cell-cell communication

Age-associated repression of HNF4α is a driver and potential therapeutic target in liver metabolic dysfunction

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.

PRISM: probabilistic cell-type resolution with integrated spatial modelling for simultaneous ambient RNA decontamination and doublet correction in spatial transcriptomics

PRISM simultaneously decontaminates ambient RNA and corrects doublets in spatial transcriptomics data, achieving high accuracy and purity in a mouse cerebellum dataset.

Therapeutic anti-IgE antibodies generate distinct functional immune complex signatures

This study shows that therapeutic anti-IgE antibodies form immune complexes with distinct functional properties, influenced by allergen incorporation and receptor binding patterns.

SPARK: Systematic Profiling of Antibiotic-Phage Response Kinetics

SPARK quantifies phage-antibiotic interactions using growth curves and shows synergy, antagonism, and dynamic changes across bacterial isolates and time.

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

Cholinergic modulation engages a CHRM1-IL-17 neuroimmune axis to promote diabetic wound repair

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

Epidermal Langerhans Cells Act as Neuroimmune Regulators of Pain and Itch

This study identifies Langerhans cells as immune-derived amplifiers of cutaneous sensory signaling and identifies semaphorin 7A as a mediator of LC-induced itch potentiation.

Mutant Isocitrate Dehydrogenase 1 Alters Extracellular Vesicle Secretion and Cargo Composition in Cellular Models

This study shows mutant IDH1 increases sEV secretion and alters their cargo composition in glioma and chondrosarcoma cells, with D2HG packaged into sEVs and cell-type-specific cargo remodeling.

CD300f is required for efficient lipid handling during cuprizone-induced demyelination

This study shows CD300f is essential for microglial lipid handling and remyelination during demyelination, with deficits in lipid metabolism and motor coordination in its absence.

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

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.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

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.

MitoDecode: quantitative phenotypic decoding of mitochondrial stress states from fluorescence images

MitoDecode assesses mitochondrial stress types and severity from fluorescence images without segmentation, showing adaptability across cell types and stress conditions.

Systematic comparison of gliflozins identifies a selective anti-calcifying effect of canagliflozin beyond canonical SGLT2 inhibition

This study compares gliflozins and finds canagliflozin uniquely reduces vascular calcification through mechanisms beyond SGLT2 inhibition, affecting VSMC metabolism and calcification.

Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile

The paper identifies subgroup-specific isoform usage and switching in SLE patients with distinct autoantibody profiles, highlighting their functional relevance in autoimmune pathogenesis.

Virtual dynamics of spatiotemporal single-cell interactions

CytoBridge reconstructs continuous virtual cell dynamics from sparse spatial transcriptomic data across development, regeneration, and neurodegeneration.

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

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.

Persistent hippocampal traces of lifelong spatial memory

The paper shows that mice retain spatial memory in the hippocampus after long absences, with neural patterns persisting despite changes in individual neuron activity.

Temporal Structure in Resting-State fMRI under Marginal and Cross-Spectral Surrogate Controls

The paper evaluates temporal complexity measures in resting-state fMRI to identify disease-related changes, finding that real data show greater outliers than randomized controls.

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.

Deducing splicing events from transcript sets with splicelogic

splicelogic converts transcript-set comparisons into interpretable splicing events, enabling downstream analysis of isoform changes in RNA-seq data.

Automahout: an autonomous image analysis system for cell tracking

Automahout autonomously tracks cells in time-lapse images using a self-tuning system that annotates, trains, and refines models without human input, achieving high TRA scores on public datasets.

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.

RadMultiBench: A Reproducible Dual-Task Benchmark Exposing the Limits of Pre-Trained Vision-Language Models Across Thoracic and Breast Imaging

RadMultiBench evaluates pre-trained vision-language models on medical imaging tasks, showing performance gaps in report generation and classification across thoracic and breast imaging.

40 Hz visual stimulation increases gamma-band functional connectivity between visual, parietal and frontal regions

This study shows that 40 Hz visual stimulation increases gamma-band functional connectivity between visual, parietal, and frontal regions, with the visual-parietal connection being most significant.

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

Simple, static, spiking nonlinearities can account for seemingly complex interactions between visual, motor and cognitive variables in the visual cortex.

The paper shows that simple nonlinearities in the visual cortex can explain complex interactions between visual, motor, and cognitive variables through additive input modulation.

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.

XRN1 couples RNA granule remodelling to global mRNA decay triggered by the activity of a viral endoribonuclease

The paper investigates how XRN1 links RNA granule remodeling to global mRNA decay triggered by the viral endoribonuclease vhs, revealing a sequential model of translational arrest and degradation.