DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics biorxiv.org 2026-06-11 De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides witho
Mechanisms of viral budding through cellular membranes biorxiv.org 2026-06-11 Budding is a fundamental membrane remodeling process central to many cellular functions and is exploited by numerous enveloped viruses to acquire thei
Covalent Inhibition of New Delhi Metallo-β-Lactamases NDM-1 and NDM-5 by 3-Bromopyruvate biorxiv.org 2026-06-11 Resistance to {beta}-lactam antibiotics, including carbapenems, mediated by metallo-{beta}-lactamases (MBLs), including the New Delhi metallo-{beta}-l
: A standardized bath challenge of Atlantic salmon reveals distinct infection dynamics and mortality across ten HPR-deleted infectious salmon anaemia virus isolates. biorxiv.org 2026-06-11 Infectious salmon anaemia virus with highly polymorphic region deletions (ISAV-HPR{Delta}) is classified as pathogenic, yet field outbreaks display wi
Cross-protection against Bundibugyo by Ebola and Sudan vaccines biorxiv.org 2026-06-11 Ebola outbreaks continue to expand across Central Africa, yet available countermeasures remain limited and virus-specific.
Laboratory adaptation and complete genome assembly of a Beposo, Ghana strain of the human hookworm Necator americanus biorxiv.org 2026-06-11 Laboratory models are invaluable tools for studying parasite biology and pathogenesis, especially for helminth infections.
Infection-specific long-chain fatty acid metabolism as a broad anti-enterovirus target biorxiv.org 2026-06-11 Enteroviruses are arguably the most numerous group of viruses infecting humans.
Plasmid copy numbers reflect distinct evolutionary strategies biorxiv.org 2026-06-11 Different plasmids exist at different copy numbers per cell, and there is an inverse relationship between a plasmid's copy number and its size.
Mutations associated with streptomycin resistance predicted to be highly prevalent and evolvable across bacteria biorxiv.org 2026-06-11 Antimicrobial resistance is an evolutionary response to antimicrobial exposure that has been extensively studied across some bacteria, including patho
Ancient DNA perspectives on North American cervids identify dispersal waves and fluctuations in diversity biorxiv.org 2026-06-11 North American fauna experienced major changes over the last two million years.
The Origin and Evolution of Protein Synthesis: A Co-Adaptation Flexible-Rigid Docking Model Based on First-Principles Reasoning biorxiv.org 2026-06-11 Although the "RNA World" hypothesis suggests that RNA played a crucial role in the origin of life [7], the functional framework of RNA in prebiotic pr
Multimodal phenotyping defines variant-to-function maps for RBM20 in dilated cardiomyopathy biorxiv.org 2026-06-11 Multiplex assays of variant effects have linked thousands of genotypes to fitness effects, yet we lack profound understanding of how variants impact m
Controlling metal-carbonate phase, form, and function through de novo protein design biorxiv.org 2026-06-11 Biomineralization enables living systems to construct hybrid materials by controlling the location, orientation, and polymorph of inorganic crystals w
Sequence-encoded H2A.Z nucleosome dynamics control DNA unwrapping and SUV420H1 recognition biorxiv.org 2026-06-11 H2A.Z and canonical H2A adopt nearly identical nucleosomal folds, yet their distinct chromatin functions are not captured by static structural analysi
Viability of engineered AAVs via protein language models biorxiv.org 2026-06-11 Capsid engineering has greatly improved the performance of recombinant AAV vectors used for gene therapy.
HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design biorxiv.org 2026-06-11 AlphaFold3 has revolutionized the prediction of biomolecular structures and interactions, including atomic-level modeling of nucleic acids.
