Han Kim

Proud of @Yena__Oh, who spearheaded this project, and @RimshahAbid @saif_dababneh @marwanbakr_ @termehaslani for all their contributions. Congrats!

Very proud of @hamna_ammar! Her undergraduate research has just been published as her first paper, with Hamna as the first author. Hamna uncovered a requirement for Ezh2 in Isl1-expressing progenitors for proper cardiac and hindlimb development. journals.biologists.com/bio/article/15…

@SChenlab @BrainCanada @rungtalab @BAmilhon Congrats, Simon!

It's an honor to receive this Momentum Grant from @BrainCanada And congrats to other recipients @rungtalab @BAmilhon :)

Our new study @NatureMedicine from the Human Phenotype Project: Analyzing diet and microbiome data from 10,000+ people, we found that what you eat is strongly linked to which microbes live in your gut, down to specific foods like coffee, yogurt, and milk driving distinct microbial signatures. We also simulate personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health Read here: nature.com/articles/s4159… HPP: humanphenotypeproject.org/home

Excited to share our new paper published today in Nat. Commun. We show that homoharringtonine (HHT), an FDA-approved leukemia drug, selectively eliminates senescent adipose cells and improves metabolic health. (1/4) #Aging #Senescence #Metabolism nature.com/articles/s4146…

New study in @Nature CV Research: Our team at Ottawa @HeartInstitute discovered that bone-marrow derived cIAP2 drives damaging inflammation after a #HeartAttack. Blocking cIAP2 with newSmac mimetics, protects the heart and prevents #HeartFailure. rdcu.be/e8a2S

Must-read Review in Nature Medicine from @DanielJDrucker: a masterclass on how GLP-1 medicines moved from glucose control to reshaping obesity, CV, liver, kidney, neuro and addiction care. nature.com/articles/s4159…

[1/n] Super excited to introduce PaperBanana 🍌! (PKU x Google Cloud AI) As AI researchers, we often spend way too much time crafting diagrams and plots instead of focusing on the ideas 🤯. To rescue us from this burden, we built an Agentic Framework to auto-generate NeurIPS-quality paper illustrations! 📄 Paper: huggingface.co/papers/2601.23… 🌐 Page: dwzhu-pku.github.io/PaperBanana/ Key Features: 🌟 Human-like Workflow: Retrieve 🔍 -> Plan 📝 -> Style 🎨 -> Render 🖼️ -> Critique 🔄. This ensures both academic fidelity and aesthetics. 🌟 Versatile: Supports both illustrative diagrams and statistical plots. 🌟 Polishing: Also effective for polishing existing human-drawn diagrams. Here are some example diagrams and plots generated by our PaperBanana:

👏Huge congratulations to the @GoogleDeepMind team on the formal publication of AlphaGenome model - a big milestone for DNA sequence-to-function modeling and variant function interpretation. 💡At the same time, I want to highlight that many core questions in gene regulation hinge on more than DNA sequence alone: DNA sequence provides the basal and shared genetic blueprint, while the regulatory logic that defines cell-type-specific gene expression and gives rise to diverse cellular phenotypes is executed by the 100s-1000s of chromatin proteins that differentially read the DNA sequences. 🏗️That motivation to mechanistically understand gene regulation drives us to develop multi-modal AI tools rooted in the fundamentals of chromatin biology, bridging DNA sequence with chromatin states and protein features to let the model learn the core regulatory mechanisms of gene expression. 📰Read more Chromnitron: Decoding the gene regulatory landscape through multimodal learning of protein–DNA interactions. 👉 Link to preprint: biorxiv.org/content/10.110… And my prior post of Chromnitron model: x.com/BoXia7/status/…

Hepatic adaptation to chronic metabolic stress primes tumorigenesis: Cell cell.com/cell/fulltext/…

Temporal inhibition of ADAM17 in fibroblasts reduces stiffness and promotes vascularization following myocardial infarction academic.oup.com/cardiovascres/…

Thanks to the authors for sharing all components of this mouse embryo spatial transcriptomics data from cell gene counts to per-molecule coordinates: ahajournals.org/doi/full/10.11… 🥳 So I vibe coded an app to explore the 3D subcellular transcript organization: jef.works/CellCarto-Mous…

Our body (cells) have fuel preference, e.g., burning fat vs. carbohydrates, which depends on the environment and nutritional states. How do cells decide which fuels to use?  Our new study found that carnitine biosynthesis is crucial for fuel switching science.org/doi/10.1126/sc…

A tour-de-force circadian proteomics study shows daily rhythms in ~19,000 proteins across 32 tissues in mice, revealing the pervasive reach of the circadian clock. #CircadianBiology #Proteomics #SystemsBiology @MolecularCell cell.com/molecular-cell…

🚀 Excited to share our latest work now on bioRxiv: the computational de novo design of tissue‑specific mammalian enhancers that work in vivo in the mouse embryo. 🐭 We use compact CNNs and transfer learning (pre‑trained on genome‑wide ATAC‑seq and fine‑tuned on validated enhancers from VISTA enhancer browser) to program tissue‑specific enhancers. Transfer learning reveals clear shifts in motif importance between sequence‑to‑accessibility and sequence‑to‑activity models, highlighting the specific features that drive enhancer function. 100% (15/15) of designed enhancers for heart, limb, and CNS are active in their intended tissues in mouse embryos. 🎯 We hope this approach will help enable the design of more versatile and precise synthetic enhancers across mammalian tissues, cell types, and dynamic cell states. Grateful for the amazing guidance from @AlexanderStark8 and @Loubiere20! 🙏 Huge thanks to all co-authors and collaborators, especially Evgeny @evgenykvon and Jacob @jmschreiber91, for making this work possible. 🙏 More details in the preprint and code: bioRxiv: biorxiv.org/content/10.648… #DeepLearning #Genomics #SyntheticBiology

💉 GLP-1 works—but muscles decide the outcome. 🔬 A new meta-analysis (18 RCTs, ~3,800 participants) shows significant weight regain and worsening metabolic health after GLP-1 discontinuation thelancet.com/journals/eclin…

Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collaboration led by @AlexanderStark8 lab. @UCIBioSci @IMPvienna

Agents are finally starting to work in biology. We’ve partnered with Anthropic and major biotech vendors - Vizgen, AtlasXOmics, Takara, 10x Genomics - to build a tool that allows scientists to steer their own analysis with natural language. Raw spatial data to publication quality figures. Our team believes this will soon be the standard way biologists interact with data. Spatial biology agents look a bit different from coding products: - tailored to the molecular details of each kit type - run in sandboxes on very large machines - orchestrate data infra, eg. bioinformatics workflows, with tool calls - build graphical analysis notebooks to communicate results Detailed breakdown of engineering decisions, product philosophy and concrete flows follows:

#DBfeature Exploring the differentiation potential of EomesPOS mouse trophoblast cells in mid-gestation By Avery McGinnis, Megan Cull, Nichole Peterson, Matthew Tang, Bryony Natale, and David Natale tinyurl.com/vcp23d95 #Extraembryonic

In the latest issue! A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells dlvr.it/TNlqDB

Big, beautiful trees!! SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life. biorxiv.org/content/10.110…