Thrilled to share our new paper on spatialMNN! . It's a fast, scalable, and accurate method to integrate multiple spatial transcriptomics (SRT) datasets and identify shared spatial domains. #SpatialTranscriptomics #Bioinformatics #Genomics #RStats

🚨 We’re hiring in Dr @Wi_Roman's Group. The Roman group study how cells communicate to keep organs healthy – and how this goes wrong in disease & ageing. Work with iPSCs, biomaterials, organ-on-chip & spatial transcriptomics to advance muscle biology & regenerative medicine.

(1/12) Over a year ago, we launched a new project to explore whether the tissue microenvironment could predict cellular behaviour and whether reprogramming might unlock new therapeutic avenues. 🧬 Spatial transcriptomics provides deep insights into tissue organisation. We

New online! Mapping trait-associated cells with spatial transcriptomics

Systematic evaluation of robustness to cell type mismatch of deconvolution methods for spatial transcriptomics data. #SpatialTranscriptomics #DeconvolutionMethods @biorxiv_bioinfo .

Plant-Compatible Xenium In Situ Sequencing: Optimised Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules . .♻️

PathCLAST: Pathway-Augmented Contrastive Learning with Attention for Spatial Transcriptomics

🌱 Xenium breaks barriers in plant spatial biology!. Thick cell walls, autofluorescence & complex tissues have long challenged spatial transcriptomics. A new bioRxiv preprint shows an optimised @10xGenomics Xenium workflow for Medicago truncatula roots & nodules.

STORIES: learning cell fate landscapes from spatial transcriptomics

Integration of spatial protein imaging and transcriptomics in the human kidney tracks the regenerative potential of proximal tubules | ⁦@ScienceAdvances⁩

🧬 STIM, a new tool developed by researchers at Janelia & the Max Delbrück Center, aligns sections of irregularly spaced 2D spatial transcriptomics data & renders them as images to reconstruct 3D volumes of gene expression. ➡️

Spatial Transcript Omics DataBase (STOmics DB) is a comprehensive repository of literature and Datasets related to spatial transcriptomics topics, and provides convenient tools for Data analysis, search and visualization.

SpaFoundation: a visual foundation model for spatial transcriptomics

PhenoGraph: A Multi-Agent Framework for Phenotype-driven Discovery in Spatial Transcriptomics Data Augmented with Knowledge Graphs

LSGI: interpretable spatial gradient analysis for spatial transcriptomics data.

#UTSW team led by Prithvi Raj, Ph.D., now boasts innovative tools like NanoString’s CosMx and 10x Genomics’ spatial transcriptomics systems—enabling researchers to map gene expression at single-cell and spatial resolution. Learn more: #BiomedicalResearch.

DiffusionST: A deep generative diffusion model-based framework for enhancing spatial transcriptomics data quality and identifying spatial domains

Very proud to have participated in this amazing work showing how we can combine the strengths of multiple spatial transcriptomics technologies! Congratulations to Qiao and to the wonderful leadership of Ben Humphreys!!.

In the Brain Resilience Lab, Shon has contributed to flagship projects that mapped the molecular landscape of human brain aging and led collaborations using next-generation sequencing, histology & spatial transcriptomics. He’s now starting his neuroscience PhD at @UCSF. Congrats!