An Itch Receptor Drives Melanoma biorxiv.org 2026-06-07 Mas-Related GPCR X4 (MRGPRX4) is a sensory neuron-restricted receptor for cholestatic itch.
Mechanistic pathway modeling reveals how IL-10 generates pleiotropic immune responses biorxiv.org 2026-06-07 IL-10 is a key anti-inflammatory cytokine whose activity is impaired in autoimmune diseases.
Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions biorxiv.org 2026-06-07 Lacticaseibacillus rhamnosus GG (LGG) is an important gut commensal bacterial strain that has been extensively studied in both industrial and health s
Megalin (LRP2), prenatal betamethasone, and injury susceptibility in the developing kidney biorxiv.org 2026-06-07 Preterm infants undergo postnatal nephrogenesis and are often exposed to gentamicin (gent).
Fusion peptides of enveloped viruses actively mediate membrane fusion in model cell membranes biorxiv.org 2026-06-07 Enveloped viruses can enter host cells by fusing their membrane with that of the host cell, a process known as membrane fusion.
Soil microbial diversity alters soil microhydrology through extracellular polymeric substance production biorxiv.org 2026-06-07 Soil microbial communities have a variety of mechanisms to deal with emerging drought stress.
Bat-mediated pest regulation in understudied pasture agroecosystems biorxiv.org 2026-06-07 Pastureland provides critical resources for livestock production.
High nitrogen deposition is associated with phosphorus-efficient ectomycorrhizas in Europe's Scots pine forests biorxiv.org 2026-06-07 Atmospheric inorganic nitrogen (N) deposition has been linked to increased tree phosphorus (P) deficiency and shifts in ectomycorrhizal (ECM) fungal c
Still Lost in Definitions: How Resilience Is Used in Ecology biorxiv.org 2026-06-07 Resilience is a central concept in ecology and environmental policy, yet its meaning and quantification remain inconsistent across subfields.
Chemical Mixtures in River Basins: Combining Additive and Independent Effects with Probabilistic Risk Modelling biorxiv.org 2026-06-07 Chemical mixtures and potential cocktail effects in aquatic ecosystems are recognised as a threat for river basins world-wide.
Small patches dominate the Natura 2000 network of protected areas in Europe biorxiv.org 2026-06-07 The Natura 2000 network for protected areas is one of Europe's main tool to address the loss of Biodiversity.
BacteReason: A Reasoning Model for Antimicrobial Resistance Prediction biorxiv.org 2026-06-07 The rapid global spread of antimicrobial resistance (AMR) has placed unprecedented pressure on clinical decision-making.
CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer biorxiv.org 2026-06-07 A substantial fraction of disease-associated genetic variants reside in non-coding regions of the genome, where they act by perturbing cis-regulatory
Fasting Status and Epigenetic Clock Stability: Implications for Aging Research biorxiv.org 2026-06-07 Background: Epigenetic clocks are DNA methylation-based biomarkers increasingly used in aging research and clinical trials.
Synaptic Plasticity as a Function of the Temporal Derivative biorxiv.org 2026-06-07 A major outstanding question in neuroscience is whether the neocortex uses the same powerful learning algorithm as current AI models: error backpropag
Compartment-Specific Assembly and Functional Potential of the Bacteriome of Citrullus colocynthis in a Semi-Arid Ecosystem biorxiv.org 2026-06-07 Plants inhabitng in arid and semi-arid ecosystems, such as Citrullus colocynthis (L.) Schrad., are adapted to drought, heat, salinity, and nutrient li
A Web-based software toolkit for accessible and best-practice machine learning analyses in biomedical research biorxiv.org 2026-06-07 Machine learning is increasingly central to biomedical research, but using machine learning well often requires substantial computational expertise an
Multimodal physical evidence uncovers interpretable gene regulatory networks for perturbation prediction biorxiv.org 2026-06-07 Gene regulatory networks govern cell fate transitions through dynamic causal mechanisms.
Anthocyanin-associated cellular programs underlying terroir variation in Cabernet Sauvignon grape berry revealed by SEED-based deconvolution biorxiv.org 2026-06-07 Plant tissues consist of diverse cell populations that collectively contribute to development, metabolism, environmental responses, and phenotype form
VelocityFM: Short-Horizon Protein Trajectory Prediction via Flow Matching in Velocity Space biorxiv.org 2026-06-07 Protein dynamics is fundamentally a trajectory prediction problem, but molecular dynamics (MD) simulation remains expensive and static structure predi
Polynomial Trajectory Compression for Protein Language Model Embeddings biorxiv.org 2026-06-07 Protein language models (PLMs) generate rich, layer-wise embeddings that capture diverse biological information but are expensive in terms of storage
Metadata Collector: An Open-Source Platform for Standardized Metadata Management in Multi Centre Sequencing Projects biorxiv.org 2026-06-07 Background: Next-generation sequencing (NGS) projects generate increasingly complex metadata that are critical for reproducibility, interoperability,
CytoGem-XAI:A Hypergraph Neural Network Framework for Genome-Scale Metabolic Modeling and Interpretable Analysis biorxiv.org 2026-06-07 Genome-scale metabolic models are essential for understanding cellular metabolism, yet existing deep learning approaches remain black boxes, and tradi
Single-cell gene regulatory network reconstruction and key regulator identification using a dual-channel fusion graph convolutional network biorxiv.org 2026-06-07 Background and objective: Gene regulatory networks are formed by complex regulatory relationships between transcription factors and their target genes
CiliAI: Automated segmentation and compartment specific fluorescence quantification of primary cilia in confocal microscopy images biorxiv.org 2026-06-07 Primary cilia regulate essential signalling pathways controlling cell proliferation, differentiation, and tissue homeostasis.
