Microglia serve as conduits for the export of toxic protein aggregates from neurons and the import of healthy organelles, keeping neurodegeneration at bay go.nature.com/4dXkIuh

Celcomen: our new tool for spatial causal disentanglement and identifiability in spatial transcriptomics to perform spatial counterfactuals such as localised gene knoc-outs! by Stathis Megas and team Wellcome Sanger Institute Cambridge Stem Cell Institute

Our recent work (led by Lauren Patel comentored by Chris Benner), is out .Nature Biotechnology rdcu.be/dTTWs. We aim to increase rigor in scientific studies. Here we show that spike-in normalization is commonly used improperly, and conclusions may actually be incorrect (1/2)

FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics nature.com/articles/s4159…

Cross-disorder and disease-specific pathways in dementia revealed by single-cell genomics cell.com/cell/abstract/…

Subcellular Level Spatial Transcriptomics with PHOTON biorxiv.org/content/10.110…

🗺️ Meet MapMyCells! 🗺️ Save time mapping gene expression data to reference taxonomies. Outputs incl. cell identity and confidence scores. Available on the Brain Knowledge Platform: portal.brain-map.org/atlases-and-da… #studyBRAIN

🧵 1/8 🎉 Our latest collaborative publication, "Challenges and recommendations for the translation of biomarkers of aging", has just been released in Nature Aging (Nature Aging). Biomarkers of aging predict biological age and its response to interventions but face challenges in

Our next Center for Integrated Cellular Analysis Virtual Seminar (12PM on 10/1) AbdulAbdul introduces IRISeq, a new technology to perform spatial transcriptomics in a highly scalable and cost-effective way (<$50/tissue section)- no optics or imaging required! Free registration: nygenome.zoom.us/meeting/regist…

Finally out in Nature Protocols : our group's workflows for end to end computational pathology. Compatible with UNI and other foundation models. Led by Omar S.M. El Nahhas from katherlab journal link: nature.com/articles/s4159… full text: rdcu.be/dT35l

Thrilled to share our „PRedictor Of PHEnoTypes“ model Prophet! Led by Alejandro Tejada Lapuerta & Yuge Ji, Prophet is a transformer-based model that predicts outcomes for unseen experiments. It aims to understands biology by learning across assays and phenotypes over 4.7M+ experiments.

How can we build an Al Virtual Cell 🔮🧬 that simulates all functions and interactions of a cell? How will it transform research and drive breakthroughs in programmable biology, drug discovery and personalized medicine? 🚀 Take a look at our Perspective! arxiv.org/pdf/2409.11654

Excited to share our research on extracellular vesicle-mediated cellular crosstalk in the developing brain (organoids)!!! Great work led by the wonderful scientists Andrea Forero & Fabrizia Pipicelli cell.com/cell-reports/f…

In Joseph Rich et al. biorxiv.org/content/10.110…, we assessed the Seurat and Scanpy single-cell packages, finding that they produce very different results on standard analyses. A new paper in eLife - the journal looking at clustering finds the same elifesciences.org/reviewed-prepr…

Excited to share our first preprint on a novel spatial multi-omics technology that co-profiles five modalities within the same tissue section. Great collab w/ Marek Bartosovic and Mingyao Li . Kudos to my postdoc Pengfei Guo and PhD student Liran Mao ! biorxiv.org/content/10.110…

Search and match across spatial omics samples at single-cell resolution nature.com/articles/s4159…

CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics nature.com/articles/s4159…

📢Out now! Gennady Gorin, Lior Pachter and colleagues from Caltech propose a method to cluster cells from multimodal single-cell data under a self-consistent, biophysical model. nature.com/articles/s4358…

Gene-level alignment of single-cell trajectories nature.com/articles/s4159…

CAST enables physical alignment of spatial omics data across replicates, techs, modalities at single-cell resolution. Such accurate alignment enables spatial atlas searching, unbiased DEG identification, and reconstruction of spatial multi-omics. DM for questions and collabs!