Fault-tolerant 3D reconstruction from 2D spatial proteomics sections biorxiv.org 2026-06-28 Reconstructing 3D molecular volumes from sparsely sampled 2D tissue sections is limited by per-section marker dropout and tissue loss.
Ptolemaea: consensus, comprehensive annotation of antiviral defence systems in bacterial genomes biorxiv.org 2026-06-28 Motivation: Bacteria carry a large repertoire of antiviral defence systems, our knowledge of which is expanding rapidly.
Desktop-Scale Hit-Point Discovery for Intrinsically Disordered α-Synuclein Using State-Space Compression and a Discrete Phase-Interference Search Operator biorxiv.org 2026-06-28 The accessible chemical space dwarfs any tractable screening budget, and most artificial intelligence drug discovery pipelines respond by docking and
Towards a Unified Exact Solution of Rearrangement Small Parsimony for Natural Genomes biorxiv.org 2026-06-28 Phylogenetic reconstruction is a fundamental problem in comparative genomics.
CarveMe-GutMicrobes: Automated Metabolic Model Reconstruction for Gut Microbial Species and Communities biorxiv.org 2026-06-28 Genome-scale metabolic models (GSMMs) are important aids towards system-level understanding of the metabolic physiology of the gut microbes and for ra
MassSpectrum Analyzer: An interactive platform for proteomic searching parameter refinement and peptide modification focused re-scoring biorxiv.org 2026-06-28 Peptide spectrum annotation is critical for the assignment of peptides and the localisation of modifications.
Dual Carbohydrate Recognition by the Chitinase-like Protein CHI3L1 Through Distinct Glycosaminoglycan and Chitin-Binding Interfaces biorxiv.org 2026-06-28 CHI3L1 (YKL-40) is a chitinase-like glycoprotein involved in immune regulation, tissue remodeling, and cancer, yet the molecular principles governing
Loop-Directed Cofactor Binding Enables Programmable Multico-factor Protein Design biorxiv.org 2026-06-28 The emergence of respiratory, photosynthetic, and assimilatory complexes in evolution required proteins capable of binding multiple catalytic and elec
Redox-modulated bacterial deubiquitinase ElaD: Target recognition and suppression of K63-linked polyubiquitin accumulation in yeast. biorxiv.org 2026-06-28 Bacterial deubiquitinases (DUBs) are important virulence effectors that manipulate host ubiquitin signaling during infection.
Peri-Locus Coeruleus Controls Endothelial Cell Heterogeneity in Enriched Environments via Region-Specific Norepinephrine Signaling biorxiv.org 2026-06-28 The brain acts as a central integrator that enables organisms to interpret environmental stimuli and coordinate adaptive responses across the body.
A novel wild-derived MHC-linked locus regulates host immunity to gammaherpesvirus infection biorxiv.org 2026-06-28 Inefficient host control of infection by gammaherpesviruses is a risk factor for lymphoproliferative disease, autoimmunity, and cancer, yet naturally
Stroke-induced lipocalin-2-expressing red pulp macrophages reprogram peripheral immunity biorxiv.org 2026-06-28 Acute ischemic stroke (AIS) induces profound systemic immune alterations that contribute to infection susceptibility.
Restriction-site-based enrichment coupled to adaptive sampling enables long-read transposon-insertion sequencing biorxiv.org 2026-06-28 Long-read Transposon insertion sequencing is essential for linking genotypes to phenotypes, as short- read approaches struggle with complex genomic re
Genetic architecture of the murine serum metabolome reveals carboxyl esterases as master regulators of circulating fatty acid metabolism biorxiv.org 2026-06-28 Background The systemic biochemical diversity of circulating metabolites and lipids reflects the integrated effects of genetic variation and environme
GR-SAFS: A Graph-Regularized Stacking Framework with Adaptive Feature Selection for High-Dimensional Prognostic Biomarker Discovery biorxiv.org 2026-06-28 Identifying prognostic biomarkers from high-dimensional transcriptomic data poses a triple challenge: achieving sparsity, preserving biological networ
High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends biorxiv.org 2026-06-29 High-fidelity detection of rare structural variants (SVs) remains challenging because library preparation and sequencing techniques generate artifactu
Determining Reliable Neural Targets for enhancing Motor Sequence Learning: A preparatory study for focal tDCS biorxiv.org 2026-06-29 Background: Motor sequence learning (MSL) underlies the acquisition of everyday skilled movements, and transcranial direct current stimulation (tDCS)
Genomic predictions of climate change vulnerability in the emblematic mountain butterfly Parnassius apollo biorxiv.org 2026-06-28 The unprecedented rate of climate warming threatens many species, and assessing their vulnerability to climate change represents a critical challenge
Promoter Structural Variants are Drivers of Genome-Wide Differential Expression in Maize biorxiv.org 2026-06-28 Background: Structural variants (SVs) are large insertions or deletions of DNA sequences.
