The recount3 Python package for programmatic access to uniformly processed RNA-seq data biorxiv.org 2026-06-20 The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositori
Vessel Spatial Analysis (VeSpA): a tool for whole slide image segmentation, morphometry, and QuPath extension. biorxiv.org 2026-06-20 Quantifying vascular architecture in histological whole slide images is needed to study tissue organisation, tumour microenvironment biology, and dise
From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference biorxiv.org 2026-06-19 Biobank-scale datasets now routinely include hundreds of thousands to millions of individuals, and as sample sizes grow, close relatives become increa
DNA methylation regulates a key sex differentiation gene in Pogona vitticeps, a dragon lizard with sex reversal biorxiv.org 2026-06-19 During embryonic development bipotential gonads differentiate into either testes or ovaries under the direction of mutually exclusive gene networks.
Whole genome sequencing of endometrial cancer identifies novel subgroups, drivers, and actionable alterations biorxiv.org 2026-06-19 Endometrial cancer (EC) is the most common gynaecological malignancy in high income countries, and is increasing in incidence.
Organisational principles of long non-coding RNAs revealed by exon deletion biorxiv.org 2026-06-19 Long non-coding RNAs (lncRNAs) regulate cell phenotypes in health and disease, yet how function is encoded in their sequence remains poorly understood
Nonlinear influence of reward volatility on arbitration between multiple learning strategies reflects cost-benefit optimization biorxiv.org 2026-06-19 Action selection involves two systems: a model-free reinforcement learning strategy, which relies on experience with action-outcome pairs, and a model
High side chain promiscuity of the terminal enzyme in the homologation pathway for L-phenylalanine and L-tyrosine biorxiv.org 2026-06-19 Natural product (NPs) and their derivatives are a major source of small-molecule drugs, and the building blocks of these NPs are often amino acids.
A Reusable Non-Adhesive Chest-Wall Acoustic Wearable Estimates Respiratory Rate During Rest and Exercise biorxiv.org 2026-06-19 Respiratory rate is a clinically and behaviourally informative signal, yet continuous monitoring outside quiet rest remains difficult.
Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights biorxiv.org 2026-06-19 Urease is a nickel-dependent enzyme that plays an important role in urea hydrolysis and in a process named as microbial-induced calcium carbonate prec
ContinuumCellAgent: A Framework-Guided Agent for Long-Horizon Scientific Research biorxiv.org 2026-06-19 AI-scientist systems are beginning to automate parts of scientific research.
Perturbation Curve models continuous transcriptional response trajectories and improves prediction of genetic modulations biorxiv.org 2026-06-19 Single-cell CRISPR screens, Perturb-seq, have revolutionized functional genomics by revealing biological causality.
FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis biorxiv.org 2026-06-19 Liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics detects thousands of metabolic features, but converting these chemical signals
Geroprotective interventions preserve trabecular bone during ageing in female mice biorxiv.org 2026-06-19 Geroprotectors extend lifespan and improve several aspects of healthspan, yet their effects on skeletal ageing remain poorly understood.
Identification of srh-30 as a 2-nonanone receptor in C. elegans biorxiv.org 2026-06-19 C. elegans detects food, mates, and danger through a large repertoire of chemosensory receptors.
Inhibitory Gain and Hub Architecture Confer Dynamic Resilience to Microcircuit Degeneration biorxiv.org 2026-06-19 Neurodegeneration progressively removes synapses and neurons, yet neural circuits can retain stable collective dynamics despite substantial structural
Killer-cell dominance dichotomy governs tumor immune networks and stratifies inflamed cancers biorxiv.org 2026-06-19 Cancer immunotherapy benefits remain limited, even among hot tumors with high killer lymphocyte infiltration.
A gavage-fomite based method to generate mouse models with natural microbiota biorxiv.org 2026-06-19 Laboratory-raised specific pathogen-free (SPF) mice have been indispensable for fundamental immunology research, yet their reliability in predicting h
Polymorphonuclear neutrophils modulate the responses of human immune cells to vaccines in an in vitro blood cell culture system biorxiv.org 2026-06-19 Vaccine-induced immune responses are the result of an intricate interplay between different cell populations of the innate and adaptive immune system,
Cross-species chromatin accessibility pinpoints HIVEP3 as a driver of thymic epithelial maturation and self-antigen expression, preventing chronic inflammation biorxiv.org 2026-06-19 Promiscuous expression of tissue-specific antigens (TSAs) by medullary thymic epithelial cells (mTECs) underpins central T-cell tolerance, relying on
RNAquarium: an archive-scale atlas of zebrafish gene expression coupled with pan-taxonomic profiling reveals diverse viral drivers of transcriptomic states biorxiv.org 2026-06-19 Zebrafish RNA-seq studies span diverse developmental, physiological, and disease contexts, yet most analyses remain confined to individual experiments
The road to nowhere: geolocation-by-genotype traces large-scale yellow-browed warbler vagrancy to central Siberia biorxiv.org 2026-06-19 Vagrant animals - individuals found far outside their normal range - offer powerful natural experiments for understanding migratory mechanisms.
Children's DNA Methylation and Family Dynamics in a Congo Basin Subsistence Community: Links with Parental Conflict and Fathers' Caregiving biorxiv.org 2026-06-19 Family environments may contribute to children's long-term health through biological processes, including epigenetic regulation such as DNA methylatio
Diagnosing Neurodegenerative Diseases by Label-Free 3-D Imaging of Intestinal Samples biorxiv.org 2026-06-19 Early diagnosis of Parkinson's disease (PD) remains challenging because motor symptoms appear only after extensive neurodegeneration, and a definitive
Differentiating Hepatic and Renal Toxicity Reveals CYP-Independent Mechanisms of Acetaminophen-Induced Acute Kidney Injury biorxiv.org 2026-06-19 Acetaminophen (APAP) overdose is the leading cause of acute liver failure (ALF), with acute kidney injury (AKI) contributing substantially to morbidit
BAYESIAN STATE-SPACE MODEL FOR JOINT INFERENCE OF OSCILLATORY DYNAMICS AND POINT-PROCESS COUPLING biorxiv.org 2026-06-19 Under a range of behavioral and physiological conditions, spike times and local field potential (LFP) oscillations exhibit phase coupling within speci
HTS-Oracle v2: Prospective AI-Guided Discovery and Experimental Validation of Small Molecule Modulators Across Multiple Targets biorxiv.org 2026-06-19 High-throughput screening (HTS) remains the cornerstone of early-phase small molecule discovery yet consistently underperforms against immunotherapy t
Accurate detection of tumor clonality and ongoing expansion mode from genomic data biorxiv.org 2026-06-19 Recent evidence shows that despite considerable effort, currently available algorithms for estimating intra-tumor heterogeneity (ITH) remain limited.
Emergent Tissue Rheology in a 3D Mechanically Adaptive Viscoelastic Cell Network Model biorxiv.org 2026-06-19 We introduce a 3D mechanically adaptive viscoelastic cell-network model that links single-cell interactions to emergent tissue rheology.
Mouse dehydration as a consequence of water bottle design biorxiv.org 2026-06-19 Animal care technicians reported that accidental deaths of mice occur more frequently under certain weather conditions.