differential expression

A candidate HNRNPU-CHD2 RNA-processing axis in neurodevelopmental disease

The paper identifies a HNRNPU-CHD2 RNA-processing axis linked to neurodevelopmental disease by showing HNRNPU depletion causes splicing changes in CHD2 that may lead to nonsense-mediated decay.

Shared and divergent features of the immune response to acute and chronic Trypanosoma cruzi infection in mice revealed by cardiac transcriptomics

This study uses cardiac transcriptomics in mice to compare immune responses during acute and chronic Trypanosoma cruzi infection, identifying shared and divergent features.

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

The paper shows PROM1 activation in liver cancer cells shifts their state along a preexisting differentiation axis, suggesting CD133's role extends beyond being a stem-like marker.

A Reproducible Pre-Transplant γδ T-cell Effector Signature Reveals Immune-Metabolic Programs Associated with Kidney Allograft Rejection

The paper identifies a pre-transplant γδ T-cell effector signature associated with kidney allograft rejection using multi-omics data from transplant recipients.

Species-specific WNT requirements shape somite morphogenesis in mammalian embryo models

This study compares somitogenesis across human, pig, sheep, and cow stem cell-derived embryo models, revealing species-specific WNT signaling and extracellular matrix requirements for axial segmentation.

LplA-mediated rescue of lethal myopathy and cardiomyopathy in mitochondrial lipoylation-deficient mammalian caused by Lipt1

This study uses AAV-delivered LplA to rescue lethal mitochondrial lipoylation defects in Lipt1-deficient mice, improving survival, motor function, and cardiac health.

Latent Transforming Growth Factor Binding Protein-2 promotes microfibrillar TGF-β bioavailability to drive pathologic fibrosis in remote regions of infarcted hearts

This study shows that LTBP2 promotes fibrosis in remote myocardium after MI by sequestering latent TGF-β, and its deletion reduces fibrosis and improves cardiac function.

Gentamicin impairs nephron development in iPSC-derived kidney organoids and disrupts proximal tubular lysosomal function

Herboxidiene and EGFR expression in A172 glioblastoma cells

This study investigates how herboxidiene affects EGFR expression and proliferation in A172 glioblastoma cells, finding that it inhibits growth without causing intron 2 retention seen in lung adenocarcinoma cells.

Sodium arsenite requires redox sensitization to cause developmental dopaminergic neurotoxicity in Caenorhabditis elegans

This study shows that sodium arsenite requires additional mitochondrial or redox stress to cause dopaminergic neurotoxicity in C. elegans, but not fluoroacetic acid.

NPlasmid-seq: Cas9-encoded terminal signatures enable molecule-level nanopore quality control of vector and IVT-template plasmids

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

NTAD: A longitudinal neuroimaging dataset of Alzheimer's disease pathology

The paper introduces a longitudinal neuroimaging dataset of Alzheimer's disease pathology, including multimodal data from patients and controls, to identify and validate novel biomarkers.

GMP-Cor: Quantifying Transcriptional Dysregulation in Antibiotic Tolerance and Persistence

This study quantifies transcriptional dysregulation in antibiotic tolerance using single-cell RNA-seq and introduces GMP-Cor to analyze gene-gene correlations in disrupted growth-arrest states.

RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

Knockdown of fibrillarin reveals cell- and virus- dependent restriction of henipavirus replication and enhanced antiviral immune signalling

This study shows that fibrillarin depletion affects henipavirus replication differently across cell types and viruses, and enhances antiviral immune signaling.

Donor Aware Reanalysis of Neuronal Nuclei Supports STMN2 Depletion Associated with Nuclear TDP 43 loss in FTD and ALS

The paper reanalyzes RNA-seq data from neuronal nuclei to identify gene expression changes associated with nuclear TDP-43 loss in FTD and ALS, finding STMN2 depletion and other transcriptomic variations.

Characterizing nascent readthrough transcripts in human cells

The paper identifies widespread readthrough transcription in human cells and shows that depletion of specific factors increases its extent.

Whole methylome changes in Barrett's metaplasia, dysplasia, and cancer

The paper identifies methylation changes associated with dysplasia and cancer progression in Barrett's esophagus using whole-genome methylation profiles.

Quantum Dot-Based Non-invasive Monitoring of Sinusoidal Endothelial Scavenger Function in Steatohepatitis

This study develops a non-invasive method using quantum dots to assess liver sinusoidal endothelial cell scavenger function in MASH, showing reduced retention correlates with disease progression.

An RNA-centric atlas of human cell cycle regulation

The paper defines an RNA-centric landscape of human cell cycle control by profiling various RNA features and identifies key RNA elements involved in cell cycle regulation.

Development and cross-cohort evaluation of a multimodal deep-learning model for ER, PR and HER2 status classification in breast cancer

This paper develops a multimodal deep-learning model for breast cancer biomarker classification and evaluates its performance across cohorts, finding high discrimination but limited incremental value over a simpler transcript-based model.

irAEGIS: Pathway-guided interpretable prediction of immune-related adverse events

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.

The mouse Cdh23ahl allele drives early cochlear dysfunction and phenotypic heterogeneity before progressive hearing loss

This study shows the Cdh23ahl allele causes early cochlear dysfunction and phenotypic variability in mice before progressive hearing loss, with altered mechanoelectrical transduction and transcriptional changes.

Circadian feeding rhythm loss drives sex-specific β-cell dysfunction in diet-induced obesity

This study shows that diet-induced obesity disrupts circadian β-cell function more in male mice than females, with time-restricted feeding partially restoring these effects.

Embodied Dynamic Causal Modelling: Brain and Cardiac Effective Connectivity

This paper introduces Embodied Dynamic Causal Modelling to estimate effective connectivity across the brain-heart axis using multimodal data from an auditory Go/No-Go task.

Cigarette smoke extract and palmitic acid exposed patient-derived iPS- RPE cells as a model for AMD

This study examines how cigarette smoke extract and palmitic acid affect patient-derived iPSC-RPE cells, showing increased susceptibility in AMD-derived cells with altered stress responses and function.

Anorectal care products cause variable inflammation and adverse barrier effects in a mucosal epithelial model

This study evaluates the effects of anorectal care products on mucosal epithelial models, finding that hyperosmolar and surfactant-containing products cause inflammation and barrier disruption, while isotonic formulations are less harmful.

Short-term changes in a chicken comb vascular model mimicking port-wine stain after synchronous ultrasound parallel beam treatment: an exploratory study

This study examines the short-term effects of SUPERB ultrasound treatment on a chicken comb model, finding reduced vascular caliber and VEGF-A expression but no consistent collagen changes.

VIGAT: VLM-guided gene activity quantification from single-cell ATAC-seq

VIGAT uses a vision-language model to quantify gene activity from single-cell ATAC-seq by analyzing accessibility patterns and genomic annotations across marker genes.

Paraquat Inhalation Produces Male-Biased Dopaminergic Neuron Loss and Motor Deficits in Mice: Relevance to Parkinsons Disease

This study shows that prolonged low-dose inhalation of paraquat in mice causes male-specific dopaminergic neuron loss and motor deficits, linking it to Parkinson's disease.