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A dream come true: in 2004 I started thinking about counting microstates to predict gene expression with Jane Kondev Rob Phillips Hernan Garcia. 20 years later we can measure them: nature.com/articles/s4158… Thank you William J. Greenleaf Benjamin Doughty Michaela Hinks Julia and all co-authors!

📣 Two ERC-funded positions are available in the lab! If you’re interested in exploring the mechanisms underlying mutation, we’d love to hear from you. ibe.upf-csic.es/work-with-us/j… RTs and shares would be greatly appreciated!

Welcome onboard Hsiu-Chuan Lin 🤗 Here's to exciting discoveries and collaborations ahead! 🚀🔬

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. nature.com/articles/s4158…

📢 There are 2 open PhD positions in my group at CRG Barcelona! We are looking for candidates interested in cell fate engineering, gene regulation, and single-cell technologies with experience in both wet/dry labs. Please help spread the word! Apply ➡️ crg.eu/en/content/tra…

We have many fully-funded PhD positions open at our research labs here in Barcelona. If you'd like to find out more, we're hosting an online workshop on the 13th of December 2025 (3PM CET) to learn how to find the right lab and experts tips on how to prepare an outstanding

1/🚀 Excited to share RegVelo, our new computational model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇 biorxiv.org/content/10.110…

📣 Hiring, please forward widely!! Two postdoc openings to work on genomics of diabetes 1. computational regulatory genomics/statistical genetics. 2. Experimental cell-based modeling DM if interested Centre for Genomic Regulation (CRG) shorturl.at/O3wMi shorturl.at/ieyZy

Interested in single cell genomics but need help getting started? Check out my lab's Single Cell Genomics Day on April 25. Talks will feature recent exciting computational and experimental advances and will be live-streamed at satijalab.org/scgd. Please RT/spread the word!

A fun collaboration with Nadezhda Azbukina ZhiSong He 何志嵩 at Treutlein lab Gray Camp for our posterior brain organoid atlas and morphogen screens!

How can causal machine learning be applied to single-cell genomics to understand the true biological mechanisms underlying cellular processes?Nature Genetics TU München "Causal machine learning for single-cell genomics" • Advances in single-cell '-omics' technologies combined

1/ Excited to share CellFlow, a new approach for complex perturbation modeling in single-cell genomics based on flow matching. From cytokine screens to cell fate and organoid engineering, we show CellFlow’s broad power across many diverse tasks. 👉 Paper: biorxiv.org/content/10.110…

I'm thrilled to share our new #bioRxiv preprint from ⁦Junyue⁩ lab at ⁦Rockefeller University⁩! We present PerturbFate, a high-throughput single-cell CRISPR platform profiling nascent/pre-existing RNA, steady-state RNA & chromatin accessibility. biorxiv.org/content/10.110…

Modular integration of epithelial, microbial, and immune components to study human intestinal biology. Amazing team project with Rubén López Sandoval, Marius Harter, Qianhui Yu, Mike Nikolaev, Matthias Lutolf, Nikolche Gjorevski, and many others Institute of Human Biology biorxiv.org/content/10.110…

Integrated Organoid Atlas benchmarks new protocols, even more impressive as a Highly Variable Cohort for comparison against perturbation and disease models: nature.com/articles/s4158… Lead by Quan Xu 许泉 Lennard Halle, MD Collaboration with Fabian Theis Treutlein lab Institute of Human Biology

Plasmid-based reporter assays are the bedrock of regulatory genomics. But a basic question has gone unanswered for decades: Do chromatin architectures form on plasmids transfected into mammalian cells—and does it matter? We finally have answers. biorxiv.org/content/10.110…

Very important report Nicoletta I Petridou linking #mechanochemical signalling to fate transitions biorxiv.org/content/10.110… wide/significant implications. Perhaps the clearest indication so far of HOW mechanical signalling can control patterning of gene expression #MustRead #NotInTheGenes

Very happy to share it’s online! If you read the bioRxiv, updates include tracking cells and tissue flow, Histo4i time course (69 Abs) comparing spatial patterning and a new WLS KO ipsc line establishing mechanosensing via YAP-WNT caudalizes organoids nature.com/articles/s4158…

New OpenProblems paper out! 📝 Led by Malte Lücken with Smita Krishnaswamy, we present openproblems.bio – a community-driven platform benchmarking single-cell analysis methods. Excited about transparent, evolving best practices for the field! 🔗 nature.com/articles/s4158…