Joined November 2023
Super excited to share what we’ve been working on in collaboration with @SynBioGaoLab over the past few months on de novo antibody design. Check out this great thread by our team lead @santimillef highlighting the technical aspects of the pipeline!
The ability to design antibodies against any protein of interest has major implications for medicine, biotech, and basic science. Today, we introduce Germinal, a pipeline for epitope-targeted de novo antibody design achieving  4–22% success rates with efficient experimental validation.
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John Wang retweeted
Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.
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John Wang retweeted
I am honored to have been selected as one of MIT Technology Review's Innovators Under 35 this year. 🔗ter.li/05p3ttfg 🔗technologyreview.com/superto… This recognition is shared with the many amazing people I get to work with everyday as a @bioe_stanford PhD student and at @arcinstitute. Doing research alongside my brilliant labmates and advisor @BrianHie has been the best part of my PhD, and the science is truly a product of that. My research has been driven by the insight that biology operates on design principles that can be leveraged to transform medicine, sustainability, materials, and beyond, and that computational modeling, including AI, will help us decipher those design principles at scale. Nature's innovations are written in genomes, and we have a long way to go in understanding them. You can read more about some of our efforts developing AI to understand and design genomes in my comment below. Thank you to everyone at the @techreview and all the judges for organizing this, especially @AmyNordrum and @antonioregalado, for your support. I can't wait to see all the incredible things the other Innovators do!
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John Wang retweeted
Following the publication of our phage gen paper, I wrote some personal thoughts on biosafety and biosecurity as generative biology improves. Given the trajectory of progress, there should be concern and urgency -- but also optimism. brianhie.com/present_and_fut…
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John Wang retweeted
Our work led by @talaldotpdb on aligning protein generative models to experimental fitness with ProteinDPO is now published in @naturemethods! New in the published paper includes stabilizing mutations to H5 hemagglutinin, a component of flu vaccines. nature.com/articles/s41592-0…
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John Wang retweeted
Today in @ScienceMagazine, we report the first functional AI-generated genomes. 🧵 science.org/doi/10.1126/scie…
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John Wang retweeted
Introducing Kimi K3: Open Frontier Intelligence 🔹 2.8 Trillion Parameters, 1 Million Context, Native Multimodal 🔹 Kimi Delta Attention enables up to 6.3x faster decoding in million-token contexts 🔹 Attention Residuals deliver ~25% higher training efficiency at <2% additional cost 🔹 Built for long-horizon agentic coding and self-evolving workflows Kimi K3 is now live on on Kimi.com, Kimi Work, Kimi Code, and the Kimi API. Open Weights by July 27, 2026. 🔗 API: platform.kimi.ai 🔗 Tech blog: kimi.com/blog/kimi-k3
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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/s41587-0…
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🐐 team!!
Replying to @dan_guo_
Special shoutout to my incredible PI @brianhie, my co-first authors @aditimerch @bviggiano_13 and the rest of the amazing Proto team @leba1127, @ev_hur, @tinabmai, @peteryin21, @samuelhking.
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John Wang retweeted
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
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A bit of news: After nearly 9 years, I have decided to leave Google DeepMind and join Anthropic (after taking some time to recharge). I am incredibly grateful for my time at GDM. @demishassabis took a real chance letting me lead the AlphaFold team just six months after finishing my PhD, and the entire GDM team taught me so much about how to do great science. GDM is a special place, and I’ll still be excited to hear about what amazing things they discover next.
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John Wang retweeted
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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John Wang retweeted
🚀 Excited to share our new work: Absolute Stability Predictor! 📊: forms.gle/4ZnXZSnTBvaykkAi9 Built the MGnify Stability Dataset (1.8M+ measurements) and developed stability prediction models, together with @grocklin, @KotaroTsuboyama, @sokrypton, and teams.
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John Wang retweeted
BREAKING: Victor Wembanyama has joined Anthropic.
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John Wang retweeted
We present SWE-chat: the first large-scale dataset of coding agent interactions from real users in the wild. In 40% of real coding sessions, the agent writes ~all the code. Users push back 39% of the time – agents almost never stop to check. Data, paper, & findings in the 🧵👇
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John Wang retweeted
Hang it in the Louvre, because that's Aert
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🤯🤯🤯
That was probably my favourite celebration from Tadej Pogačar, ever. No prepared salutation to the audience, no grandiose gesture, just a pure, authentic human reaction to winning the hardest-to-win monument in professional cycling. #MilanoSanremo
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First concrete evidence I’ve seen of sequence and structure co-design being superior to backbone generation + redesign, very cool!
🧵 We ran the largest head-to-head benchmark of protein binder design methods in the wet lab. Project page: research.nvidia.com/labs/gen… 1 million designs. 127 targets. RFdiffusion, BindCraft, BoltzGen, and Proteina-Complexa — all tested side by side.👇
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Evo 2, the largest fully open biological AI model to date, is now published in @Nature.
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John Wang retweeted
Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions. We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.
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