snRNA-seq

Single-cell spatiotemporal transcriptomics reveals the origin, cellular heterogeneity and regulatory network of seed fiber cells in poplar

This study uses single-nucleus RNA sequencing and spatial transcriptomics to map seed fiber development in poplar, identifying their origin and regulatory network.

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.

Spatial proximity to AD pathology defines cell-type and genotype-specific characteristics in human AD hippocampus

The paper analyzes spatial relationships between AD pathology and gene expression in human hippocampus using MERFISH and snRNA-seq data, identifying cell-type and genotype-specific effects of A{beta} and tau pathology.

Spatial Transcriptomics Reveal Developmental Dynamics of the Human Cerebral Cortex and Striatum

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

A single-nucleus and spatial transcriptomic atlas of the Syrian hamster preoptic area across hibernation states

This study creates a transcriptomic atlas of the Syrian hamster preoptic area using snRNA-seq and spatial transcriptomics, comparing seasonal and hibernation states.

Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

This study identifies conserved neuronal-like and secretory programs in GEP-NETs and links them to spatial microenvironmental niches and metastatic potential.

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

This study shows that cellular senescence disrupts liver zonation and hepatocyte function with age by altering gene expression and cell signaling.

Invasion status stratifies the composition of the human pancreatic cancer perineural niche

Xenium and single-nucleus profiling of 14 human pancreatic tumors shows invaded nerve neighborhoods enriched for classical cancer cells, myCAFs and lipid-handling macrophages but depleted of lymphocytes.

A consensus atlas of human brain development defines cell type-specific maturation trajectories across the lifespan

Reprocessing nine human brain datasets (2,157,582 cells, 156 donors, GW6 to adulthood) under one marker-based taxonomy yields 35 replicable cell types with cell type-specific timing of adult-like maturation.

Multi-omics characterization of astrocyte subtypes reveals spatially coordinated astrocyte downregulation in depression

The paper identifies spatially localized astrocytic dysfunction in depression using multi-omics data and shows its role in disease pathology.

Decoding Lymphangioleiomyomatosis (LAM) Niche Environment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics

This study identifies two distinct LAM subtypes and their microenvironmental interactions using multi-omics and spatial transcriptomics, revealing key regulatory networks and potential therapeutic targets.

Prenatal e-cigarette exposure induces region- and cell type-specific metabolic and developmental reprogramming

This study shows prenatal e-cigarette exposure causes region- and cell type-specific metabolic and developmental changes in neonatal rat brains, linked to neurodevelopmental disease risk.

HESTA: a curated and reusable database for the human early organogenesis spatiotemporal transcriptome atlas

The paper presents a spatiotemporal transcriptome database of human embryogenesis, providing spatial gene expression and substructure data across 50 developing organs.

Multimodal analysis identifies pericyte-centered signaling programs altered by sex and brain region in Alzheimer's Disease

The paper identifies sex- and brain region-specific pericyte signaling changes in Alzheimer's Disease using single-nucleus RNA sequencing and spatial transcriptomics.

Single-cell spatial transcriptomics and snRNA-seq decoding the organizational principles of functional modules in the mouse amygdala

This study combines spatial transcriptomics and snRNA-seq to map cell type organization and functional modules in the mouse amygdala, revealing developmental origins and spatial patterns.

Early Pulmonary Fibrosis is Defined by Niche- and Cell-Specific Molecular Programs

This paper identifies compartment- and cell-specific molecular programs in preclinical familial pulmonary fibrosis using multi-omic profiling and finds these signatures are partially represented in peripheral blood.

Interleukin-1β Drives Disease Progression in Arrhythmogenic Cardiomyopathy

Human arrhythmogenic cardiomyopathy hearts harbor a lesion niche of POSTN fibroblasts and NLRP3+ inflammatory macrophages; IL-1β neutralization in Dsg2-mutant mice reduced fibrosis, dysfunction, and ventricular ectopy.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Identification and Characterization of Neoplastic Cells in Keratin-Positive Giant Cell-Rich Tumors

This paper uses single-nuclei RNA sequencing and spatial transcriptomics to characterize KPGCT, showing neoplastic cells express HMGA2::NCOR2 fusions and activate the hippo pathway, driving CSF1 production and macrophage recruitment.

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The paper integrates single-cell and spatial multiomic data to show widespread reactivation of developmental programs in diseased human hearts, with insights into transcriptional factors and localized fetal reactivation.

Spatial multi-omics unveils the monoclonal origin, neuroendocrine plasticity, and microenvironment niches in combined small cell lung cancer

This study uses spatial multi-omics to show cSCLC has a monoclonal origin, lineage plasticity, and distinct microenvironment niches, leading to a new diagnostic assay.

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions

The paper presents OWHA, a 4D multimodal atlas of wound healing in mice, revealing a conserved Basal IV/SEMA3C circuit that coordinates repair, and shows its disruption in diabetic wounds.

Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction

This study uses snRNAseq to identify cell-specific pro-repair responses induced by an infusible ECM biomaterial after myocardial infarction.

A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder

The paper creates a poly(A) isoform-aware single-cell and spatial atlas of the human bladder, identifying fibroblast niches and their spatial relationships.

RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair

RamanOmics integrates snRNA-seq, spatial transcriptomics, and Raman imaging to map spatial biochemical and molecular changes in aging and repair, identifying senescent cell signatures and their functional roles.

A Multi-omic Atlas of Human Choroid Plexus in Alzheimer's Disease

This study creates a multi-omic atlas of the choroid plexus in Alzheimer's disease, identifying disease-associated cell state transitions and functional impairments.

APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

The paper investigates how APOE genotype affects gene expression in the human entorhinal cortex, identifying an oligodendrocyte subtype as a potential mediator of Alzheimer's disease risk.

SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs

SpaTM is a topic modeling framework for spatial transcriptomics data that supports both annotation-guided and annotation-free analysis, showing competitiveness in spatial label prediction and clustering.

Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology

Nephrobase Cell+ is a kidney-specific foundation model that outperforms existing models in single-cell analysis, cross-species transfer, and batch effect correction.

Transcriptomic Signatures of Hippocampal Subregions and Neuronal Nuclei in Active Place Avoidance Memory Maintenance

This study identifies transcriptomic changes in hippocampal subregions and neurons during offline memory maintenance using spatial transcriptomics and snRNA-seq.