CLASPP: A unified model for predicting post-translational modifications biorxiv.org 2026-06-07 Post-Translational Modifications (PTMs) are a fundamental mechanism for regulating cellular pathways and increasing the functional diversity of the pr
Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis biorxiv.org 2026-06-06 We present Ontologizer 3, an easy-to-use cross-platform desktop application for Gene Ontology (GO) overrepresentation analysis.
Using protein language models for pangenome construction biorxiv.org 2026-06-06 Current pangenome construction methods rely largely on nucleotide or protein sequence alignment, limiting their ability to detect remote orthologs and
Neural synchrony between prefrontal and visual cortex supports visual working memory biorxiv.org 2026-06-07 Working memory appears to depend on neural mechanisms that are distributed across the brain.
Neurophysiological Functional Connectivity Changes during Difficult Listening in Older and Younger Adults biorxiv.org 2026-06-07 Older adults often report increased difficulty understanding speech in noisy listening environments.
Cortical folding patterns are encoded in the geometry of the unfolded neocortex. biorxiv.org 2026-06-07 Cortical folding patterns are conserved across individuals of gyrencephalic species and are closely related to cytoarchitectural organisation, connect
Thalamic Nuclei Differentially Coordinate Propagation of Cortical Slow Oscillations biorxiv.org 2026-06-07 Sleep slow oscillations (SOs) vary in the spatial extent of their cortical propagation, ranging from widespread Global events to spatially restricted
Hippocampal CA2 modulates trace fear conditioning through circuit-specific control of CA1 biorxiv.org 2026-06-07 Forming associations between temporally separated events depends on pathways linking the CA1, the subiculum (SUB), and the entorhinal cortex.
Connectional neuroanatomy of U-fibers in the rhesus monkey brain biorxiv.org 2026-06-07 The superficial white matter (SWM), the region of white matter immediately beneath the gray matter-white matter (GM-WM) border, contains short cortico
Repurposing drugs to treat Amoebic Gill Disease in Atlantic Salmon biorxiv.org 2026-06-07 Neoparameoba perurans causes Amoebic Gill Disease (AGD), a major parasitic disease of marine-phase Atlantic salmon and rainbow trout worldwide.
The Sorghum Lipid Database (SoLD): population-scale lipidomics linking environmental and genetic variation in the Sorghum Association Panel biorxiv.org 2026-06-06 Sorghum (Sorghum bicolor ) is a climate-resilient crop whose acclimation to nutrient limitation and low temperature likely involves extensive lipidome
HOPE: Interpretable Histology Analysis with Spatial Omics-Derived Signatures for Precision Oncology biorxiv.org 2026-06-06 Hematoxylin and eosin (H&E) stained images are fundamental clinical tools for disease assessment.
Temporal Biodynamics: An AI Platform for Identification of Stage-Relevant Targets and Biomarkers biorxiv.org 2026-06-06 Temporal modeling of disease progression is poised to revolutionize the process of target identification, leading to better characterization of and in
EnzOracle: Mechanism-aware prediction of enzyme environmental adaptation via a classification-guided mixture-of-experts framework biorxiv.org 2026-06-06 Industrial biocatalysis increasingly requires enzymes capable of operating under extreme physicochemical conditions, yet most natural sequence data re
STITCH: Spatial Transcriptomics Imputation via Flow Matching with Internal Learning biorxiv.org 2026-06-06 Spatial transcriptomics datasets frequently suffer from spatial gaps and missing regions due to sectioning artifacts, tissue damage, and the high cost
PAG-Agent: a biologist-oriented research assistant for context-aware pathway-level analysis and interpretation biorxiv.org 2026-06-06 Pathway analysis is a critical step for translating gene-level omics results into biological mechanisms, yet existing workflows often leave researcher
Correcting for Global Synonymous Selection Improves the Accuracy of Episodic Positive Selection Inference biorxiv.org 2026-06-06 The ratio of nonsynonymous to synonymous substitution rates ({omega}) constitutes a fundamental parameter for inferring adaptive protein evolution, pr
Ignet 2.0 and Vignet: An Ontology-Driven Web Platform for Biomedical Gene Interaction Discovery and Visualization biorxiv.org 2026-06-06 Background: The expansion of biomedical literature demands systematic ontology-guided discovery of gene interactions, vaccine mechanisms, drug associa
Nonlinear rheology of laminin-111-modified hyaluronan hydrogels biorxiv.org 2026-06-06 We experimentally assess the nonlinear rheology of composite biopolymer hydrogels composed of thiolated hyaluronic acid, poly(ethylene glycol) diacryl
The hypertrophic cardiomyopathy mutation G768R makes cardiac myosin a high duty ratio motor biorxiv.org 2026-06-06 {beta}-cardiac myosin is the primary motor protein in the human heart responsible for force generation by converting chemical energy from ATP hydrolys
Broadband amplification of organ of Corti vibrations in the mouse cochlear apex biorxiv.org 2026-06-06 Mammalian hearing depends on the active amplification of sound-evoked waves as they travel along the basilar membrane within the cochlea.
