differential expression

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.

Caudate nucleus aging and its association with brain disorders

This study examines caudate nucleus aging across species and diseases, identifying shared and disorder-specific age-related changes in cell types and regulatory features.

Age-related biological dysregulation quantified using metabolomics is composed of distinct subsystems with synergistic associations to health outcomes: An analysis of the Canadian Longitudinal Study on Aging

The paper quantifies age-related biological dysregulation using metabolomics in older adults and shows it has distinct subsystems linked to health outcomes and DNA methylation.

LabWeaver: reliable agentic data analysis grounded in laboratory knowled

LabWeaver improves agentic data analysis by organizing experimental context around laboratories, enhancing reliability in single-cell RNA-seq analysis of synovial sarcoma.

Quantitative Donor Histology and Transcriptomics Link Pancreatic Composition and Precancers Across the Adult Lifespan

The paper quantifies PanIN burden and pancreatic composition across age to identify high-risk demographics associated with increased precancer burden.

Lesion-Derived Estimated Functional and Structural Connectomes Predict Post-Stroke Recovery Outcomes

The paper develops a pipeline to estimate structural and functional connectomes from lesion masks to predict post-stroke recovery outcomes, showing better performance than traditional methods.

Edi-Set-Flow: detecting differential RNA-editing at scale

Edi-Set-Flow detects differential A-to-I RNA editing in bulk RNA-seq data across tissues and conditions, revealing distinct editing signatures and known protein-recoding events in brain samples.

Organelle Aging Predicts Human Disease

The paper models subcellular aging across 10 organelles using proteomic data from 61,931 individuals and finds that premature organelle aging is associated with increased disease risk and mortality.

ORTHOTOPIC TUMOUR INDUCTION PROTOCOL SHAPES TUMOUR MICROENVIRONMENT

This study shows that varying the number of tumor cells implanted affects the tumor microenvironment, with implications for disease progression and therapeutic response.

ROCK inhibitor Ripasudil reduces Alzheimer pathological proteins and enhances cellular bioenergetics

This study shows ripasudil reduces tau pathology and improves mitochondrial function in AD models.

RyR2-Mediated Ca2+ Leak Drives Progressive Arrhythmogenic Cardiomyopathy

This study shows that RyR2-mediated Ca2+ leak causes arrhythmias and progressive cardiomyopathy in rabbits, identifying RyR2 as a therapeutic target.

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.

Brain mitovesicles undergo stage-specific remodelling during the progression of amyloid-β pathology

This study shows that mitovesicles from Alzheimer's disease mouse models undergo stage-specific proteomic changes that reflect mitochondrial dysfunction and provide a conserved disease signature in humans.

The Reasoning Paradox in Scientific Sandboxes: Why Extended Reasoning Fails in Autonomous Bioinformatics and How to Fix It.

This paper identifies two failure modes in extended reasoning models within bioinformatics tasks and introduces DTDR to improve accuracy and reduce errors.

Phylogeny-Guided Global-Local Shrinkage for Microbiome Feature Selection

This paper introduces PGL, a Bayesian regression method for microbiome feature selection that uses phylogenetic trees to improve detection of exposure-associated ASVs.

Serial dependence carries the action that produced the previous report

This study investigates serial dependence by showing that previous judgments influence subsequent ones through the action used to express them, not just the stimulus or decision.

Polycomb Marked Promoter Methylation Gains in Aging and Cancer are Independent of Replication

This study shows that Polycomb-marked promoter methylation gains in aging and cancer occur independently of replication and are driven by age-related epigenetic drift rather than oncogenic signaling.

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

This study profiles human cartilage across OA grades, revealing changes in fibronectin expression, splicing, and receptor signaling during disease progression.

ssGSEA3.0: Feature-Level Bootstrap Resampling for Robust Assessment of Statistical Significance

ssGSEA3.0 improves statistical significance assessment in ssGSEA by using feature-level bootstrap resampling, enhancing detection power while maintaining calibration across weighting schemes.

KH1 Domain of Poly C Binding Protein 1 (PCBP1) Interacts with Utrophin-A mRNA and Modulates Utrophin-A Expression in Mouse Myoblasts

This paper shows PCBP1 interacts with utrophin-A mRNA, represses its expression by promoting nuclear retention, and identifies the KH1 domain as critical for this interaction in mouse myoblasts.

Loss of stromal VEGFR2 protects against ischemic acute kidney injury by preserving the renal microvasculature

This study shows that loss of stromal VEGFR2 protects against ischemic AKI by preserving the renal microvasculature through enhanced endothelial function and communication.

Pharmacological activation of mitophagy prevents calcific aortic valve disease by targeting dysregulated mitochondrial-to-nuclear communication

This study shows that activating mitophagy with TJ0113 prevents calcific aortic valve disease by restoring mitochondrial-to-nuclear communication disrupted in diseased valves.

Ontogenetic and time-course transcriptomic analyses of maize leaf primordia reveal regulators of transverse vein development

This study identifies regulators of transverse vein development in maize through transcriptomic and anatomical analyses, revealing EREB41 and EREB114 as essential genes.

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.

MaxCAT-Net: Hybrid Transformer-Based Skin Lesion Classification and Lightweight Segmentation with Calibration and Cross-Dataset Validation

MaxCAT-Net improves skin lesion classification and segmentation with hybrid architecture and calibration, showing performance on benchmark datasets but with preliminary results.

Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress

The paper compares gene expression in salt-tolerant and salt-sensitive birch species under salt stress to identify genetic regulators of their response.

EigenBrain maps cortical molecular architecture from functional, geometric, and structural eigenmodes

The paper shows functional MRI eigenmodes can approximate specific receptor and transporter distributions in the cortex, while structural and geometric eigenmodes cannot, and applies this to detect molecular differences in autism and schizophrenia.

Immuno-Proteomic Age of Cardiovascular Etiology (iPACE) Signature Predicts Cardiovascular Risk in Elderly Patients

The paper develops an immune proteomic signature (iPACE) from serum proteins in elderly patients that predicts cardiovascular risk and mortality.

Long-PDE4D degradation attenuates left ventricular cardiomyocyte hypertrophic remodelling

This study shows that targeted degradation of long PDE4D isoforms reduces cardiac hypertrophy without affecting contractile function in rat and human cardiomyocytes.

Human and zebrafish data corroborate gene x gene interactions in ameliorating Duchenne muscular dystrophy disease progression

The paper investigates gene-gene interactions in Duchenne muscular dystrophy using human and zebrafish data, finding interaction effects for six gene pairs and rescue of muscle organization in zebrafish for MAN1A1 and ACTN3.