the pipeline — an increase in throughput even though latency remains. In Machines of Loving Grace, I wrote about AI’s potential to “cure most diseases in 5-10 years” — a goal that sounds impossible, but one I believe is just barely possible if AI is applied to every stage of the pipeline. The first step is showing that AI can first help with, and then drive, biological discoveries. Claude’s discovery is the latest in a line of related prior work that goes back decades, beginning with systems like CRISPR, and continuing with discoveries like the bridge recombinase and VIPR in the past few years. Recently, there has been heightened interest in systems based on reverse transcriptase (RT) enzymes, the enzyme underlying the system Claude identified. And most recently, a Stanford team working independently described a novel RT system with an associated non-coding array that is in some ways similar to the one Claude found, though they are distinct systems that evolved independently from each other. I believe that we’re at the very beginning of finding such systems and developing them into powerful tools for biotechnology. I’m proud of the resources Anthropic has invested in accelerating the public benefits of AI through the life sciences, and we’re aiming both to grow our life sciences team and to work with other scientists to extend this approach to a broad range of problems. If you have a proposal for a research collaboration or are interested in joining our life sciences team, please reach out.
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I think they set the limit to 20 papers per author and still to this day I think that is an insanely large number. Why can't it be no more than 3 papers? These conferences happen every 4 months; there's no way people meaningfully contribute to more than 3 papers every 4 months
60k+ ICLR 2027 submissions is more than all prior ICLRs combined
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Proteina-Complexa adds exciting new experimental results with a very large protein all co-designed!
Our wet-lab validation campaign for Proteina-Complexa is now on bioRxiv! It includes some new exciting experimental results, from large protein structures (fully codesigned!) to functional carbohydrate binders. biorxiv.org/content/10.64898… Thread with some of the additions 🧵1/n
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I'd like to see AI companies do a benchmark where they do training cutoff 1 year before a discovery, and see if their models can come up with that discovery themselves. Without researcher guidance, I doubt they can do that.
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Protein design requires feedback from the lab🔬 Reinforcement Learning from Experimental Feedback (RLXF) demonstrates this can help generate proteins that fluoresce much more than wild-type. Check it out! nature.com/articles/s41467-0… Great work by the @romerolab1
really excited to share our work is in press @NatureComms today. when i met with @romerolab1 back in sep 2022, hoping to rotate in the lab, one of my first questions was “have you thought about RLHF?” his eyes lit up and he said “YES!”. fast forward to sep 2026, i can truly say this project challenged me in every way possible. this was a real labor of love. i learned so much about myself, the field, and where it’s heading working on this with @NathanielBlalo2 and the rest of my amazing colleagues. i hope you find this work insightful if you happen to give it a read. nature.com/articles/s41467-0…
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*trains on interaction data from researcher very close to Navier-Stokes solution* *probably has some sort of internal attempt already going* *hears another researcher is close to solving* *launches 10,000 agents with info about approach and scoops in 10 days* lol
We’re sharing a solution to the Navier-Stokes Millennium Prize Problem, one of the deepest problems at the frontier of mathematics. The proof was produced by a group of agents, using an OpenAI next-generation model significantly more capable than GPT-6 Astra. The problem concerns whether the description of smooth three-dimensional fluid motion modeled by the Navier-Stokes equations can break down. It has remained unresolved for roughly 90 years.
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Few/one step code generation with PlaidQ Check it out!
This quoted post is unavailable.
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A very well written guide to different use cases of PyLabRobot Check it out!
Very excited to announce the PyLabRobot Cookbook from the Chory Lab! This cookbook showcases many usage examples and design patterns that should help you get started writing PyLabRobot code quickly. I strongly recommend this cookbook to anyone interested in lab automation!
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Don't get me wrong, this is very cool. But if you read into it, the workflow is: * prompt claude about thing X you want to control and how to use it * it writes code to operate it and a background agent to control/monitor it That's standard claude code right?
Today, we're kicking off the first phase of the research preview for Model Hardware Standard (MHS): a new standard for AI agents to safely operate physical equipment in scientific research and advanced manufacturing. Read more: anthropic.com/news/model-har…
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Binder design is nice and all, but here we have three agents sharing data and autonomously controlling a lab to design enzymes with shifted substrate scopes and high activity! @cobanbrooks @NotinPascal @romerolab1
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Claude Science when it becomes a wrapper on existing tools
Many drugs work by binding to a specific target in the body and blocking or changing what it does. An important first step in the drug development process is designing a molecule that can bind tightly to its target. Traditionally, that's meant weeks or months of expert work per target, sifting through a large number of candidates to identify the few that work. We wanted to test if Claude could successfully design novel protein binders from scratch (also called de novo design). With a protein design prompt written by a human expert, Claude autonomously designed protein binders against 14 out of 15 targets. We then worked with Adaptyv Bio and Twist Bioscience, who independently built and tested the proteins Claude designed.
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Benjamin Perry retweeted
I’m really excited to share our new preprint, out today, where we built a fully autonomous system for enzyme engineering — integrating a self-driving lab with a generative protein language model that worked together over a month to engineer substrate specificity in glycoside hydrolase (GH1) enzymes. biorxiv.org/content/10.64898… [1/n]
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Nature is full of super rare proteins in metagenomics data that don’t cluster with anything else. Often these “singleton” proteins are thought to be fragments or errors. Turns out, they are useful! Check it out below
When training protein language models, people usually discard metagenomic proteins that don't cluster with at least 1 other protein (singletons). With @riavinod_ @Samir_char @avapamini @lorin_crawford , we show that this is probably not the right strategy.
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Enzyme design just got fully automated🧪🤖 AI protein engineering is great but you still have to synthesize the designs in the lab, get data, and update your model. The latest work from @cobanbrooks, @NotinPascal, and @romerolab1 changes this. 📝Paper: biorxiv.org/content/10.64898…
I’m really excited to share our new preprint, out today, where we built a fully autonomous system for enzyme engineering — integrating a self-driving lab with a generative protein language model that worked together over a month to engineer substrate specificity in glycoside hydrolase (GH1) enzymes. biorxiv.org/content/10.64898… [1/n]
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