scRNA-seq

Label-free flow operators and stability operators from single-cell time courses: what local dynamical operators can and cannot identify

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

Human organoid screen links transient translational modulation to progenitor progression in corticogenesis

The paper screens human cortical organoids with small molecules to identify translational modulators affecting progenitor progression in corticogenesis, finding Emetine promotes neuronal differentiation.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

Rapid, accurate, and memory-frugal sub-gene-level quantification of probe-based, multiplexed single-cell data

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

Single-Cell Transcriptomics Reveals Tumorigenic Lineages and Interactions Persisting and Evolving From Premalignancy to Cancer in the Stomach

The paper uses single-cell transcriptomics to track molecular changes from premalignancy to cancer in gastric tissue, identifying persistent and evolving tumorigenic lineages and markers like EMB.

Microglial AhR Drives Sex-Biased Amyloid Pathology

This study identifies microglial AhR as a regulator of sex-biased amyloid pathology, showing that AhR activation exacerbates amyloid deposition and that AhR deficiency reduces amyloid burden.

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

LCN2+ Astrocytes Mark a Pro-inflammatory Astrocyte State Associated with Secondary Brain Injury After Cerebral Venous Thrombosis

Cytomegalovirus Infection in Human Cortical Organoids Induces Unique Developmental and Viral Substates

This study uses single-cell RNA sequencing to analyze HCMV infection in cortical organoids, identifying viral sub-states and cell type changes.

Response to azacitidine and the TIM-3 inhibitor, sabatolimab, in MDS and CMML is associated with distinct immune and antigen-presentation states

This study identifies immune and antigen-presentation states associated with response to azacitidine and sabatolimab in MDS and CMML using single-cell RNA sequencing.

Single-Cell Transcriptome-Wide Mendelian Randomization and Colocalization Analysis Reveals Immune Cell-Specific Mechanisms in Alzheimer's Disease

This paper uses single-cell eQTL-MR and colocalization analysis to identify immune cell-specific genetic mechanisms associated with Alzheimer's disease risk.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

Sex-specific gene and isoform expression characterizes hippocampal aging in rhesus macaques

This study identifies sex-specific gene and isoform expression changes in hippocampal aging of rhesus macaques and finds shared transcriptional signatures with Alzheimer's disease.

Benchmarking Statistical Methods for Differential Composition Analysis in Population-Scale Single-Cell Data

This study benchmarks 12 methods for differential composition analysis in scRNA-seq data, finding LOCOM performs best in controlling false discovery rate and maintaining power.

SPECHTacle: An Efficient Detection and Visualization of Cell Specific Regulation in Single Cell-Based Experiments Using a Novel Combinatorial Computational Tool

SPECHTacle efficiently identifies and visualizes cell-specific regulatory changes in single-cell experiments using optimal transport and entropy analysis.

Vorinostat Can Reduce an Ongoing Fibrosis and Preserve Key Liver Metabolic Functions by Selectively Altering Mesenchymal Cell Differentiation

This study shows Vorinostat reduces ongoing liver fibrosis and preserves metabolic functions by altering mesenchymal cell differentiation in a human iPSC-derived model.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Single-Cell RNA Sequencing Reveals Distinct Cellular and Molecular Features of Steroid-Induced Osteonecrosis of the Femoral Head Compared to Alcohol-Induced Osteonecrosis and Hip Osteoarthritis

This study uses single-cell RNA sequencing to compare cellular and molecular features of steroid-induced and alcohol-induced osteonecrosis of the femoral head with hip osteoarthritis, identifying distinct immune and stromal cell signatures.

Uncovering cross-signal interactions in single-cell and spatial omics

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

A fibroblast-CD8+ T cell circuit drives a Type 1 shift in allergic inflammatory memory

This study identifies a fibroblast-CD8+ T cell circuit that drives a Type 1 immune shift in allergic inflammatory memory through mechanistic and translational analysis in murine and human models.

High-fat diet promotes exhaustion-associated T-cell remodeling across vascular and lymphoid tissues in atherosclerosis-prone mice

This study shows that a high-fat diet causes T-cell exhaustion in multiple tissues of atherosclerosis-prone mice, which partially reverses with dietary changes.

Live Droplet Single-Cell RNA Sequencing

The paper introduces Live D-seq, a method for longitudinal, non-destructive single-cell RNA sequencing, and demonstrates its ability to track cellular dynamics over time.

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

This study identifies MET signaling as a targetable vulnerability in rhabdoid tumors through integrated single-cell multi-omic and spatial transcriptomics analyses.

Early Progression Cells mark a stem-like state associated with pancreatic cancer initiation and progression

The paper identifies Early Progression Cells (EPCs) as stem-like cells in pancreatic cancer that drive progression and are associated with specific gene programs and interactions.

Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

This study compares molecular features of SSc-NSIP and SSc-UIP with IPF, finding shared epithelial changes and distinct fibroblast programs.

Perturbation-induced gene programs map the hidden regulatory architecture of complex diseases

This paper introduces Perturbscape, a framework that uses perturbation-induced gene programs to identify disease-relevant genes and pathways, showing higher heritability informativeness than steady-state approaches.

CD200R1 Marks a Branchpoint During Human Natural Killer Cell Development in Tonsils

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

Single-cell geometry of drug responses across malignant glioma states

The paper analyzes drug response direction across glioma states using single-cell RNA-seq data, finding that response direction is consistent across states but magnitude varies.