snRNA-seq

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 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.

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

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.

Pathology-defined cell states reveal reproducible transcriptomic signatures across ALS cortical single-nucleus RNA-seq studies

The paper shows that using pathology-defined cell states improves reproducibility of transcriptomic signatures in ALS snRNA-seq studies compared to conventional case-control analyses.

The extreme diversity of retinal amacrine cells has deep evolutionary roots

The paper reconstructs the evolutionary origins of retinal amacrine cell diversity using transcriptomic data from 24 vertebrate species, identifying 42 orthologous cell types and suggesting a hybrid precursor origin.

Constructing a full-length single-nucleus transcriptomic atlas of the obese mouse by UURNA-seq

This paper introduces UURNA-seq, a high-throughput single-nucleus RNA sequencing method, and constructs a comprehensive obesity atlas revealing transcriptional changes and metabolic pathway dysregulation.

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.

Cluster replicability in single-cell and single-nucleus atlases of the mouse brain

The paper evaluates cluster replicability across two mouse brain atlases using single-cell and single-nucleus RNA sequencing, identifying 2009 reciprocally matched clusters with consistent spatial and gene expression 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.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

Semi-parametric Empirical Bayes Method for Multiplet Detection in snATAC-seq with Probabilistic Multi-omic Integration

SEBULA detects multiplets in snATAC-seq using a semi-parametric empirical Bayes model and integrates with scRNA-seq data, showing superior performance on benchmark datasets.

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.

Fixative eXchange (FX)-seq: Scalable Single-nucleus RNA Sequencing Analysis of PFA-fixed or FFPE Tissue

FX-seq improves snRNA-seq from FFPE and PFA-fixed tissues by removing crosslinks and preventing RNA leakage, enabling analysis of 321,710 nuclei from mouse and human samples.

Precision-Based Filtering Facilitates Integration of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations

The paper introduces a coefficient of variation-based filter for RNAseq data to retain low-variation genes, enabling better identification of cell populations in Arabidopsis snRNAseq data.

Ablation of Prdm16 and beige fat causes vascular remodeling and elevated blood pressure

Adipocyte-specific deletion of Prdm16 ablates beige fat identity, derepresses the secreted enzyme Qsox1, and induces vascular fibrosis, angiotensin II hyperreactivity, and elevated blood pressure in mice.

Factorization of Alzheimer's disease genetic risk influences allow patient stratification, predicting disease onset, cognitive decline, and cell-type specific responses

The paper uses matrix factorization to analyze genetic risk variants in Alzheimer's disease, identifying factors that predict disease onset, cognitive decline, and cell-type specific responses.

Central T3 deprivation disturbs cortical cilia formation, oligodendrocyte lineage and neuronal cell-cell-communication in a MCT8/OATP1C1 deficient Allan-Herndon-Dudley Syndrome mouse model

This study uses single nucleus RNA sequencing to analyze cortical and striatal development in a mouse model of Allan-Herndon-Dudley Syndrome, identifying disruptions in oligodendrocyte lineage, cell-cell communication, and cilia formation.

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.

Mouse Cortical Cellular Diversification Through Lineage Progression of Radial Glia

This study uses scRNA-seq and snATAC-seq to show that radial glia sequentially generate neurons and glia through lineage progression, with chromatin accessibility regulating cell fate decisions.

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.

Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentation

This study compares rhesus macaque and human placental organoids to identify evolutionary differences in trophoblast gene expression and differentiation pathways.

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.

Molecular Deconstruction of the Medullary Raphe Magnus in the rat: Transcriptional Responses to Repeated Seizures

The paper uses snRNA-seq to analyze transcriptional changes in the rat brainstem's Raphe Magnus region after repeated seizures, identifying altered neuronal function without changes in other cell types.

Nuclei Isolation Protocol for Single-Nucleus RNA Sequencing of Human Stem Cell-Derived Grafts

This paper describes a protocol for isolating nuclei from human stem cell-derived grafts in rat brains for single-nucleus RNA sequencing.

Spreading alpha-Synuclein Oligomers Trigger Astrocyte Changes and Astrocyte-Glutamatergic Neuron system dysfunction in an Age-related Manner

The paper investigates how alpha-synuclein oligomers spread in a mouse model of Parkinson's disease, identifying age-related astrocyte changes and dysfunction in the astrocyte-glutamatergic neuron system.

Age-associated microglia populations identified from several single cell transcriptome data

The paper identifies common and dataset-specific age-associated microglia populations across mouse and human datasets using integrative single-cell transcriptomic analysis.

Alveolar epithelial cell plasticity and injury memory in human pulmonary fibrosis

Single-nucleus multiomic and ex vivo lung slice profiling of human idiopathic pulmonary fibrosis identifies Alveolar Intermediate cells bridging alveolar and Aberrant Basaloid states and reveals AP-1 chromatin injury memory.