Building AI agents for biomedical science @phylo_bio

Joined June 2011
Gregory Minevich retweeted
Introducing Biomni-Tuso, a new recipe for auto-research in biology AI model. We asked Biomni to develop a genetic perturbation prediction model and let it run for five days. It explored 500 configurations and discovered a new method that outperformed the leading methods across multiple benchmarks. We've since applied the same recipe to protein structure representation learning, enhancer–gene linking, ligand binding, and more, consistently discovering new leading models. Biomni-Tuso doesn't just tune hyperparameters. It works like an AI bio researcher for you: reading literature, thinking about orthogonal bio data sources, and testing fundamentally different modeling ideas. We believe this is where bio AI model research is headed. Instead of spending months building models by hand, researchers can describe a problem in natural language and let Biomni explore hundreds of ideas on their own data, while handling all the ML infra. Biomni-Tuso is now available as an auto-research skill (under "tusoskill") in Biomni Lab for all enterprise users. On the public platform, it is available to all users on CPU-based tasks. As we prepare for a broader rollout for GPUs, we're giving 500 GPU hours each to 100 Biomni Lab users to start building today. Apply here: forms.gle/ZzMsChN8ByqWSRGW9 Amazing work led by Alistair Turcan with @martinjzhang Example replay: biomni.phylo.bio/replay/shar… Open sourced genetic perturbation model: github.com/phylobio/TusoPert… Learn more: phylo.bio/blog/biomni-tuso
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Gregory Minevich retweeted
Today, we're excited to share that Biomni is published in @ScienceMagazine. Biomedical research is still fragmented, manual, and difficult to scale. In this work, we introduce Biomni - the first general-purpose biomedical AI agent with an integrated biology environment that can reason, plan, and execute end-to-end scientific workflows. We show that, with the right environment and harness, AI can automate large-scale omics analyses, orchestrate laboratory robotics, optimize molecular properties, and even train new AI models for biology. We also introduce a reinforcement learning recipe for continually improving biomedical AI agents, enabling open-source models to achieve frontier-level performance. It's surreal to look back. We started the Biomni project in early 2024, when agentic AI was still nascent. It is exciting to see tens of thousands of biologists collaborating with agents every day to accelerate science. Try Biomni: biomni.phylo.bio Read more: science.org/doi/10.1126/scie… This work is not possible without this truly inter-disciplinary team: @serena2z @hcwww_ @YuanhaoQ Minta Lu, Ryan Li, @yusufroohani Lin Qiu @shiyi_c98 Gavin Junze Di @rickwierenga @kavi_deniz Sherry @TianweiShe Shruti Jennefer Xin Zhou @MWheelerMD Jon Bernstein @MengdiWang10 @PengHeAtlas @zhou_jingtian @SnyderShot @lecong Aviv Regev @jure @StanfordAILab @genentech @phylo_bio @arcinstitute @UW @berkeley_ai @RetroBio_ @tamarindbio @Princeton @UCSF
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Gregory Minevich retweeted
5M+ researchers open GeneCards when they look up a gene. Today we are excited to integrate it in the Biomni Lab. Our agents are now grounded in one of the most comprehensive, expert-curated human gene knowledge bases - 200+ integrated data sources spanning genomic, transcriptomic, proteomic, clinical, and functional data. Try it at: biomni.phylo.bio Learn more at: phylo.bio/blog/biomni-lab-x-…
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Gregory Minevich retweeted
Biomni Lab lets biologists collaborate with AI agents to finish complex tasks end-to-end. Here are 15 popular use cases, each link is a full replay so you can watch the agent work through every step: 1. Spatial transcriptomics analysis: map gene expression across tissue architecture from spatial transcriptomics data, with spatial clustering and neighborhood analysis. biomni.phylo.bio/replay/shar… 2. Binder design: design de novo protein binders against a target structure using computational protein design tools. biomni.phylo.bio/replay/shar… 3. Biomarker panel design: identify and optimize a multi-marker diagnostic or prognostic panel from omics