scRNA-seq

This study identifies CD73 as a regulator of metaplasia and immune remodeling in chronic pancreatitis, showing its role in tissue recovery and fibrosis.

The paper uses CRISPR-based lineage recording and single-cell RNA sequencing to show that mesodermal cell diversity in mouse embryos arises from spatially distinct, fate-biased progenitor pools rather than simple branching lineages.

Bloom is a transformer-based model that unifies brain cell representations across modalities and contexts, outperforming unimodal models in cell type resolution and annotation tasks.

This study presents a multi-omic analysis of the bent-wing bat genome to explore immune-related adaptations and viral interactions.

Chimera measures gene expression deployment across species, showing differences between predicted and observed expression patterns, revealing new insights beyond sequence conservation.

The paper identifies PKR as a critical mediator of mitochondrial neuropathology in a mouse model of Leigh syndrome, showing its role in neuroinflammation and disease progression.

The paper introduces scTPPM, a single-cell multi-omics approach that co-profiles transcriptomes, proteomes, eight PTMs, and metabolomes, revealing dynamic crosstalk during mouse oocyte meiosis.

This paper introduces stochprofIC, an algorithm for noise-corrected state variability inference in single cells, validated using mini-bulk data from mouse brains and human breast cancers.

The paper identifies age-associated differential transcript usage in mouse tissues, showing regulatory isoform switching with tissue-specific structural consequences.

This study examines transcriptional and DNA methylation changes in the hippocampus and prefrontal cortex of irradiated mice, identifying cell-type-specific gene expression and methylation patterns linked to cognitive deficits.

The paper identifies a STAT1-CEBPB-NF-κB signaling pathway in diabetic kidneys that mediates FGF23's pro-inflammatory effects, suggesting CEBPB as a therapeutic target.

The paper identifies plasma B cells as the dominant immune subset in fibrotic hearts of chronic Trypanosoma cruzi-infected mice, revealing their role in sustaining cardiac fibrosis through interactions with fibroblasts.

This study uses single-nucleus long-read RNA sequencing to identify isoform usage shifts in mouse kidneys during acute injury, revealing changes in gene expression and isoform composition.

This study identifies IL13 as a critical cytokine for the antitumor activity of polyfunctional CD4+ T cells modified with constitutively active Stat5, showing its role in enhancing immune responses and tumor control.

The paper compares larval single-cell transcriptomes of sponges and cnidarians to explore the evolutionary origins of neural and sensory cell types.

ProClust assesses the statistical significance of clusters in scRNA-seq data to refine overclustering and distinguish biologically meaningful subpopulations.

The paper uses in vivo single-cell CRISPR screens to study how tumor suppressor loss and genetic perturbations affect glioma states and immune recruitment in mice.

This study identifies age-associated repression of HNF4α as a driver of liver metabolic dysfunction and shows that restoring HNF4α can reverse some age-related liver defects.

This study generates transgene-free iPSCs from the fat-tailed dunnart, demonstrating their pluripotency and potential for use in conservation biotechnology.

This study links cochlear immunity to adjacent bone marrow through anatomical and day-night profiling in mice, revealing synchronized clocks and immune cell dynamics.

The paper compares gene regulatory networks in mouse and pig limb development to reveal conserved and divergent regulatory programs and mechanisms of developmental robustness.

The paper identifies a PTN-rich MSC subtype that enhances cartilage repair in KOA by modulating key inflammatory and repair pathways.

The paper identifies a CHRM1-IL-17 neuroimmune axis that promotes diabetic wound healing through cholinergic modulation and local AChE inhibition.

The paper identifies a dynamic stem cell state marked by Panx3 that responds to environmental cues and enables regeneration in aged and osteoarthritic joints.

This study uses single-cell multi-omics to identify OTP and NOVA1 as key regulators of leptin action in hypothalamic feeding circuits, revealing cell-type-specific transcriptional and regulatory changes.

ORBIS reconstructs 3D tissue geometry from single-cell gene expression without spatial references, achieving lower shape error and faster sampling than existing methods.

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

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.

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.