Beta-Adrenergic Stimulation and MYH7 G256E Mutant Gene Dosage Drive Hypertrophic Cardiomyopathy Phenotype Penetrance biorxiv.org 2026-06-06 Aims Hypertrophic cardiomyopathy (HCM) is the most prevalent genetic heart disorder, characterized by significant phenotypic variability even among in
Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Reduced Neuroaxonal Integrity biorxiv.org 2026-06-06 Despite sustained viral suppression with effective antiretroviral therapy (ART), neuroaxonal integrity persist in a subset of people with HIV-1 (PWH).
Demographic history, geographic distance, and landscape features shape the genetic divergence of wild tigers in northeast India biorxiv.org 2026-06-06 Habitat fragmentation creates small, isolated populations that are vulnerable to inbreeding, genetic drift, and a high genetic load.
Mapping Chemical Diversity: Descriptor-Guided Clustering of Natural Products in the COCONUT Database biorxiv.org 2026-06-06 Natural products represent a major source of bioactive compounds for drug discovery, yet their exploration remains challenging due to extensive struct
Multivariate integration of histological images and gene expression data: a comparative review biorxiv.org 2026-06-06 Integrating histological images with gene expression data offers a promising approach for linking tissue morphologies to molecular signatures and impr
An inflammatory gene set driven epigenetic clock tracks down disease progression and rejuvenation biorxiv.org 2026-06-06 Chronic, low-level inflammation, characterized by elevated pro-inflammatory programs, including epigenetic changes, in the absence of infection, is a
samsampleX: Distribution-aware downsampling for benchmarking next-generation sequencing data biorxiv.org 2026-06-06 High-throughput next-generation sequencing (NGS) is essential for genetic variant discovery across diverse applications.
Comparative Proteomics Across Tissues and Crop Agroecosystems Reveals Agricultural Stressor Responses in the Western Honey Bee biorxiv.org 2026-06-06 Maintaining honey bee health in crop production systems is increasingly difficult because worker bees encounter multiple chemical and biological press
Revised Adaptive Immune Receptor Data in the Immune Epitope Database biorxiv.org 2026-06-06 The Immune Epitope Database (IEDB, iedb.org) is a freely available resource that catalogs experimentally defined immune epitopes and - if available -
TetraFuse: A Synergistic Four-Dimensional Dynamic Fusion Framework for Efficient and Robust Medical Image Classification biorxiv.org 2026-06-06 Accurate and robust classification of medical pathology images is pivotal for computer-aided diagnosis.
Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders biorxiv.org 2026-06-06 Light microscopy of tissue sections stained with hematoxylin and eosin (H&E) has been the foundation of histopathology for over 150 years and rema
Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling biorxiv.org 2026-06-06 Background.
Cell type-centric interaction networks define spatial architecture of intrahepatic cholangiocarcinoma biorxiv.org 2026-06-06 Tumor spatial organization critically shapes disease progression and therapeutic response, yet remains poorly defined.
Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025 biorxiv.org 2026-06-05 Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade.
