scRNA-seq

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.

A multipotent mouse distal airway secretory cell population that contributes to both airway and alveolar regeneration

This study identifies a multipotent secretory cell population in mouse distal airways that contributes to both airway and alveolar regeneration after injury.

Regenerative epithelial spike cells instruct immune niche homeostasis in zebrafish fin epidermis

The paper identifies a novel epithelial cell type in zebrafish fins, spike cells, and shows their role in maintaining immune cell niche homeostasis through interactions with mpeg1+ immune cells.

Multicellular Perturb-seq Reveals Lineage-Specific Transcriptional Control During Human Cardiac Organoid Development

This study uses Perturb-seq with CRISPRi to analyze how cardiac and vascular transcription factors coordinate lineage commitment and cross-lineage signaling in human cardiac organoids.

TRACE: a framework for traceable biomedical resource construction demonstrated through single-cell glaucoma data

TRACE provides a framework for creating traceable biomedical resources, demonstrated with a single-cell glaucoma dataset, enabling reproducible analyses and resource reuse.

Human lymphatic organoids reconstruct convergent developmental routes to functional lymphatic vessels

This study generates human lymphatic organoids from pluripotent stem cells using two mesodermal routes, showing they form functional vascular networks and support immune interactions.

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.

Lineage tracing in rhabdoid tumor organoids and orthotopic xenografts reveals convergent transcriptional states

The paper uses lineage tracing and single-cell RNA sequencing to show that rhabdoid tumors converge on a limited set of transcriptional states despite clonal diversity.

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.

Single-cell transcriptomics of enriched rare neural lineages of Tribolium castaneum

The paper develops workflows for targeted single-cell and single-nucleus RNA sequencing of rare neural populations in Tribolium castaneum using reporter and antibody-based enrichment strategies.

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.

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.

A subtype-specific gene regulatory program controls differential circuit integration of deep CA3 pyramidal neurons

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

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.

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.

Sex-specific bone marrow populations regulate skeletal phenotype and identify CD74-marked osteoclast precursor subsets

The paper identifies sex-specific bone marrow cell populations that regulate bone mass and shows CD74 marks osteoclast precursor subsets.

Disentangling Context-Specific Alzheimer's Disease Progression Signatures through an Explainable AI Framework

ADVISE identifies context-specific Alzheimer's disease progression signatures using an explainable AI framework and validates ROBO2 as a candidate regulator in excitatory neurons.

gcat, its_a_scam: modular tools for single cell data processing and per-cellquality control

The paper introduces gcat and its_a_scam, modular tools for single cell genomic data processing and quality control, showing they produce results comparable to proprietary pipelines.

Distinct processing of visual motion by transcriptomic cell types in the superior colliculus

The paper identifies how three transcriptomic cell types in the superior colliculus process visual motion with distinct feature selectivity, morphology, and connectivity.

CD40 ligand and IFN-γ induce proinflammatory activity and microglia-mediated neurodegeneration in human stem cell models

This study shows CD40L and IFN-γ induce inflammation and neurodegeneration in human stem cell-derived microglia, suggesting CD40L blockade as a potential MS therapy.

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

This study assesses whether hydroquinone induces aneuploidy in hematopoietic stem cells using KaryoTap and FISH, finding no reproducible increase in whole-chromosome aneuploidy.

Single-cell characterization of 3D CLL spheroid model that recapitulates lymph node microenvironment-driven phenotypes and in vivo drug responses to ibrutinib

The paper uses a 3D CLL spheroid model to study how lymph node microenvironmental signals influence CLL cell phenotypes and drug responses to ibrutinib.

CTLA-4 checkpoint signalling modulates germinal centre dynamics and antibody avidity during Borrelia burgdorferi infection in mice.

This study shows that CTLA-4 signaling impairs antibody quality during Borrelia infection by affecting germinal center dynamics and T cell responses in mice.

Aging reshapes cardiac extravascular leukocyte transcription through bidirectional remodeling during LPS-induced endotoxemia

This study shows aging causes bidirectional transcriptional changes in cardiac immune cells during LPS-induced endotoxemia, with shared mitochondrial remodeling and cell-type-specific functional shifts.

Patient-Derived Synovium-on-a-Chip Recapitulates Disease and Treatment Response and Permits Study of Resistance

This paper develops a patient-derived synovium-on-a-chip model to study RA disease and treatment response, finding that it correlates with clinical outcomes and identifies ECM signaling as a resistance mechanism.

Molecular dissection of the ChAHP complex subunits Adnp and Chd4 reveals common and divergent functions in retinal development

This study investigates the role of the ChAHP complex in retinal development by analyzing Adnp and Chd4 knockouts, revealing shared and distinct functions in cell proliferation and fate.

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.