scRNA-seq

Islet size, cellular composition, and spatial location are interconnected in the human pancreas

The paper examines how islet size, endocrine cell composition, and spatial location are interconnected in human pancreata using single-cell analysis of non-diabetic donors.

Linking live-cell imaging to single-cell sequencing using genetic barcoding

This paper introduces Waldo, a genetic barcoding system that links live-cell imaging phenotypes to single-cell sequencing data for the same cells.

COPD Preferentially Disrupts Constitutive Redox Support Relative to Inducible Antioxidant Defense

The paper identifies a cell-selective loss of constitutive redox support in COPD, with reduced PGC-1 target-program output in fibroblasts.

Evolutionarily informed gene sets reveal conserved and lineage-modified transcriptional programs during vertebrate forebrain evolution

This study uses a multispecies comparative framework to analyze forebrain cell types across vertebrates, revealing conserved transcriptional programs and lineage-specific modifications.

Age-associated transcriptional programs in tumor-associated macrophages are associated with tumor progression in HPV-negative oral cancer

The paper identifies age- and smoking-associated SPP1high tumor-associated macrophages in HPV-negative oral cancer that promote tumor progression by remodeling the extracellular matrix and suppressing antitumor immunity.

Mechanisms Matter: Transportability of Cellular Perturbation Effects

The paper shows deep learning models struggle to generalize cellular perturbation responses across contexts, highlighting the importance of causal mechanisms over distributional similarity.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs

FlyAnatoView projects Drosophila scRNA-seq data onto anatomical diagrams to restore spatial context and enable exploration of gene expression patterns across tissues.

Preferential formation of NUP98::KDM5A condensates at specific H3K4me3-rich loci drives leukemogenic gene expression

This study shows NUP98::KDM5A forms condensates preferentially at H3K4me3-rich loci, driving leukemogenic gene expression through chromatin engagement.

Characterizing and Mitigating Protocol-Dependent Gene Expression Bias in 3' and 5' Single-Cell RNA Sequencing

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.

Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma

The paper uses spatial and single-cell transcriptomics with mitochondrial lineage tracing to uncover fate switching and premetastatic niche formation in osteosarcoma.

Estimating the completeness of large-scale single-cell sequencing projects

This paper estimates the completeness of large-scale single-cell sequencing projects using ecological richness metrics applied to cellular diversity data.

Dietary magnesium supplement enhances memory through Hippo signaling

This study shows dietary magnesium enhances memory by modulating Hippo signaling in Drosophila neurons, specifically in β Kenyon Cells.

scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

Accurate Reconstruction of Adaptive Immune Receptor Repertoires from FACS-partitioned B and T Cell Subsets

The paper develops computational methods to accurately reconstruct adaptive immune receptor repertoires from partitioned B and T cell subsets, showing improved accuracy compared to pooling sub-repertoires.

Connectomics by Sequencing Reveals Self-Organizing Principles of Neuronal Networks in Cerebral Organoids

The paper develops COSCO to map neuronal connectivity in cerebral organoids and shows self-organizing network motifs and disease-related topological changes.

Transient Vascular Cell Integration and Intrinsic Media-Stimulated Endothelial Activation Reveal Diabetic Retinopathy Signatures in Human Retinal Organoids

The paper develops vascular organoids that integrate into retinal organoids, revealing diabetic retinopathy-like gene expression patterns in endothelial-like cells.

HyperCom: a hypergraph-based method to infer cell-resolved cell-cell communication

HyperCom infers cell-resolved cell-cell communication using hypergraphs from single-cell transcriptomics data, providing a continuous sender-receiver score for ligand-receptor pairs.

Single-cell informed metabolic modeling reveals organ-specific metabolic adaptations in breast cancer organotropism

This study uses single-cell transcriptomics and metabolic modeling to identify shared and organ-specific metabolic adaptations in breast cancer metastasis to the liver, bone, and brain.

Dynamic Schlafen 11 (SLFN11) expression revealed by single-cell RNA sequencing of clonal human cancer cells

The paper uses single-cell RNA sequencing to show heterogeneous SLFN11 expression in cancer cells, linking it to stress response and genome maintenance.

Exploring the Comedone Switch through Single-Cell Resolution of Human Acne Lesions

The paper investigates the molecular mechanisms of comedogenesis in human acne using single-cell transcriptomics, identifying a microcomedone-like cell population and supporting the comedone switch hypothesis.

Myeloid cell reprogramming drives enhanced defense against Streptococcus pneumoniae lung infection following exposure to commensal Prevotella

The paper shows that exposure to Prevotella melaninogenica reprograms myeloid cells to enhance defense against Streptococcus pneumoniae lung infection.

A Measure of Transcriptional Dyscoordination for Quantifying Aging in Single Cells

This paper introduces a measure of transcriptional dyscoordination to quantify aging in single cells, showing it increases with age and is linked to cellular processes like senescence and genome instability.

One-carbon metabolism sustains effector T cell function through cell-surface glycosylation

This study shows folate deprivation impairs CD8+ T cell function by disrupting cell surface glycosylation, and increasing folate uptake enhances T cell anti-tumor activity.

AmbiDose: per-cell removal budgets for ambient RNA contamination

AmbiDose removes ambient RNA contamination in single-cell RNA sequencing by using cell-specific removal budgets and ambient profiles, achieving high specificity for same-species UMIs.

Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions

The paper creates a single-cell and spatial transcriptomics atlas of the ileum during diverse infections, revealing novel cell states and immune responses.

Conserved cellular architecture and developmental mechanisms of the zebrafish meninges

This study defines zebrafish meningeal development, identifies conserved Foxc1 and Wnt signaling roles, and reveals limited regenerative capacity and developmental defects upon meningeal loss.

"Double-dipping" in testing for phenotypic differences with scRNA-Seq

The paper identifies a 'double-dipping' issue in scRNA-Seq where cell-type clustering and phenotype testing are performed on the same data, leading to inflated false discovery rates, and proposes solutions to mitigate this problem.

Realigning representational drift in mouse visual cortex by flexible brain-machine interfaces

This study uses flexible electrodes to track and model representational drift in mouse visual cortex, enabling a stable decoder for brain-machine interfaces.

Conserved Fibroblast Subsets Drive Shared Fibrotic Mechanisms in Osteoarthritis Synovium and Systemic Sclerosis Skin

This study identifies conserved fibroblast subsets and fibrotic mechanisms in osteoarthritis and systemic sclerosis using single-cell RNA-seq and spatial transcriptomics.