Sociality changes Gene Essentiality biorxiv.org 2026-06-28 Transposon insertion sequencing (Tn-seq) has become a powerful tool for assigning gene fitness and essentiality in bacteria, and has recently been ext
A cis-regulatory variant in ASIP causes gray coat color in the donkey biorxiv.org 2026-06-28 Background Gray is one of the relatively rare coat colors in donkeys.
Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease biorxiv.org 2026-06-28 Gene expression evolves dynamically along cell lineages, yet most analysis methods treat single-cell RNA-seq (scRNA-seq) data as static snapshots and
The genomic origins and evolutionary path to a key innovation in the world's most venomous snakes biorxiv.org 2026-06-28 Evolutionary innovation is a key driver of the colonization of new environments and the adaptive radiations of major groups.
Inference of fitness landscapes with heterogeneous patterns of epistasis across sites biorxiv.org 2026-06-28 Fitness landscapes provide a framework for understanding how genetic variation shapes evolutionary outcomes.
Processed pseudogenes as dynamic substrates of vertebrate genome evolution biorxiv.org 2026-06-28 Pseudogenes, gene copies presumed nonfunctional, are widespread products of genome evolution, yet their retention under selection and functional signi
Short-Read Sequencing Benchmarking with Donor-Specific Assemblies biorxiv.org 2026-06-28 Background High-throughput short-read sequencing has become a core technology for genomics, but the rapid expansion of available platforms has made it
LOESS and DE-SWAN can induce artifactual "waves" of molecular aging biorxiv.org 2026-06-28 A growing literature has investigated the relationship between age and biomolecular changes, leading to conclusions that aging occurs in discrete mole
Client-server interfaces enable efficient agent-driven variant calling biorxiv.org 2026-06-28 Background: Large language model (LLM) agents increasingly automate bioinformatics analyses, but most existing bioinformatics tools were built for sta
PARROT: Phase-Altering Regulatory Rewiring Over Time biorxiv.org 2026-06-28 Motivation: Gene regulatory networks undergo dynamic restructuring during development and disease.
Real Science Is Harder Than Benchmarks: Evaluating Advanced AI Frameworks on Published Studies. I. Uncertainty Quantification, ML on Therapeutic Data Commons, and Agent-Based Modeling biorxiv.org 2026-06-27 Artificial Intelligence (AI) frameworks for automating scientific research have shown strong performance on benchmarks, but their capacity to routinel
Ire1-triggered hxl1 mRNA splicing coordinates stress tolerance and virulence in the pathogenic fungus Trichosporon asahii biorxiv.org 2026-06-27 The pathogenic fungus Trichosporon asahii causes severe mycoses in immunocompromised hosts, such as neutropenic patients.
Isolation of bioconcrete-producing bacteria for urea-free marine applications biorxiv.org 2026-06-27 Manual intervention for concrete repair and replacement comes at high environmental and economic costs.
GpsB acts as an adapter for MacP-mediated activation of class A penicillin-binding protein aPBP2a in Streptococcus pneumoniae, independently of MacP phosphorylation biorxiv.org 2026-06-27 Regulation of class A penicillin-binding proteins (aPBPs) in peptidoglycan biosynthesis is incompletely understood in Gram-positive bacteria.
Inhibition of RNA splicing is a novel therapeutic strategy for disruption of nuclear replicating viruses biorxiv.org 2026-06-27 RNA splicing is a fundamental feature of eukaryotic gene expression that is co-opted by many nuclear-replicating viruses to produce viral transcripts.
Pulse-driven and persistent antimicrobial resistance markers in a transboundary Great Lakes connecting channel: pulse-week-stratified water-quality thresholds for One Health surveillance biorxiv.org 2026-06-27 Surface waters in urban watersheds receive episodic inputs of wastewater, runoff, and road-salt residues during spring, yet the contribution of these
Gram-negative-dominated polymicrobial microbiome of necrotizing soft tissue infections from North India: an integrated culture and 16S rRNA metagenomics prospective cohort study biorxiv.org 2026-06-27 Necrotizing soft tissue infections (NSTIs) carry 10 to 30% mortality.
Limited horizontal transmission of an obligate, free-living bacterial symbiont biorxiv.org 2026-06-27 Nutritional symbionts can be essential for their animal hosts.
West Nile virus response to mosquito and avian biodiversity in rural environments biorxiv.org 2026-06-27 Context.
Maintenance of viral diversity through influenza transmission bottlenecks: a within-host branching-process model biorxiv.org 2026-06-27 Viral populations can experience a dramatic reduction in population size and genetic diversity during transmission between donor and recipient hosts.
Comparing genomic inbreeding of an isolated rhesus macaque study population to wild populations biorxiv.org 2026-06-27 Long-term studies of isolated animal populations have greatly improved the understanding of various evolutionary processes.
Bacteriophage Heteroresistance as a Cause of Treatment Failure in Urinary Tract Infections biorxiv.org 2026-06-27 With the rise of antimicrobial resistance, urinary tract infections (UTIs) have become increasingly more difficult to treat, prompting renewed interes
Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea biorxiv.org 2026-06-27 In fungi, hyphal fusion is beneficial within an individual, but fusion between individuals comes with the risks of infection or exploitation.
Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array biorxiv.org 2026-06-27 Selection for disease resistance forms one of the most highlighted areas of aquaculture breeding.
Targeted epigenetic repression of oncogenic transcription factors via CRISPR/dCas9 locus-specific silencing biorxiv.org 2026-06-27 Despite the revolutionary impact of genome engineering tools in medicine, the safe and effective intracellular delivery of CRISPR remains a major obst
Cryo-electron microscopy structure of the bovine ephemeral fever virus RNA-nucleoprotein assembly biorxiv.org 2026-06-27 Bovine ephemeral fever virus (BEFV), a member of the Rhabdoviridae family, is an arthropod-borne pathogen that causes acute febrile disease in cattle.