data. biomni.phylo.bio/replay/shar… 4. Clinical trial landscaping: search and summarize the trial landscape for a disease area, mapping phase, endpoints, and sponsor activity. biomni.phylo.bio/replay/shar… 5. Survival analysis: pull clinical and expression data, fit Cox models, generate Kaplan-Meier curves, and identify prognostic markers. biomni.phylo.bio/replay/shar… 6. scRNA-seq processing and annotation: from raw counts to UMAP clustering, marker gene detection, and automated cell type labeling. biomni.phylo.bio/replay/shar… 7. Cell-cell communication: infer ligand-receptor interactions between cell types from single-cell data and map intercellular signaling networks. biomni.phylo.bio/replay/shar… 8. Primer design for novel Cas13: analyze a putative Cas13 protein from a metagenomic screen—verify the ORF, identify HEPN domains, and design cloning primers with restriction sites and a FLAG biomni.phylo.bio/replay/shar… 9. Proteomics differential expression: normalize mass spec data, run statistical tests, and visualize differentially abundant proteins. biomni.phylo.bio/replay/shar… 10. Gene regulatory network inference: reconstruct transcription factor-target gene networks from expression data and identify key regulators. biomni.phylo.bio/replay/shar… 11. Gene co-expression network analysis: build weighted co-expression networks, identify gene modules, and correlate them with phenotypic traits. biomni.phylo.bio/replay/shar… 12. Microbiome analysis: process 16S/metagenomic sequencing data to profile microbial communities, diversity, and differential abundance. biomni.phylo.bio/replay/shar… 13. Polygenic risk scores: compute and evaluate PRS from GWAS summary statistics against a target cohort. biomni.phylo.bio/replay/shar… 14. Variant annotation: annotate genetic variants with functional predictions, allele frequencies, and clinical significance. biomni.phylo.bio/replay/shar… 15. Fine-mapping: narrow GWAS loci to credible causal variants using statistical fine-mapping methods. biomni.phylo.bio/replay/shar… Each of these would normally take days to weeks of scripting, debugging, and iteration. In Biomni Lab, the agent handles the full execution while you steer the science. Learn more: phylo.bio/use-cases
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Gregory Minevich retweeted
viruses from various families have repeatedly converged on capsids with icosahedral symmetry in the course of evolution. i wrote about why it might be so asimov.press/p/viral-capsids
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Gregory Minevich retweeted
We've been building nonstop since our public launch, and this week we're officially celebrating with the Biomni community! 🚀 On Thursday, join us virtually for a live demo of Biomni Lab by co-founders @KexinHuang5 and @YuanhaoQ, plus recent product updates and how we think about evaluating AI agents in biology. On Friday, we'll feature demos + lightning talks from scientific co-founders @jure and @lecong, plus free swag, drinks, small bites, and plenty of time to mingle. We only have a few spots left, so RSVP soon. • Virtual: luma.com/l5ryjaij • South SF: luma.com/n8k8qb0n We can't wait to see you there!
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Gregory Minevich retweeted
Excited to share one of the first examples of agents transforming clinical trial & EHR data analysis at scale. Biomni leverages 12M+ patient EHRs at Mount Sinai to scale complex trial emulation end-to-end:
Introducing agentic trial emulation: Biomni scaled clinical trial emulation using 12M patients EHR data at Mount Sinai. Researchers used Biomni to autonomously emulate multiple landmark anticoagulation RCTs end-to-end within their EHR—turning months of manual target trial analysis into scalable, agent-driven workflows that can extend across large numbers of trials and diseases. Running many emulations in parallel enabled something new: learning a stable institutional transport signal that quantifies how published trial effects systematically translate in local care. Read more: phylo.bio/blog/scaling-agent… Exciting work with @BenGlicksberg @joshualampertmd Justin Kauffman et al
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Gregory Minevich retweeted
Congratulations to the @phylo_bio team on launching a super useful and thoughtfully designed tool for life science!
