scRNA-seq

Joint recording of past and present transcriptomes reconstructs single-cell trajectories

This paper introduces scReMeMber-Seq, a method to reconstruct single-cell trajectories by linking past and present transcriptomes using methylation-based memory recording.

Chikungunya Virus Infection of Monocytes Generates a Persistent Macrophage Reservoir That Promotes IFN-π/IL-27-STAT1- and NF-κB-Driven Chronic Arthritis

This study shows CHIKV infection transforms monocytes into persistently infected macrophages that drive chronic arthritis through IFN-π/IL-27-STAT1 and NF-κB pathways.

Single-Cell Omics to Uncover Cell-Type-Specific Gene Regulatory Networks Driving Mucilage Production in Specialized Roots

This study uses single-cell RNA sequencing to identify gene regulatory networks in mucilage-producing roots across maize, sorghum, and Medicago truncatula, revealing shared and species-specific regulators.

RNA splicing factor mutations drive myeloid neoplasm oncogenesis through protein complex poisoning

This study identifies how RNA splicing factor mutations drive myeloid neoplasm by disrupting proteomic networks through mis-splicing, validated via single-cell transcriptomics and proteomics.

Desmoglein-1 coordinates cell proliferation and actin dynamics to promote epidermal morphogenesis.

This study uses scRNA-seq to show Dsg1 coordinates cell proliferation and actin dynamics to drive epidermal morphogenesis through a Dsg1-Nck1-N-WASP axis.

ProxiNet transfers spatially learned cellular proximity to dissociated single-cell transcriptomes

ProxiNet transfers spatially learned cellular proximity from spatial transcriptomics to dissociated single-cell transcriptomes, revealing tissue organization and age-related changes in Alzheimer's.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

Multi-Model Machine Learning Consensus Identifies a Dual-Interferon Gene Signature in Ischemic Stroke: An Integrative Single-Cell Transcriptomic Analysis

This paper uses a multi-model consensus framework to identify a dual-interferon gene signature in ischemic stroke using single-cell RNA sequencing data from a mouse model.

Single-cell transcriptomics reveals life cycle and cell cycle gene expression dynamics during in vitro growth of two Leishmania species

This study uses single-cell transcriptomics to analyze life cycle and cell cycle gene expression dynamics in two Leishmania species during in vitro growth, revealing developmental endpoints and cell cycle-related gene expression patterns.

Endothelial AMBRA1 loss contributes to vascular dysregulation facilitating metastatic progression in early-stage melanoma

This study shows that endothelial AMBRA1 loss leads to vascular dysfunction and promotes metastasis in early-stage melanoma.

Cell-of-origin shapes tumor subtype in BRCA1-associated triple-negative breast cancer

This study identifies two cell-of-origin-driven subtypes of BRCA1-associated TNBC, showing that tumor subtype depends on the cell type initiating the cancer.

Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues

The paper constructs a single-nucleus multi-omic atlas of adult human tissues, identifying regulatory elements and variant effects across 21 tissues.

Accurate and scalable demultiplexing of single-cell RNA sequencing using BEACON

BEACON improves demultiplexing accuracy in single-cell RNA sequencing by learning background counts, outperforming existing methods and enabling new biological insights.

CycloCross: Adversarial single-cell RNA-seq data translation across species

Translating cells between mouse, macaque and human scRNA-seq with a CycleGAN, without ortholog mapping, preserved developmental time structure, imputed missing states and produced more realistic synthetic cells than scGAN.

CHACAM: a cell-cell interaction-guided hierarchical attention model for high-precision cell identity annotation of scRNA-seq data in early C. elegans embryogenesis

CHACAM improves cell identity annotation in C. elegans scRNA-seq data by integrating cell-cell interactions and gene expression to resolve ambiguous lineages.

Ancestral secretory programs underlie the evolution of morphological innovations across Spiralia

This study identifies shell-forming cell types in Pacific oysters and shows they evolved from ancestral epithelial-secretory systems in Spiralia.

The Metabolic Organ Clock: A Computable Framework Linking Cell-Lineage Architecture to Emergent Organ Bioenergetics

The paper develops a computable framework linking cell-lineage architecture to organ bioenergetics, finding that compartment identity explains most of the variance in metabolic tier.

Epigenetic progression of pancreatic cancer to aggressive subtypes involves alternate routes of lineage reprogramming in subtype-intermediate progenitor cells

The paper identifies subtype-intermediate progenitor cells in pancreatic cancer with distinct epigenetic profiles linked to clinical outcomes and lineage reprogramming.

Mapping the response of primary human chondrocytes to an osteoarthritis-relevant stimulus by single-cell RNA sequencing

This study uses single-cell RNA sequencing to analyze how fibronectin fragment treatment alters chondrocyte states and transcriptional programs in primary human cells.

Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum

This study uses single-cell RNA sequencing and TCR profiling to analyze immune changes in Parkinson's disease across different stages and identifies sex-dependent immune alterations and TCR diversity.

TNFα drives platelet hyperreactivity and thromboinflammation through regulation of hematopoietic stem and progenitor cells.

This study shows TNFα increases platelet reactivity and thromboinflammation by expanding and reprogramming hematopoietic stem and progenitor cells, not directly affecting megakaryocytes.

An FEV-Associated Metastasis-Initiating-Like State Linked to Tumor Cell Plasticity and Immune Niche Remodeling in Prostate Cancer

The paper identifies a metastasis-initiating-like state in prostate cancer linked to FEV, tumor plasticity, and immune niche remodeling through integrated multi-omics analysis.

Utilizing single-cell data for per-cell type eQTL mapping in the human pancreas

This study identifies cell type-specific eQTLs in the human pancreas using single-cell RNA-seq data and deconvoluted bulk RNA-seq data, revealing new genetic signals and associations with metabolic disease.

Sex-stratified adipose-liver circuits in human MASLD

This study identifies sex-specific transcriptional differences in liver and visceral adipose tissue in MASLD and shows coordinated cross-tissue states.

Isogenic forebrain organoids uncover early neurodevelopmental alterations and imbalances in neuronal function leading to hyperexcitation in Gaucher disease

This study uses isogenic brain organoids to identify early neurodevelopmental changes and hyperexcitability in Gaucher disease, linking lipid dysregulation and neuronal function imbalances to clinical symptoms.

Single-cell profiling resolves gain- and loss-of-function mechanisms in CASR to advance mechanism-aware variant classification

The paper uses single-cell RNA-seq and machine learning to classify CASR variants as gain- or loss-of-function, achieving high accuracy and clinical validation.

Keto-gluconeogenic metabolic axis mirrors renal homeostasis and post-injury response in spatial transcriptomics

This study identifies a keto-gluconeogenic metabolic axis that mirrors renal homeostasis and injury responses using spatial transcriptomics and biochemical analyses in AKI to CKD transition.

TxCyto: A machine learning framework for estimating cytokine activity from whole transcriptome

A fully connected neural network trained on 9491 TCGA bulk tumor transcriptomes estimates activity of 645 cytokines and secreted proteins, checked against perturbation and protein data.

Integrating morphology and gene expression of neural cells in unpaired single-cell data using GeoAdvAE

GeoAdvAE integrates unpaired single-cell morphology and transcriptomics to align cell types and reveal disease-associated microglia signatures.

Inferring cascade drivers of VEXAS syndrome by a causal machine learning tool CauNagi

The paper introduces CauNagi, a causal machine learning tool, to identify causal drivers of VEXAS syndrome using single-cell transcriptomic data, revealing key regulatory hubs involved in myeloid dysfunction.