spatial domain detection

This paper introduces RIDGE, a deconvolution framework that generates spatially continuous cell-type maps of the human cortex, revealing both global organization and regional specialization.

This study shows that speech motor cortex encodes sentence-level linguistic structure and semantic content through single-unit activity in three BrainGate2 participants.

This study introduces DynaClade, an algorithm for analyzing human motion in virtual environments, revealing non-random action sequences with higher-order structure and context-dependent behavior.

SpaAxFormer improves spatial transcriptomics by integrating gene-level and cell-level representations, achieving better imputation and spatial-domain identification in some datasets.

This paper introduces f-LENNS, an AI framework that enhances fMRI resolution without retraining, improving spatial fidelity and generalizing to atypical brain function.

SigDoTS is a statistical framework for spatial domain detection in spatial transcriptomics that controls for post-selection bias and improves domain recovery.

MorphoANOVA systematically analyzes spatial gene-expression patterns in relation to tissue morphology, identifying genes with location-specific associations and spatial expression beyond morphology.

This study maps human lung fibrosis in 3D, showing how structural changes in tissue microarchitecture drive maladaptive repair states and disease progression.

The paper identifies a pre-fibrotic stage in scleroderma by analyzing spatial transcriptomic changes in clinically uninvolved skin, showing early loss of fibroblast niches and vascular reprogramming.

The paper examines age-related accumulation of Biondi bodies in human choroid plexus epithelial cells, finding nonlinear increases in prevalence and load, and suggesting prion-like spread mechanisms.

MorphoProt predicts spatial protein abundance using RNA expression, multiscale histology, and tissue neighborhoods, outperforming baselines in human and mouse tissues.

This study introduces QUEST, a model that uses H&E histology to predict spatial protein expression, enabling virtual staining and analysis across biological scales.

This paper introduces vTRM, a framework to characterize WMH spatial patterns across age and sex, revealing distinct associations with aging, vascular, and neurodegenerative processes.

This study uses spatial transcriptomics to identify a hypoxia-associated SPP1-enriched microenvironment in pediatric TB granulomas that may contribute to incomplete bacterial clearance.

This paper develops a forward-operator model to predict signal mixing in fMRI and shows that correcting for it improves coarse-resolution cortical mapping.

The paper shows that nociceptive signaling is essential for the brain to represent and replay inflammatory states using human fMRI and mouse activity mapping.

This study evaluates probe registration accuracy in newborn fNIRS and HD-DOT, showing significant cap misalignment affecting spatial accuracy of functional images.

This study develops a non-invasive method using quantum dots to assess liver sinusoidal endothelial cell scavenger function in MASH, showing reduced retention correlates with disease progression.

This study shows that dogs and humans have similar neural representations of human bodily emotions, with happiness and anger encoded asymmetrically in distinct brain regions.

This study uses optical clearing and light-sheet fluorescence microscopy to visualize 3D microanatomy of human head-and-neck tissues and correlate it with conventional histology.

TileScope quantifies spatial gene expression relationships beyond simple colocalization, distinguishing regional enrichment from internal covariation in glioblastoma and other tissues.

This study develops a cross-species framework linking collagen structure to mechanical vulnerability in intervertebral discs using multiscale imaging and modeling.

The paper introduces TSNR, a method for spatial protein prediction that uses protein-specific signals and broad molecular context, achieving high correlation on a benchmark.

The paper uses expansion microscopy to reveal the repeat-subunit organization and multi-domain architecture of human mitotic centromeres, including specialized histone modifications.

InSpace quantifies subcellular organization by preserving localization and molecular co-occurrence, revealing spatial programs in B and plasma cells across cancers.

This study identifies divergent brain pathology in preterm infants with NEC, showing distinct cellular and molecular changes in the pons and cerebellum.

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

The paper shows that the human gut microbiota recovers to an individual-specific state after antibiotics, not to a generic healthy state.

The paper maps m6A modifications in lncRNAs at single-base resolution, revealing distinct patterns linked to transposable elements, RNA structure, and splicing.

This study identifies c-MYC as a non-canonical origin licensing accelerator, showing it increases licensing speed through TRRAP/GCN5 and histone H1 eviction, particularly in heterochromatin.