We have developed a new workflow to map whole human organs at single-cell resolution, while integrating spatial transcriptomics, proteomics, and metabolomics. We applied this workflow to map precancerous lesions of the fallopian tubes. More here: www.biorxiv.org/content/10.1...

The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data! Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models. Start mining data now: dataminer.depmap.sanger.ac.uk

📢 NEW! Visium HD 3’ + Long Reads from @10xgenomics.bsky.social Explore whole transcriptome spatial analysis at single-cell resolution. Now sequence full-length transcripts to uncover isoforms & SNVs. 👉 Protocols: shorturl.at/E3A4G #SpatialTranscriptomics #VisiumHD #LongReadSeq #ONT #PacBio

GHIST: a deep learning-based method to predict spatial gene expression at high resolution using histology data. www.nature.com/articles/s41...

Read the News & Views highlighting both of these papers, here: www.nature.com/articles/s41...

iSCALE: a tool leveraging histology and spatial transcriptomics data to infer gene expression at super resolution in tissues. www.nature.com/articles/s41...

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

A rapid imaging-based screen for induced-proximity degraders identifies a potent degrader of oncoprotein SKP2 go.nature.com/4mTBGhr

Multiplexed Perturbation Enables Scalable Pooled Screens https://www.biorxiv.org/content/10.1101/2025.08.14.669942v1

Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates - @ethz.ch @uzgent.be go.nature.com/41GoBiX

Targeted delivery of diverse biomolecules with engineered bacterial nanosyringes - @zhangf.bsky.social go.nature.com/46OFcoj

🚨 Our new #preprint is out! doi.org/10.1101/2025... We used #PerturbMap spatial functional genomics in pancreatic cancer to track tumor clone dynamics and uncover how extracellular factors like Serpine1 and Serpinb2 drive immune evasion. 🧵 (1/8)

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

We developed MouseMapper AI, a deep learning ensemble for the analysis of whole-body systems, including the nervous and immune systems, to map disease/drug perturbations tissue by tissue, organ by organ, at the cellular level in 3D. biorxiv.org/content/10.1...

Now online! Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue

High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer | Science www.science.org/doi/10.1126/...

@czbiohub.bsky.social The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies

🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41... 🧵Walk-through thread below ⬇️

🚀 First MOSAIC consortium paper and MOSAIC Window: a rich 60-patient public (multimodal) dataset accessible via EGA. 📄 www.biorxiv.org/content/10.1... #CancerResearch #SpatialTranscriptomics #SingleCell #PrecisionOncology #AI cc: @owkin.bsky.social @10xgenomics.bsky.social

On 3/7/23, I searched Olfr1000 in Loupe Browser #10xGenomics. That simple query sparked a hunch: maybe RUBIX and PERTURB-CAST actually work. Learn how 🍫-G2P took shape: doi.org/10.1038/s415... Take a look at 🍫-G2P: chocolat-g2p.dkfz.de

Spatial transcriptomics holds great promise to understand biological tissue function, but the assignment of transcripts to cells has been a substantial bottleneck. For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger. www.biorxiv.org/content/10.1...

Cancer recurrence predicted by spatial biology of the immune response nature.com/articles/d41... nature.com/articles/s41...

3. Defining cell circuits @cellpress.bsky.social www.cell.com/cell/fulltex...

GASTON Gradient Analysis of #Spatialtranscriptomics Organization with Neural networks "models gene expression as a Piecewise linear function of the Isodepth" Work with Visium Xenium MERFISH Slide-seq V2 Stereo-seq @uthsav.bsky.social @naturemethods.bsky.social 2025 www.nature.com/articles/s41...

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE https://www.biorxiv.org/content/10.1101/2025.02.25.640190v1

Today, we're launching the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements. arc-website-git-ben-virtual-cell-atlas-tool-arc-institute.vercel.app/news/news/ar...

Can we perform genome-wide screens in any cell type in the body?! Excited to share our roadmap for leveraging advances in sgRNA delivery, library design, and phenotypic selection to enable unprecedented genetic dissection of organismal physiology and disease. www.cell.com/cell-genomic...

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling https://www.biorxiv.org/content/10.1101/2025.02.20.639398v1

New online! Decoding cell–cell communication using spatial transcriptomics

In silico generation of synthetic cancer genomes using generative AI https://www.biorxiv.org/content/10.1101/2024.10.17.618896v2 🧬🖥️🧪 https://github.com/LincolnSteinLab/oncoGAN

A little MYC goes a long way! Check out this absolute tour de force from colleagues Miryam Müller, Stephanie May, Tom Bird and team who assembled an compendium of liver cancer mouse models mirroring a spectrum of human HCC subtypes: www.nature.com/articles/s41...

@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...

Our lifestyle and environmental exposures are the predominant influencers of healthy aging and premature mortality, compared with polygenic risk, in the first comprehensive assessment www.nature.com/articles/s41... open-access

Excited to share SpaceBar - our new method for labeling and detecting clones with imaging-based spatial transcriptomics platforms! w/ Yael Heyman and @arjunraj.bsky.social www.biorxiv.org/content/10.1... 🧵

#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology

Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.

I missed this one last month. New AI tool predicts gene expression from pathology slide images: Digital profiling of gene expression from histology images with linearized attention https://www.nature.com/articles/s41467-024-54182-5 🧬🖥️🧪 https://github.com/gevaertlab/sequoia-pub

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms 🧬🖥️🧪 biorxiv.org/cgi/content/...

Cassini: Streamlined and Scalable Method for in situ profiling of RNA and Protein https://www.biorxiv.org/content/10.1101/2024.12.14.628484v1

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation

💥🚀 www.biorxiv.org/content/10.1...

www.nature.com/articles/s41... A collaborative project incepted by Michael Kosicki, and executed by Ananth Pallaseni (both Ph.D students at @sangerinstitute.bsky.social at the time) and Elin-Madli Peets.

Only a subset of patients respond to immunotherapy Why? Which ones? We conducted an unbiased analysis of response biomarkers and found that hundreds of possible biomarkers collapse into five latent, orthogonal factors that underlie immunotherapy response. www.nature.com/articles/s41...

#snPATHO… www.nature.com/articles/s42...

Check out this preprint on Perturb-multi (doi.org/10.1101/2024...), a multi-year collaborative effort that enabled multi-modal in vivo genotype-phenotype mapping by pooled genetic perturbations and high-dimensionality phenotype readout by imaging and sequencing. bsky.app/profile/weal...

@rongfan8.bsky.social's Perturb-DBIT www.biorxiv.org/content/10.1...

—Please give me an A.I. that automatically detects, interprets all types of medical. images (scans, retina, endoscopy, skin) that I can interact with, can integrate data from other sources, saves a lot of time, and improves accuracy —Sure, here it is www.nature.com/articles/s41...

Checkout our updated preprint! Now live on BioRxiv. www.biorxiv.org/content/10.1... @kampmann.bsky.social We present our new and improved technique to do large-scale (5000+ genes) CRISPR screens directly in a mouse brain, all with cell type-specific resolution using a Cre-responsive sgRNA. Enjoy!