#spatialTranscriptomics

We are excited to share our new preprint about our development of a new #spatialTranscriptomics method (sphere-sequencing) to unveil local tissue microenvironments at single cell resolution! See below the #tweetorial from our very own @handlerkristina 👩‍🔬

Excited to share our new preprint on #thalamus development! 🧠 We reveal how sensory and non-sensory circuits are specified early in embryogenesis using #mutiomics, #spatialtranscriptomics, #lineagetracing. @GLB_Lab @JPLopezAtalaya @NeuroAlc

Are you interested in the role of #spatialtranscriptomics in the study of #colorectalcancer Check out our paper 👇👇👇 on deconvolution of the TME Great effort from @drcolinwood @hollyleslie_ @LabEdwards @grisurgery @ColinWSteele @LabSpatialNBJ

Have a look at this exciting manuscript on 3D reconstruction of intra-tumor heterogeneity! #SpatialTranscriptomics

Can allele-specific CNV analysis help decode tumor clonal heterogeneity from #SpatialTranscriptomics? Here is a re-analysis of a recent @10xGenomics Visium dataset from Barkley et al using Numbat, along with some thoughts and recommendations.

Stoked to share our new paper w/ @TiroshLab in @NatureGenet! Using spatial multi-omics we characterized two distinct modes of p-EMT in HNSCC, each with their own distinct ecosystems and drivers. #SpatialTranscriptomics #HNSCC #Visium #CODEX #EMT

DeepSpaceDB >2k #SpatialTranscriptomics Visium samples 👉Interactive, downloadable data analysis QC➡️ manual/LLM image annotation➡️ in-sample or cross-sample spot clustering BASS BayesSpace➡️ Spatially variable genes singleCellHaystack SPARK-X binSpect➡️ Cell type deconvolution RCTD SPOTlight 👉Cross-sample/Cross-study comparison 👉Analyze your own data 👉Database-wide gene/pathway inquiry @alexisvdb #NucAcidRes 2026

Curious about what we can do? #SpatialTranscriptomics - all mRNAs spatially resolved. See our showcase:

Excited to share our latest study in Cardiovascular Research (@escardio)! 🎉 Using CosMx WTX #spatialtranscriptomics (@brukerspatial) and paired plaque-PBMC #scRNAseq, we reveal critical cellular drivers of plaque instability beyond stenosis severity.

Check out our updated scatterbar package for visualizing proportional data across spatial coordinates like deconvolved cell types in #spatialtranscriptomics using stacked bar plots (alternative to scatterpies)! Preprint: Tutorials:

A guidebook of spatial transcriptomic technologies, data resources & analysis approaches🤠 A great ending for my 2-wk learning of #SpatialTranscriptomics tools Start reading real-world #SpatialOmics & preparing for @IVBM2024😆 @CSB_Journal 👉Jan 2023

I am updating my lecture slides on #spatialtranscriptomics to use author names + remove journal names to de-emphasize brands and re-emphasize people per #HHMI recs. In the process, I realized ALL the seminal techdev work has been led by co-first authors contributing equally 🧵1/3

De-spot Projecting sc-/sn-RNAseq (paired/unpaired) to #SpatialTranscriptomics Visium ST Stereo-seq MERFISH-> Spatial Multi-modality Data Sharpen the spatial cell-type boundaries Improve detection of low-proportion cell-type spatial domains Jian Liu lab @CellRepMethods 2024

THRILLED to share our latest work at the @hoheyn lab: "SPOTlight: Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell Transcriptomes". THREAD (1/n) #singlecellcnag #spatialtranscriptomics #visium

Imaging-based #SpatialTranscriptomics #Segmentation Segger 👉Attention-based #GraphNeuralNetwork 👉Learn a transcript-cell/boundary joint latent space 👉Unassigned transcripts➡️fragments➡️ median 20 transcripts/fragment vs 50 transcripts/cell vs Baysor BIDCell CellPose 10X Cell/Nuclei protocol 30 times faster than Baysor (on 4x @NVIDIAAI A100 GPU...🤧💸💸💸🤑) @HeidariElyas @MoritzGerstung bioRxiv 2025

In this blog post, I use our recent SEraster #Rstats tool to perform spatial bootstrapping to evaluate the stability of cell-type proportion estimates from #singlecell #spatialtranscriptomics data. Try it out for yourself: #bioinformatics #codetutorial

I record myself live coding in #Rstats to explore the impact of normalizing #spatialtranscriptomics data in dim reduction + clustering vs deconvolution #dataanalysis 📽️ Follow along and try out the code for yourself! #AcademicTwitter #Bioinformatics

Excited to share our lab's new preprint led by Ting @huanting_ong introducing paired-surface spatial mechanomics! We link nanoindentation stiffness maps with #SpatialTranscriptomics to connect local tissue mechanics with molecular state. 🔗 🧵1/7

We introduce EYKTHYR, a computational method that integrates gene expression and chromatin accessibility in a spatially aware model to identify transcription factors shaping spatial gene programs. Led by Lane Fellow @SpencerKrieger #spatialtranscriptomics

#SpatialTranscriptomics Visium @10xGenomics Vascular SpatialTime CD201/PROCR+ human perivascular mesenchymal progenitors Located at the outer adventitia of artery/vein in adipose tissue Wnt-hi A potential hierarchy of adventitial CD34+CD31-CD45-CD146- cell progenitorness CD201➡️CD304/NRP1 or CD141/THBD @NThottappillil @AaronWJames_Lab @Dev_Cell 2024