Predicting Gravitational Self-Motion: Falling Down versus Falling Up biorxiv.org 2026-06-05 Humans have been shown to use an internalized representation or prior of Earth gravity to predict object motion.
Single-Cell Multi-Omics Dissection of Malignant Evolutionary Mechanisms and Construction of a Prognostic Model for Clear Cell Renal Cell Carcinoma biorxiv.org 2026-06-06 Clear cell renal cell carcinoma (ccRCC) exhibits pronounced heterogeneity across WHO histological grades, yet systematic single-cell multi-omics studi
Robust Multi-Mutant Protein Stability Prediction from a Fine-Tuned Evolutionary Scale Model biorxiv.org 2026-06-05 Recently, high-throughput experimental techniques have propelled improvements in deep learning-based prediction of mutation effects on protein stabili
A Crossed Laser Phase Plate for CryoEM biorxiv.org 2026-06-05 The laser phase plate (LPP) enables phase-contrast imaging in cryogenic electron microscopy (cryoEM), enhancing image contrast without compromising hi
Encoding neuronal shape in the stochastic dynamics of branching processes biorxiv.org 2026-06-05 Cell shape critically influences function, yet how complex and reproducible morphologies emerge from stochastic cellular dynamics remains unclear.
A co-proteomic view of metabolite-specific interactions in the Botrytis cinerea-Arabidopsis pathosystem biorxiv.org 2026-06-06 To successfully infect their myriad hosts, generalist plant pathogens must tolerate a vast arsenal of plant specialized defense metabolites.
Genomic Prediction Enables Same-Season Selection for Reduced Glycosidic Nitrile in Eastern U.S. Winter Barley biorxiv.org 2026-06-06 Glycosidic nitriles (GN) in barley are precursors to carcinogens formed during distillation, making GN reduction a critical breeding objective for mal
Aerial imagery and deep learning accurately estimate maize foliar disease severity biorxiv.org 2026-06-06 Southern leaf blight (SLB) is a foliar disease of maize (Zea mays L.) caused by the necrotrophic fungal pathogen Cochliobolus heterostrophus.
LC-MS Metabolomics Reveals No Significant Impact of Microbial Inoculation with Bacillus velezensis and Lachnum sp. on Cranberry Metabolome biorxiv.org 2026-06-06 Sustainable agriculture has driven increased exploration of microbial inoculants as a promising strategy to boost plant growth for higher yield and en
Elevated temperature drives the biosynthesis of novel acylated glucosinolates in Arabidopsis thaliana seeds biorxiv.org 2026-06-06 Glucosinolates (GSLs) are major defensive compounds massively accumulated in Brassicaceae seeds, including that of the model plant Arabidopsis thalian
Integrated Evaluation of Osmotic and Antioxidant Defense Mechanisms in Cotton Genotypes Exposed to NaCl Stress biorxiv.org 2026-06-06 Salinity stress is one of the major abiotic factors limiting cotton productivity worldwide by inducing osmotic imbalance, oxidative stress, and metabo
Nucleoporin1 maintains male germ unit organization and transport in Arabidopsis pollen tubes, likely through shaping nuclear morphology biorxiv.org 2026-06-06 The male germ unit (MGU) in Arabidopsis pollen is comprised of one vegetative nucleus (VN) and two sperm nuclei (SN).
Dynamic gene gain and loss during the divergence of obligate biotrophic powdery mildew pathogens biorxiv.org 2026-06-06 Powdery mildew outbreaks can result in devastating crop losses across both horticultural and cereal crops.
Sidekick2 facilitates multiciliated cell penetration through multicellular adherens junctions biorxiv.org 2026-06-06 Multicellular vertices are important cellular interfaces for mediating tissue dynamics across the epithelium.
Lysosomal lipid metabolism promotes tumor cell invasion through local energetics and membrane lipid remodeling biorxiv.org 2026-06-06 Metabolic vulnerabilities in cancer have been targeted primarily to suppress tumor growth, but less is known about the metabolic requirements for tumo