Germline regulation of tumor evolutionary dynamics shapes multiple myeloma progression biorxiv.org 2026-06-07 Germline variation shapes cancer risk, yet its influence on the evolutionary dynamics of established tumors remains poorly understood.
Multi-level, multi-body atomic interaction graphs for machine learning-based prediction of protein-ligand binding energies biorxiv.org 2026-06-07 Accurate prediction of binding affinity is crucial for rational drug design and discovery.
GLOF: A large-scale expert-curated benchmark dataset of gain-of-function and loss-of-function missense variants biorxiv.org 2026-06-07 Distinguishing loss-of-function (LOF) from gain-of-function (GOF) effects of missense variants is fundamental to understanding disease mechanisms and
Quantifying Evidence for Competing Biomedical Hypotheses using Large Language Models and Bayesian Analysis biorxiv.org 2026-06-07 Science fundamentally depends on the generation and testing of hypotheses, many of them controversial.
KDM: embedding DNA/RNA motifs and sequences in a shared k-mer space for unified discovery, analysis and binding prediction biorxiv.org 2026-06-07 Motif discovery and binding-site prediction in DNA and RNA sequences are central tasks in regulatory genomics, yet the methodological landscape is spl
Minimally invasive measurement of maternal transcripts enables predicting the developmental potential of mammalian zygotes biorxiv.org 2026-06-06 Maternal transcripts are stored in the oocyte cytoplasm during oogenesis and play a pivotal role in early embryonic development after fertilization.
Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling biorxiv.org 2026-06-06 BACKGROUND: Atherosclerotic cardiovascular disease remains the leading cause of death worldwide.
Expert-Guided Supervised Annotation of Erythroid Differentiation in Single-Cell RNA-seq biorxiv.org 2026-06-06 Accurate annotation of intermediate cell states remains a major challenge in single-cell RNA sequencing (scRNA-seq), particularly in continuous differ
Divergent Loop Architecture Shapes Pocket2 Variation in Shark Legumains biorxiv.org 2026-06-06 Legumain (AEP) is a cysteine protease with a highly conserved catalytic core but variable surface features whose evolutionary and structural diversity
CryoDiff: An uncertainty-aware diffusion model for Cryo-EM map enhancement biorxiv.org 2026-06-06 Cryogenic electron microscopy (cryo-EM) enables high-resolution structural determination of large macromolecular complexes.
TDKC (Target Distilled K-mer Classifier): Ultrafast and Memory-Efficient Sequence Classification for Target Pathogen Diagnostics biorxiv.org 2026-06-06 Metagenomic sequencing can identify pathogens from clinical samples without prior knowledge of the causative agent.
Finetuning masking challenges narrow-task evaluation of cell foundation models biorxiv.org 2026-06-06 Single-cell foundation models are large, self-supervised deep learning networks pretrained on millions of cellular transcriptomes.
scMTG reconstructs single-cell temporal dynamics with Markov transition generators biorxiv.org 2026-06-06 Single-cell time-series data offer a unique opportunity to study how cell states emerge, evolve, and diversify over time.
Enformer-Based Phylogenetic Tree Reconstruction biorxiv.org 2026-06-06 Enformer is a deep learning model trained on human and mouse genomes to predict regulatory activity from 196,608 bp DNA windows.
VelOT: kinetic-free RNA velocity inference via optimal transport, flow-field smoothing, and VAMP coarse-graining of cellular dynamics biorxiv.org 2026-06-06 Inferring cellular dynamics from snapshot single-cell RNA sequencing remains difficult when spliced and unspliced counts are sparse or unreliable.
Automated Retinal Dysplasia Segmentation in Mouse Optical Coherence Tomography Scans Using a UNet-Based model biorxiv.org 2026-06-06 Optical coherence tomography (OCT) is the state-of-the-art non-invasive imaging technique for preclinical retinopathy studies.
Handshake: Partner-Specific Protein-Protein Binding Site Prediction at Scale Using ProstT5 and Cross-Chain Attention biorxiv.org 2026-06-06 Partner-specific protein-protein binding site prediction, identifying which residues of a protein form the interface when bound to a specific partner,
pLM-Guided Inverse Folding for Antibody Sequence Design biorxiv.org 2026-06-06 Inverse folding, predicting amino acid sequences from three-dimensional structures, is a foundational task in computational protein design, yet it is
Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression biorxiv.org 2026-06-06 Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome.
Discovery and characterization of a pigment produced by Streptococcus pyogenes biorxiv.org 2026-06-06 Streptococcus pyogenes is a major human-restricted pathogen capable of both localized and systemic diseases, as well as causing post-infectious acute
Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM biorxiv.org 2026-06-06 Deep learning neural networks provide a powerful approach for segmenting low-contrast cryogenic electron microscopy (cryoEM) images.
CascadeMAP: Autonomous Closed-loop Optimization of Enzyme Cascades via Microfluidics, Machine Learning and Agentic AI biorxiv.org 2026-06-07 Enzyme cascades enable complex biochemical transformations, but their optimization is resource-intensive, requiring navigation through high-dimensiona
Structural insights into the inhibition of sickle hemoglobin polymerization by asymmetric hemoglobin tetramer HbFS (α2γβS) biorxiv.org 2026-06-07 Sickle cell disease (SCD) is caused by a single amino acid substitution in the {beta}S globin chain at 6th position (6E[->]V).
Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1 biorxiv.org 2026-06-07 Compound ranking in structure-based virtual screening notoriously yields highly ranked false positive binders due to variable poses or biases in scori
Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning biorxiv.org 2026-06-07 High-throughput chromatin accessibility assays such as bulk and single-cell ATAC-seq have generated large collections of processed signal tracks in bi