Variable ectopic heterochromatin islands provide an alternative route to antifungal heteroresistance in Cryptococcus neoformans biorxiv.org 2026-06-11 The fungal pathogen Cryptococcus neoformans is estimated to cause approximately 180,000 deaths annually, primarily among immunocompromised HIV patient
Phylogenomic description of three novel species of the Microbulbifer genus, phylum Pseudomonadota, isolated from marine sponges and corals biorxiv.org 2026-06-11 Understudied bacterial genera present a dynamic phylogenetic landscape and opportunities for discovering new taxa as more strains are isolated and gen
Virus-grazer interplay enhances virus production, particle aggregation, and trophic efficiency during infection of Prochlorococcus biorxiv.org 2026-06-11 Viruses and grazers are fundamental agents of mortality in the oceans, impacting phytoplankton populations and organic matter cycling.
Secreted ORF8 reprograms macrophages to enhance SARS-CoV-2 infection of lung epithelial cells biorxiv.org 2026-06-11 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily targets the respiratory epithelium, yet severe disease features diffuse lung in
Morphological and thermoregulatory responses to urbanization in the European garden spider Araneus diadematus. biorxiv.org 2026-06-11 Urbanization creates novel environments that can drive phenotypic and behavioural responses, yet how multiple traits respond across spatial scales rem
Plant MutS Homolog 1 is a mismatch-directed nuclease required for organelle genome maintenance biorxiv.org 2026-06-11 The MSH1 gene in Arabidopsis thaliana (AtMSH1) encodes a modular enzyme that consists of an N-terminal MutS DNA mismatch repair module fused to a C-te
Multimodal PET Defines a Goldilocks Thermal Window for Focused Ultrasound Ablation and Immunotherapy Combinations biorxiv.org 2026-06-11 Background: Thermally ablative focused ultrasound (T-FUS) offers a noninvasive, spatially precise strategy for local tumor destruction, with the added
Topology-aware thermodynamics for DNA probe design under fixed stringency: Retained paired boxes link mismatch placement, nearest-neighbor stability and room-temperature diagnostic specificity biorxiv.org 2026-06-11 DNA probe specificity is usually screened by mismatch number, melting temperature and full-duplex nearest-neighbor free energy.
Isolation and introductions disrupt the homogeneity of Argentine ants in Europe. biorxiv.org 2026-06-11 The introduction of alien species into new habitats stands as a pressing economic and ecological challenge but it is also essential for unveiling evol
inquiSTR: a toolkit for accurate and efficient population-scale tandem repeat genotyping and analysis biorxiv.org 2026-06-11 Tandem repeats are highly mutable genomic elements linked to human traits and diseases.
Utilizing a cell culture based novel cellular thermal shift assay to understand the isoform-dependent thermal stability of ApoE variants biorxiv.org 2026-06-11 Apolipoprotein E (ApoE) is the primary genetic risk modifier of late-onset Alzheimer's disease, with the E4 allele increasing risk up to 15-fold relat
Near-infra red light and mitochondrial large-conductance calcium-activated potassium channels: protection of hippocampal neurons, influence on channel activity and transcriptome remodelling biorxiv.org 2026-06-11 Photobiomodulation (PBM) is a therapeutic approach based on illumination with red or near-infrared (NIR) light.
Socially-mediated compensatory growth carries hidden sperm costs in male guppies biorxiv.org 2026-06-11 Phenotypic plasticity allows organisms to mitigate early-life adversity through compensatory growth, yet the long-term costs of such "catch-up" trajec
Female acoustic signaling of sexual immaturity depresses male courtship in Drosophila biorxiv.org 2026-06-11 In an early phase of life, most animals are behaviorally and physiologically not yet able to reproduce but show adaptations specific to a juvenile sta
DeePEn - A Depth sensitive benchmark for Protein Engineering biorxiv.org 2026-06-11 Recent progress in modeling techniques and high-throughput screening has significantly enhanced the accessibility of protein engineering.
Attenuation of value-to-evidence translation drives biased decision making in anxiety and depression biorxiv.org 2026-06-11 Anxiety and depression are globally prevalent conditions associated with maladaptive decision making.
