cell-cell communication

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

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

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.

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

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

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.

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

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

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

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

This study shows that platelet-derived signals cause distinct endothelial dysfunction in bicuspid aortic valve disease, leading to mitochondrial dysfunction and immune cell recruitment.

irAEGIS predicts immune-related adverse events from pre-treatment scRNA-seq data using a pathway-guided interpretable model, outperforming existing methods and identifying biologically relevant immune programs.

This paper develops an injectable, bioresorbable device for localized mRNA delivery to the heart after myocardial infarction, showing improved cardiac function and reduced remodeling in mice.

NEPTUNE identifies neuronal cell death markers from single-cell RNA-seq data, revealing non-apoptotic mechanisms in photoreceptor degeneration in rd1 mice.

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

The paper examines proximal podomere patterning in sea spiders and arachnids, finding homoplastic evolution of gene expression patterns that challenges assumptions about leg segment homology.

This study identifies regulatory interactions between sRNAs and transcription factors in S. aureus, showing their roles in stress responses and virulence.

The paper benchmarks Quantum Barcoding against mass cytometry in human and rhesus macaque blood, integrating data to reveal conserved and divergent signaling responses across species.

The paper shows that genomic context influences RNA processing by demonstrating that introns retain splicing across ectopic positions, while cryptic polyadenylation sites are less frequently used outside their native context.

This paper identifies the human-specific gene FRMPD2B as an activity- and experience-regulated modifier of cortical connectivity, showing its role in postnatal brain development.

The paper uses graph neural networks to interpret microbial association patterns in IBD, showing that coordinated associations, not just abundance shifts, are predictive.

This study edits mtDNA variants in human iPSCs to show that heteroplasmic complex I variants impair neuronal commitment.

This study identifies c-MYC as a non-canonical origin licensing accelerator, showing it increases licensing speed through TRRAP/GCN5 and histone H1 eviction, particularly in heterochromatin.

This study shows dsRNA-induced PTI in plants restricts virus movement and replication, with a JA signaling-dependent branch involving COI1 and callose deposition.

This study identifies Vago4 as a ligand that downregulates Domeless to restrain JAK/STAT signaling in invertebrates, defining an IFN-like axis.

This study identifies Pro3 as a key enzyme linking proline biosynthesis to cell wall integrity in Cryptococcus neoformans, showing its critical role in virulence and growth.

This study identifies Tie1, a fungal effector that targets OsTLP7 to suppress plant immunity by altering its localization and transcriptional activity.

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.