Today we’re launching Phylo, a research lab studying agentic biology, backed by a $13.5M seed round co-led by @a16z and @MenloVentures / Anthology Fund @AnthropicAI. We’re also introducing a research preview of Biomni Lab, the first Integrated Biology Environment (IBE), where we’re imagining a new way biologists work. Biomni Lab uses agents to orchestrate hundreds of biological databases, software tools, molecular AI models, expert workflows, and even external research services in one workspace, supporting research end-to-end from question to experiment to result. Agents handle the mechanics, while you define the question, then review, steer, and decide. Scientists end up spending more time on science: asking questions, understanding mechanisms, and eliminating diseases. Phylo (@phylo_bio) is a spin-out of @ProjectBiomni, where we will maintain the open-source community and push open-science research. I’m grateful to continue building with my co-founders @YuanhaoQ @jure @lecong and the dream founding team @serena2z @TianweiShe @huangzixin20151 @gm2123 @margaretwhua @malaygandhi. We’re also fortunate to be advised by leading scientists @zhangf, Carolyn Bertozzi, and @fabian_theis, and supported by an amazing group of investors including @JorgeCondeBio @zakdoric Matt Kraning @ZettaVentures @dreidco @conviction @saranormous @svangel @valkyrie_vc and others. Biomni Lab is available for free today: biomni.phylo.bio/ Learn more in our launch post: phylo.bio/blog/company-fundr… We are also hosting launch events - join us at South San Francisco: luma.com/n8k8qb0n Virtual: luma.com/l5ryjaij We’re also hiring! phylo.bio/careers
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Gregory Minevich retweeted
Today we’re launching Phylo, a research lab studying agentic biology, backed by a $13.5M seed round co-led by @a16z and @MenloVentures / Anthology Fund @AnthropicAI. We’re also introducing a research preview of Biomni Lab, the first Integrated Biology Environment (IBE), where we’re imagining a new way biologists work. Biomni Lab uses agents to orchestrate hundreds of biological databases, software tools, molecular AI models, expert workflows, and even external research services in one workspace, supporting research end-to-end from question to experiment to result. Agents handle the mechanics, while you define the question, then review, steer, and decide. Scientists end up spending more time on science: asking questions, understanding mechanisms, and eliminating diseases. Phylo (@phylo_bio) is a spin-out of @ProjectBiomni, where we will maintain the open-source community and push open-science research. I’m grateful to continue building with my co-founders @YuanhaoQ @jure @lecong and the dream founding team @serena2z @TianweiShe @huangzixin20151 @gm2123 @margaretwhua @malaygandhi. We’re also fortunate to be advised by leading scientists @zhangf, Carolyn Bertozzi, and @fabian_theis, and supported by an amazing group of investors including @JorgeCondeBio @zakdoric Matt Kraning @ZettaVentures @dreidco @conviction @saranormous @svangel @valkyrie_vc and others. Biomni Lab is available for free today: biomni.phylo.bio/ Learn more in our launch post: phylo.bio/blog/company-fundr… We are also hosting launch events - join us at South San Francisco: luma.com/n8k8qb0n Virtual: luma.com/l5ryjaij We’re also hiring! phylo.bio/careers
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Gregory Minevich retweeted
“The leaders of the Human Genome Project always knew they were just starting a conversation” The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do go.nature.com/3Ck1qBP
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Gregory Minevich retweeted
Not only does Bennu contain all 5 of the nucleobases that form DNA and RNA on Earth and 14 of the 20 amino acids found in known proteins, the asteroid’s amino acids hold a surprise go.nature.com/3EqQLWo
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Gregory Minevich retweeted
WHY DOES THE EPIGENETIC CLOCK TICK? While money has been poured into developing therapies to reverse the epigenetic clock (@altos_labs 🤑), why the epigenome changes with age at all is unclear. In @NatureAging today, we suggest a potential driver: somatic mutations.