Age-dependent Effects of Titrating Anodal Transcranial Direct Current Stimulation (tDCS) Intensity on Motor Sequence Learning biorxiv.org 2026-06-11 Optimising the currently heterogenous efficacy of transcranial direct current stimulation (tDCS) interventions for motor learning requires identifying
Pseudogenes confirm ongoing loss of ethylene biosynthesis in seagrasses biorxiv.org 2026-06-11 Many flowering plant species have adopted an aquatic lifestyle, contrasting with their terrestrial ancestors.
Explainable AI identifies H3K18ac as a new marker of active enhancers biorxiv.org 2026-06-11 Enhancers are non-coding regions of DNA that regulate gene transcription, yet the mechanisms underlying enhancer activity remain incompletely understo
Dairy wastewater grease stabilizes in situ mesophilic biomethanation for H2-to-CH4 conversion biorxiv.org 2026-06-11 Power-to-Gas technologies are emerging as a key strategy to integrate surplus renewable electricity into energy systems, through the conversion of gre
Tumour evolution as ground truth for cancer whole-genome sequencing biorxiv.org 2026-06-11 Cancer genomes are shaped by evolutionary processes that couple mutagenesis, clonal selection, chromosomal instability, spatial growth and treatment r
A Deep Hypergraph Learning Model for Predicting Antimicrobial Combination Effects Across Bacterial Targets biorxiv.org 2026-06-11 Antimicrobial resistance (AMR) creates an urgent need for efficient strategies to identify effective antibacterial combinations.
Amylo-Pipe: an integrated web server for mechanistic and kinetic prediction of protein and peptide aggregation biorxiv.org 2026-06-11 Protein aggregation is central to amyloid-related disorders and remains a major developability challenge for protein therapeutics.
A quantitative coordinate system for developmental dynamics biorxiv.org 2026-06-11 Quantitative comparison of morphogenesis across individuals remains a fundamental challenge, as developing embryos vary in shape, orientation and deve
PhyloZoo: a unified framework for phylogenetic network analysis in Python biorxiv.org 2026-06-11 Reticulate evolutionary processes (events in which lineages merge, such as hybridization, recombination, and horizontal gene transfer) are widespread
MARINER: a surround visual stimulator for vision research in aquatic animals biorxiv.org 2026-06-11 Aquatic vertebrates are increasingly used in neuroscience research, yet underwater visual stimulation remains a challenge.
Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System biorxiv.org 2026-06-11 Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function.
Cerebrovascular pulsatility differs across vascular compartments and is altered by hypercapnic stimuli: a BOLD fMRI study biorxiv.org 2026-06-11 Cerebral small vessel disease and neurodegenerative disorders have been associated with increased cerebrovascular pulsatility.
Starvation modulates associative short-term memory of Drosophila in a task-dependent manner biorxiv.org 2026-06-11 It is widely believed that starvation favours the processing of food-related cues, a notion here called the 'adaptive specificity hypothesis'.
Mutant SOD1 expressed by oligodendrocytes aggregates in myelinic nanochannels and accelerates disease progression in familial ALS mice biorxiv.org 2026-06-11 Amyotrophic lateral sclerosis (ALS) is a highly debilitating and fatal disease characterized by the progressive loss of motor neurons.
A systematic imputation framework for sparse, multimodal space biology datasets: application to retinal imaging and omics from the RR9 mission biorxiv.org 2026-06-11 Space biology experiments are expensive, logistically complex, and inherently limited in sample size, resulting in datasets that are frequently incomp
DyMoTree decodes early cell state transitions and drivers from single-cell transcriptomes using a tree-structured neural network biorxiv.org 2026-06-11 Inferring early cell fate from single-cell RNA-sequencing data is essential for identifying cellular origins and fate plasticity in development and di
DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data biorxiv.org 2026-06-11 Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecu
OMIO: A policy-driven Python library for reproducible microscopy image I/O biorxiv.org 2026-06-11 Modern fluorescence and multiphoton microscopy workflows operate within a heterogeneous ecosystem of file formats, partially overlapping metadata stan