spatial domain detection

MorphoANOVA: Dissecting Histology-Gene Expression Relationships in Spatial Transcriptomics

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

Microenvironmental Fingerprint of Maturing Tau Condensates from Spectral and Lifetime Phasor Analysis of a Solvatochromic Dye

This paper develops a multimodal framework using spectral and lifetime phasor analysis to characterize microenvironmental changes in Tau condensates during maturation.

Three-dimensional mapping of human lung fibrosis identifies spatial coupling between tissue microarchitecture and maladaptive repair states

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

Generalizable virtual staining from histopathology to spatial proteomics across biological scales

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

Gene expression in Anolis sagrei suggests conservation of patterning mechanisms drives formation of two high acuity areas

The paper identifies conserved gene expression patterns in the retina of Anolis sagrei that suggest shared developmental mechanisms for forming multiple high acuity areas.

Topographic reference modelling of white matter hyperintensities across the adult lifespan

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

Spatial transcriptomics of pediatric tuberculosis lymph nodes reveals a conserved hypoxia_SPP1 niche

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

Predicting cortical signal mixing in coarse-resolution fMRI: a forward-operator analysis of surface mapping and the conditional benefit of correction

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

Dog and Human Brains Represent Human Emotional Bodies with Asymmetric Encoding of Happiness and Anger

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.

Cross-species structure-mechanics prediction in the intervertebral disc

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

TSNR: Protein-Specific Signals with Broad Molecular Context for Spatial Protein Prediction

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.

Quantifying subcellular organization from localization to co-occurrence with InSpace

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

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

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

Individual-specific recovery of the healthy human gut microbiota after antibiotics

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

Single-base mapping of m6A in lncRNAs reveals a distinct landscape linked to transposable elements and RNA processing

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

Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect

This study examines how host plant, season, and urbanization affect the gut microbiome of soapberry bugs, finding that host plant is the primary driver of microbial community structure.

Full-Term and Preterm Differences in Human Brain Functional Connectivity Development Across Birth

This study compares functional connectivity development in preterm and full-term brains using longitudinal MRI scans, finding divergent patterns in connectivity trajectories.

Kontext: Kernel-based method bridging spatial domain identification and cell-cell communication

Kontext identifies spatial domains and cell-cell communication by integrating ligand-receptor interactions, outperforming existing methods in spatial transcriptomics.

PatHoST: weakly supervised reconstruction of pathogen spatial distributions from host transcriptomes

PatHoST reconstructs pathogen spatial distributions from host transcriptomes using weakly supervised learning, showing improved detection in both experimental and human SARS-CoV-2 data.

Evolution of immune infiltration and immune triad formation across early melanoma progression

The paper investigates immune infiltration and triad formation in early melanoma progression using spatial transcriptomics, finding increased immune engagement in Stage I lesions compared to Stage 0.

smoothclust: Spatial smoothing and boundary-density summaries for spatial transcriptomics

smoothclust provides a framework for spatial domain analysis in spatial transcriptomics, including a clustering workflow and a boundary density metric to summarize tissue architecture.

Somatostatin-excitatory coordination emerges with dexterous motor skill learning

The paper shows that SST neurons become selectively coordinated with behaviorally relevant excitatory populations during motor skill learning.

Torsion in motion: the visual system as a three-axis gimbal

This study estimates eye torsion during walking using head-mounted technology and shows its role in altering retinal flow for self-motion parameter extraction.

Distinct gradients of cortical architecture capture visual representations and behavior across the lifespan

The paper shows two architectural gradients in human visual cortex that correlate with structural, functional, and behavioral traits across the lifespan.

Molecule-resolved inference reveals the spatial organization of transcriptional programs

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

Tissue-specific transcriptomic responses to early Toxoplasma gondii infection in sheep during congenital toxoplasmosis

This study examines early transcriptomic responses to Toxoplasma gondii infection in pregnant sheep, identifying tissue-specific immune and stress pathways linked to fetal loss.

Algorithmic Geometry Shapes the Biological Meaning of Thalamocortical Structural Covariance

The paper compares five algorithms for deriving structural covariance networks in the thalamocortical system and finds they emphasize different neurobiological aspects based on their mathematical properties.

Brain representations of visual short-term memories during healthy human aging: occipital decline and frontoparietal compensation

This study investigates age-related changes in visual short-term memory using fMRI decoding, finding that visual cortex representations weaken with age and load, while frontoparietal regions compensate by strengthening during memory maintenance.

Osmotic Coupling of Mechanics and Epigenetics Regulates Chromatin Phase Organization

This study develops a model linking nuclear hydration to chromatin phase organization and mechanics, showing how osmotic and mechanical cues influence chromatin structure through water content and histone dynamics.

Hexagonal modulation of theta rhythmic attentional sampling of visual space

The paper shows that visual attention samples space in a hexagonal pattern guided by theta rhythms, similar to spatial navigation mechanisms.