Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches. www.biorxiv.org/content/10.1...

Our latest collaboration with @rongfan8.bsky.social, spatial triomics to investigate myelin and cortical brain development, and demyelination, spearheaded by Leslie Kirby in our lab @ki.se and Di Zhang in Rong's lab! Check it out @nature.com www.nature.com/articles/s41...

We’re releasing CytoSyn, our new diffusion model for synthetic histopathology image generation. REPA-E architecture. H0-mini conditioning. Model: huggingface.co/Owkin-Biopti... Supporting article: www.owkin.com/blogs-case-s...

A computational method designs receptors called T-SenSERs, which have predictable signalling responses to tumour microenvironment soluble factors and can be co-expressed with conventional CARs in T cells to enhance their therapeutic activity. www.nature.com/articles/s41...

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart https://www.biorxiv.org/content/10.1101/2025.11.02.686137v1

We dived into cancer cell interactions with COMPOTES. Using MOSAIC data, we uncovered 45 programs across major cancers, shedding light on immune dynamics and therapeutic paths. Pre-print at: doi.org/10.1101/2025...

Our new multimodal ML models achieve high accuracy in predicting iCCA outcomes (c-index 0.70). This collaborative study with @mskcancercenter.bsky.social enhances understanding of the disease and may guide treatment selection. Check out the paper: www.sciencedirect.com/science/arti...

High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes - @pku1898.bsky.social go.nature.com/47yENVJ

High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks. www.nature.com/articles/s41...

🧵1/17 📣Thrilled to share our latest study just out in Cancer Discovery! ➡️ aacrjournals.org/cancerdiscov...

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes @science.org @shaleklab.bsky.social www.science.org/doi/10.1126/...

Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE

Excited that the paper presenting our mouse brain in vivo CRISPR screening platform is out today in @natneuro.nature.com! Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab. www.nature.com/articles/s41...

We’re happy to share our new preprint form @N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat lab! 🎉 🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation. 🔗 biorxiv.org/content/10.1...

Tissue and cellular spatiotemporal dynamics in colon aging - @nygenome.org @flatironinstitute.org @broadinstitute.org @cancerdynamics.bsky.social go.nature.com/47I1RBF

Integrated epigenetic and genetic programming of primary human T cells - @gladstoneinst.bsky.social @ucsanfrancisco.bsky.social @j-eyquem.bsky.social @marsonlab.bsky.social go.nature.com/3WOJJAJ

CoCo-ST detects global and local biological structures in spatial transcriptomics datasets. #SpatialTranscriptomics #VarianceIdentification @natcellbio.nature.com www.nature.com/articles/s41...

We use CODA to map human endometrial tissue at single-cell resolution, a map that then serves as a blueprint to design a multi-compartment multicellular assembloid of the endometrium. Read about our approach to organoids/assembloids here: www.biorxiv.org/content/10.1...

(1/x) Excited to report VIPS (Volumetric imaging of biological specimens via photochemical sectioning) @science.org! VIPS uses light-based sample sectioning to eliminate the inherent imaging depth limit of high-resolution optical microscopes @supgokul.bsky.social: www.science.org/doi/10.1126/...

Tracing colorectal malignancy transformation from cell to tissue scale www.biorxiv.org/content/10.1...

@science.org High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer | Science www.science.org/doi/10.1126/... @lukekoblan.bsky.social @weissmanlab.bsky.social @zhuanglab.bsky.social @whiteheadinstitute.bsky.social et al.

PerTurboAgent: A Self-Planning Agent for Boosting Sequential Perturb-seq Experiments https://www.biorxiv.org/content/10.1101/2025.05.25.656020v1

The new Gemma model, Cell2Sentence, accelerates cancer therapy discovery! 🤯 It found a novel way to make "cold" tumors "hot," boosting immunotherapy effectiveness. Lab tests confirmed a 50% synergistic immune signal increase. Amazing!!! blog.google/technology/a...

We are thrilled to share our new preprint entitled “The origin and molecular evolution of the mammalian liver cell architecture” www.biorxiv.org/content/10.1...

Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening https://www.biorxiv.org/content/10.1101/2025.05.02.651939v1

Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment @cp-cellrepmed.bsky.social @harvardmed.bsky.social www.cell.com/cell-reports...

SPACE: spatially resolved multiomic analysis for high-throughput CRISPR screening in 3D models https://www.biorxiv.org/content/10.1101/2025.09.14.675819v1

Cool @srviswanathan.bsky.social Cancer target discovery enabled by transcriptome-based virtual CRISPR screening www.biorxiv.org/content/10.1...

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. www.biorxiv.org/content/10.1...

New online! Towards a reference cell atlas of liver diversity over the human lifespan

🔥 www.cell.com/cell-genomic...

Introducing CellTransformer, a new AI tool developed with UCSF that makes it easier to explore massive neuroscience datasets and identify important subregions of the brain. 🧵

generative AI model PerturbNet predicts changes in gene expression and cell state in response to unseen chemical and genetic perturbations ➡️ www.embopress.org/doi/full/10....

Discovery and protein language model-guided design of hyperactive transposases - @marcguellc.bsky.social @upf.edu @icreacommunity.bsky.social @crg.eu go.nature.com/4gXLGEw

A spatial transcriptomics analysis led by my student Zaira reveals the distinct nature (gene expression, tumour cell states and local microenvironments) of radionecrosis and recurrence in glioblastoma. 👏

New highlight video! 🧪🧬💻 RAEFISH from Steven Wang at Yale unlocks whole-transcriptome imaging at single-molecule resolution. See 20,000+ RNAs light up in cells and tissues. Plus get direct gRNA detection in high-content CRISPR screens. Spatial biology just leveled up www.youtube.com/watch?v=P2j6...

New CRISPR libraries from the @johndoench.bsky.social and Root labs — Jacquere (human) and Julianna (mouse). A perfect pairing for your next screen. 🍷🧀 https://twp.ai/9PX2kT https://twp.ai/4irnYP

Heat-rechargeable computation in DNA logic circuits and neural networks @Nature.com

Very proud to finally publish Giotto Suite after many years of hard work. It's a big milestone for our lab and will be a massive stepping stone for our ongoing projects and ideas. Take a look at giottosuite.com and feel free to share feedback and ideas for improvement.

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models https://www.biorxiv.org/content/10.1101/2025.06.11.659105v1

Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution @cellcellpress.bsky.social @sstevenwang.bsky.social @yalepress.bsky.social www.cell.com/cell/fulltex...

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. Read more: e11.bio/blog/prism

Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context https://www.biorxiv.org/content/10.1101/2025.09.26.678648v1

We have developed a new workflow to map in 3D at single-cell resolution whole human organs. Prof. Rong Fan (Yale) mapped out immune cell populations in the vicinity of ovarian precancerous lesions in healthy women and found no enrichment. More here: www.biorxiv.org/content/10.1...

Highly multiplexed 3D profiling of cell states and immune niches in human tumors @natmethods.nature.com @harvardmed.bsky.social www.nature.com/articles/s41...

Big step forward in phenotype-directed drug discovery: By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping. Super cool!! www.nature.com/articles/s41... #AI #drugdiscovery #cancer

I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...

🚨Location, location, location! Now out @natcancer.nature.com, the final version of our study showing how a tumor's anatomic site can impact the function of driver gene mutations, using SMAD4 inactivation as in pancreatic cancer as a clinically relevant example: nature.com/articles/s43.... (1/4)

For decades, human genome editing has been limited to small, localized modifications. Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.