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Gregory Minevich retweeted
Excited to report that we have discovered a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Specifically, in a new paper on BioRxiv, we show that RNA editing by the near-ubiquitous ADAR1 in unmodified human cells is sufficient to allow us to infer the ages of thousands of species of RNA. This provides a new way to infer past transcriptional dynamics, without any metabolic labeling or genetic engineering, in anything from cultured cells to patient biopsies. Work by @agreeb66, @JamesBa95200124, @AaronWagen, and many more, and funded by @LNuzhna's Impetus Grants, along with generous support from @ericschmidt and @wenschmidt. 1/
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Gregory Minevich retweeted
Super excited to share that ENGRAM is out today! ENGRAM cells are programmed to write their histories into the genome, recording the intensity, duration, and order of biological events simultaneously. nature.com/articles/s41586-0…
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It's been 60 years since Epstein-Barr virus (EBV) was discovered. Still, still scientists are continuing to learn fascinating facts about this EBV. A new paper in @Nature by Sylvain Latour and colleagues from INSERM, Paris, report a remarkable human genetics discovery that reveals an important biology of EBV infection--the role of IL27 and its receptor in EBV infection. Martin et al. Nature nature.com/articles/s41586-0… The authors found that individuals who were born with complete deficiency of a cytokine receptor, IL27RA, are highly susceptible to severe EBV infection. But the remarkable part of the discovery is that, despite severe EBV infection, none of these individuals developed cancer; they are protected from EBV-induced cancer risk. If there is one virus that oncologists might know better than virologists, it's EBV. Discovered in 1964 based on microscopy examinations of tumor cells from cancer tissue biopsied from African children, EBV was the first ever known oncogenic virus (thelancet.com/journals/lance…). If you are curious, listen to this 6 mins video where famous scientist/author Dorothy Crawford tells the story of EBV discovery (youtube.com/watch?v=_-Jx4KqC…). EBV infection is extremely common. More than 95% of the population gets it at some point in their life. Once the virus enters the body, it permanently lives dormant in your B cells until you die. In some individuals, such as those immunocompromised, reactivation of this latent infection results in uncontrolled proliferation of B cells causing lymphoma. Not just lymphoma, EBV also cause stomach cancer and nasopharyngeal cancer. Most of the knowledge on the immune pathways hijacked by EBV came to light through humans born with rare genetic mutations causing different types of immunodeficiency. All such known monogenic conditions leading to severe EBV infection almost always have led to cancer. This is the first time scientists are encountering a genetic defect which increases the risk of severe EBV infection but protects against cancer. The finding has perhaps revealed the Achilles' heel of EBV infection, which could be exploited to prevent cancer development in immunocompromised individuals with EBV infection. The other fascinating part of the finding is one of the loss of functions has drifted to higher frequency (0.7%) in Finnish population. So, there are more than 200 individuals in Finland who are knockouts for IL27RA. In the Finngen biobank, the authors found 15 homozygotes, of which two were hospitalized for EBV infection (>50-fold enrichment). The Finnish variant is probably incompletely penetrance because the variant do not completely inactivates IL27R; it leaves behind some residual activity. Just a couple of years ago, Bjornevik et al. demonstrated the strong association of EBV with multiple sclerosis (science.org/doi/10.1126/scie…). Shortly after this report, Lanz et al showed that the reason for 32-fold increased risk of MS after EBV infection is because of the resemblance of a antigen protein in EBV with a glial cell protein in the CNS, resulting in collateral damage in the immune defense against EBV (nature.com/articles/s41586-0…). Currently, mRNA vaccines are being trialed based on this finding. With the recent discovery of IL27 and its receptor IL27RA in EBV, I wonder if these genes have links to MS risk. If so, targeting these genes might also help with treating MS. We will know soon. Amazing discovery. Yet another incredible demonstration of the power of 'natural experiments' aka human genetics in understanding the fundamental biology. Martin et al. Nature nature.com/articles/s41586-0…
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Gregory Minevich retweeted
“This is crazy molecular biology. I would have never guessed this type of mechanism existed” Bacterial defensive systems scramble the standard workflow of life go.nature.com/3UVnNT4
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Gregory Minevich retweeted
1/ We are happy to share our review on “The Ouroboros of Autoimmunity” published in @NatImmunol! (nature.com/articles/s41590-0…)
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Gregory Minevich retweeted
Happy and super excited to share our discovery of a protein fractal! We unravel the surprisingly simple emergence of these marvellous structures and show it might have even been an accident of evolution. Read the full story here nature.com/articles/s41586-0… Or just stick around 🧵
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