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And with that, it’s a wrap on the very first #semmretreat24 😄 It has been a great opportunity to be part of the people behind the organization of this amazing event, enabling networking while sharing some very cool science! 🧪 Thanks to everyone in SEMM who participated!

The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳 For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread. nature.com/articles/s4159…

Virtual cell models have the potential to transform biological research. Today Chan Zuckerberg Initiative released an initial set of models, including scGenePT and SubCell, designed to be easy to run and build upon. This is a really exciting time in biology. czi.co/4g1jTSa

Benchmarking the translational potential of spatial gene expression prediction from histology | Nature Communications nature.com/articles/s4146…

AI provides a universal framework that leverages data and compute at scale to uncover higher-order patterns Today, Arc Institute in collaboration with NVIDIA releases Evo 2—a fully open source biological foundation model trained on genomes spanning the entire tree of life 🧵

Happy to share our new preprint: A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver: biorxiv.org/content/10.110…

Senescent cells contribute to disease and are found in many tissues but are hard to analyze because markers have been derived in culture and do not account for cell-type differences. Here, we define new signatures based on millions of single cells (1/5) nature.com/articles/s4146…

Excited to share our #multiomics study of who was the world's #oldest living person! Our research on this record-breaking #supercentenarian suggests that, under certain conditions, #aging and #disease can become decoupled—challenging the common belief that they are inherently

I am delighted to share a manuscript long in the making, elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm biorxiv.org/content/10.110…

STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues biorxiv.org/content/10.110…

Our work on 3D genome organization in human cancer is out! In collaboration with Yanding Zhao Howard Chang William J. Greenleaf and TCGA we used HiChIP to profile enhancer connectivity and rewiring in primary tumors. nature.com/articles/s4158…

A universal AI-powered pipeline developed by @Beghinteam enables precise 3D analysis of cell morphology and topology within organoid structures. nature.com/articles/s4159…

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with Omer Ali Bayraktar , Oliver Stegle and Moritz Mall groups. Preprint at end🧵👇

The peer-reviewed version of expansion in situ genome sequencing is now out in Science! The news is bittersweet – when we first revealed this last September, I never guessed it would be my final paper in academia, but a lot has changed. A few parting thoughts:

Out today from the Schwartz lab! A new way to study cell-cell communication from spatial transcriptomics data. Cell Neural Networks on Spatial Transcriptomics (CellNEST) can detect both signals between individual cells and relay networks of communication. nature.com/articles/s4159…

What if SCALE is a solved problem? 🤔 Sequencing-Free Single-Cell Genomics with STAMP! 💣 Now published in Cell: Our approach for scalable, cost-effective analysis of millions of single cells or hundreds of samples—without sequencing. By replacing sequencing with

Amazing days at #EACR2025! Inspiring science, excellent sessions, and such an incredible #cancerResearch community to be part of✨ huge thanks to Cereda Lab and Matteo Cereda for the constant support and IIGM . Also super happy that Fondazione AIRC per la ricerca sul cancro stopped by my poster 🌟

How to turn a layer of fibroblasts into a tulip 🌷? Check out our new pre-print on shape-programmable living surfaces. Led by Pau Guillamat IBEC biorxiv.org/content/10.110…

reprogramming cells with transcription factors is our most expressive tool for engineering cell state traditionally, we found TFs by ~guesswork ICML Conference we're sharing NewLimit's SOTA AI models that can design reprogramming payloads by building on molecular foundation models

I’d love to hear biologists weigh in on the fundamental question: can you predict the impact of cell perturbations better by studying the natural variation in a population of healthy cells (more data), or by studying cells that have been perturbed genetically or chemically?