spatial.ist_papers @spatial_papers

Impressive talk by Sammy Ferri-Borgogno on multi modality spatial profiling at PreCancer Atlas symposium @MDAndersonNews Exemplar study in #OvarianCancer: mdpi.com/2072-6694/16/5… Excited about potential of @ST_Omics Stereo-seq: Sub cellular resolution ✅ Coding & non coding RNA…

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NEW AVIAN BRAIN ALERT! Check our research on the development of the pallium in birds🐣 and reptiles🦎. Comparative neurogenesis, scRNAseq and spatial-omics showing that the pallium of amniotes develops in different ways, but converge into similar circuits! shorturl.at/bvFJL

CODA day! The CODA team at @JohnsHopkins maps pancreatic precursor lesions in 3D and at single-cell level. First 3D spatial genomic maps of large tissue samples. A human pancreas contains a staggering ~1000 lesions, some showing multifocality. Here: nature.com/articles/s4158…

How about combining single-cell and spatial transcriptomics to study tissue and cellular spatiotemporal dynamics in colon aging? Aidan Daly, @f_cambuli, @RichBonneauNYC, Aviv Regev, and I are happy to share our latest pre-print (1/16): biorxiv.org/content/10.110…

Using in situ spatial transcriptomics? Try Proseg, @danielcjones’s new cell segmentation method based on probabilistic and Cellular Potts modeling. Great for @vizgen_inc Merscope, @10xGenomics Xenium, and @nanostringtech CosMx data. Preprint & code: (1/n) doi.org/10.1101/2024.0…

“Library size confounds biology in spatial transcriptomics data” finally out in Genome biology! TL;DR - LS normalisation is bad for domain identification. - Exercise caution in adapting scRNA-seq methods to ST - New normalisation methods needed for ST rdcu.be/dE93v

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We used BARseq in situ sequencing to identify genes in ***1.2 million neurons*** throughout the mouse brain We found that cortical areas with similar cell types are also interconnected. We call this “wire-by-similarity.” biorxiv.org/content/10.110… 1/n

Xu et al. combined Stereo-seq with single-cell transcriptomic profiling to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. ➡️ nature.com/articles/s4158… #singlecell #spatialomics #spatialbiology

SpatialData is a tool developed by EMBL scientists in cooperation with multiple research institutions to unify & integrate data from different omics technologies. It provides holistic insights into health & disease and is publicly accessible. embl.org/news/science-t…

I’m very happy to share our paper in @CellCellPress on the spatial organization of GBM! bit.ly/4aKDeEp. Check out our tweetorial for a summary of our findings: bit.ly/44e0uZ9. I wanted to share a few additional thoughts on its implications and some future…

🔥Absolutely thrilled to share a pair of papers out in @CellPress of work done with @GarryPNolan. 🔬 T cell mediated restructuring of the tumor microenvironment - doi.org/10.1016/j.celr… 🧬 Extracting spatiotemporal mechanisms from spatial-omics data - doi.org/10.1016/j.cels…

A spatiotemporal atlas of mouse liver homeostasis and regeneration nature.com/articles/s4158… #journals #feedly

Excited to share Nicheformer! Led by @Alejandro__TL & @AnnaCSchaar, Nicheformer is a foundation model for single-cell & spatial omics. Its innovation is going beyond disassociated analysis to capture & predict local tissue context at single-cell level. biorxiv.org/content/10.110…

Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones nature.com/articles/s4146… #journals #feedly

1. BANKSY is out! go.nature.com/4bUR200 Our spatial clustering algo applies to any spatial RNA/protein/... assay, scales to 2M cells, detects both cell typing and spatial domains and facilitates spatial batch correction. 🧵 👇

1/n: 🔬We introduce NicheCompass (NC) a graph learning model to build spatial atlases across millions of cells, quantitatively characterize cell niches, infer cellular communication, and map new data into these atlases. NC can be used with various spatial technologies, ranging…

#CellCharter A powerful single-cell #SpatialTranscriptomics analysis framework Graph-based #DeepLearning Spatial cluster: Cell type Different expression Neighborhood enrichment AND Shape!!!👹 - curl/elongation/linearity/purity #VariationalAutoEncoder for dimension reduction,…

1/11 Check out our preprint introducing Nova-ST, a high resolution, spatial barcoding workflow developed by repurposing Illumina’s NovaSeq 6000 S4 flow cells for spatial transcriptomics profiling. biorxiv.org/content/10.110…

Our newest manuscript is out today! Very happy to share this story about the microenvironment during in vivo cardiac renewal: nature.com/articles/s4416…

🤩🤩🤩 Spatial Omics fans, I am super excited to share our latest manuscript!!! 🤩🤩🤩 #spatialomics #spatialbiology #singlecell Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues biorxiv.org/content/10.110…