Where do the ligands bind? Co-folding bitter taste GPCRs with the BitterDB chemical space biorxiv.org 2026-06-27 Bitterness is a key taste modality mediated in vertebrates by TAS2R G protein coupled receptors, which also function in diverse extraoral tissues.
Improving oral dissolution kinetics of weakly basic vodobatinib via slurry conversion to an amorphous drug-polymer salt biorxiv.org 2026-06-27 Vodobatinib (VBN) is a weakly basic (pKa {approx} 2.3), anticancer treatment with poor enteric solubility and low oral bioavailability.
ProLoc: Text-guided Localization of Protein Functional Regions biorxiv.org 2026-06-27 Motivation: Protein function is often mediated by specific sequence regions, such as domains, motifs and functional sites.
Glitch genes: embedding geometry predicts functional fragility in single-cell foundation models biorxiv.org 2026-06-27 Background: Single-cell foundation models are increasingly used for perturbation prediction and gene network inference, but their learned gene represe
The Hidden Disorder Divide: Reconciling Benchmark Inconsistencies in Intrinsically Disordered Protein Binding Site Prediction biorxiv.org 2026-06-27 Computational predictors of protein-binding sites within intrinsically disordered regions (IDRs) show highly inconsistent performance across high-qual
UTRGen: A unified framework for full-spectrum design of mRNA 5' UTRs biorxiv.org 2026-06-27 The 5' untranslated region (5' UTR) is a key regulatory element that governs mRNA translation and protein output.
Stability-driven multi-omics integration for reproducible latent structure biorxiv.org 2026-06-27 High-dimensional multi-omics data integration offers novel opportunities to characterize complex biological systems.
BoltzProt-1: Towards Efficient De Novo Binder Design with Good Developability biorxiv.org 2026-06-27 Designing binders against novel protein targets remains a central challenge in computational drug discovery.
eRNAformer enables genome-wide de novo mapping of enhancer-derived RNA loci biorxiv.org 2026-06-27 Enhancer-derived RNAs (eRNAs) are critical regulators of gene transcription, yet their genome-wide annotation remains challenging.
Influence of Non-Specific Surface Adhesion on the Shape and Microrheology of Red Blood Cells biorxiv.org 2026-06-27 Poly-L-Lysine (PLL) mediates the non-specific adhesion of cells and is commonly used in Atomic Force Microscopy (AFM) measurements, to ensure that cel
Repetitive anatomical patterns for thalamocortical projections of higher-order thalamic nuclei biorxiv.org 2026-06-28 Cortico-thalamo-cortical circuits entail extensive trans-thalamic connectivity between cortical areas, yet their structural organization and function
Individual strategies for ignoring irrelevant information are reflected in distinct neural signatures during temporal attention. biorxiv.org 2026-06-28 Attentional functions enable the nervous system to regulate incoming information, selecting what is behaviorally relevant while filtering out distract
Estimation of neuronal tuning for word meaning from passively recorded naturalistic speech biorxiv.org 2026-06-28 The ability to derive neural-level language coding models holds great scientific and clinical potential.
Instrumental-Motor Transfer: The Relative Value of Competing Movement Goals Modulates Implicit Motor Learning biorxiv.org 2026-06-28 Multiple learning signals can shape motor output, including reward and punishment (via value-based reinforcement learning) and sensorimotor error (via
Reconstruction of critical-sized mandibular defects in a sheep model using a PLLA-PGA-CC scaffold biorxiv.org 2026-06-27 Introduction: Critical-sized bone defects cannot heal spontaneously, requiring additional, often burdensome, treatment.
A Multiscale Computational Analysis of Myometrial Excitation during Late Pregnancy biorxiv.org 2026-06-27 The control of uterine activity during pregnancy is a complex process that involves regulating myometrial excitability across multiple scales.
Rapid urban evolution of the dengue mosquito in West African cities biorxiv.org 2026-06-26 Aedes aegypti is an exceptionally effective global vector of human disease because of its strong specialization on human hosts and habitats.
Thermally driven sex reversal reveals divergent sex determination dynamics in wild viviparous reptile populations biorxiv.org 2026-06-26 Climate change can threaten population viability by disrupting sex ratios in species whose sex is influenced by temperature.
Single cell genomics and fluorescence microscopy suggest a permanent plastid in a marine centrohelid biorxiv.org 2026-06-26 Photosynthetic organelles (plastids), which originated via primary endosymbiosis between an Archaeplastida ancestor and cyanobacteria, have shaped the
Transformation and allelic exchange in Orientia tsutsugamushi biorxiv.org 2026-06-26 Orientia tsutsugamushi is a mite-transmitted obligate intracellular bacterium that causes the potentially deadly zoonosis, scrub typhus.
EpiATLAS - a reference for human epigenomic research biorxiv.org 2026-06-26 The sequence of the human genome provides a foundation for understanding cellular processes in health and disease.
Mapping the genetic architecture of human cortical expansion and its links to neuropsychiatric disorders biorxiv.org 2026-06-26 Cortical expansion is a defining feature of human evolution and neurodevelopment, involving the tangential growth and gyrification of the cerebral cor
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers biorxiv.org 2026-06-26 Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated.
Mapping non-coding functional elements in allotetraploid Cyprinus carpio embryo development reveals subgenome variation of transcription regulation biorxiv.org 2026-06-26 Common carp (Cyprinus carpio) is an important freshwater species for ornamental and aquaculture purposes, and a key cyprinid model for studying allote