Food reward in Bottlenose Dolphins (Tursiops truncatus) and Belugas Whales (Delphinapterus leucas) reduces heart rate and increase heart rate variability. biorxiv.org 2026-06-28 Heart rate (HR) and its variability (HRV), mediated by the autonomic nervous system are key indicators of diving physiology and behavioral state, in v
Prefrontal activation predicts response latency and is shaped by age and lifestyle biorxiv.org 2026-06-28 Neurological and neuropsychiatric conditions affect 43% of the global population, many shaped by modifiable lifestyle exposures, yet their relationshi
Rhythmic replay of short-term memory neural patterns revealed by time-resolved error prediction biorxiv.org 2026-06-28 Theta oscillations are thought to provide a temporal scaffold for short-term memory (STM), organizing item encoding and maintenance into successive ph
Enhancing slow-wave sleep via non-invasive brain stimulation modulates brain-to-blood clearance of Alzheimer's disease biomarkers biorxiv.org 2026-06-28 Sleep disturbances and neurodegeneration form a bidirectional vicious cycle.
PLFest: A Multi-Site Validation of an Open Platform for Visual and Cognitive Assessment biorxiv.org 2026-06-28 Purpose: To evaluate the feasibility, validity, and scalability of PLFest, an open-source, Unity-based, cross-platform application designed for standa
Time space signatures of hybrid search resolution using EEG and eye movements concurrent recordings biorxiv.org 2026-06-28 Understanding how the brain supports visual search in naturalistic environments, where attention and memory must work together to find targets among d
Prenatal circadian rhythm disruption induces sex-specific substance use and mood-related phenotypes in mice biorxiv.org 2026-06-28 20% of Americans are at risk for environmental circadian rhythm disruptions (CRD) due to shift work, leading to substantial negative health outcomes.
Dozens of genetic variants sustain adaptation to urban spatial heterogeneity in Arabidopsis thaliana biorxiv.org 2026-06-28 Urbanization creates mosaics of microhabitats that sustain diverse plant communities, and offer untapped opportunities to understand contemporary ecol
Minicollagen expression dynamics reveal a transcriptional program for cnidogenesis in the sea anemone Nematostella vectensis biorxiv.org 2026-06-28 Cnidae are explosive harpoon-like organelles localized within stinging cells, or cnidocytes, of the phylum Cnidaria (jellyfish, hydroids, sea anemones
Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE biorxiv.org 2026-06-28 Cell-cell communication is fundamental to tissue organization, homeostasis, and disease progression.
OxyBLI: A Genetics-Based Approach for In Vivo Real-Time Visualization of Tissue Oxygenation Dynamics biorxiv.org 2026-06-28 Accurate measurement of cellular oxygen levels is essential for understanding the balance between oxygen demand and supply in tissues.
Transitive reasoning as linear classification biorxiv.org 2026-06-28 Transitive inference (TI) is the ability to reason about transitive relationships in an ordered set of items (e.g., if A>B and B>C, then A>C)
Temporal Gating by Chandelier Cells Encodes Signed Prediction Errors biorxiv.org 2026-06-28 The brain refines its predictions of the world by updating its internal model whenever sensory input differs from expectation.
Resting fMRI functional connectivity reflects fluctuations in inhibitory interneuron activity biorxiv.org 2026-06-28 Primate brain function relies on distributed cortical networks.
Cognitive and affective neurodevelopment in youth exposed to deprivation and threat biorxiv.org 2026-06-28 Background: Early life adversity (ELA) is associated with notable negative consequences across development.
Melanin-concentrating hormone signaling regulates prefrontal updating of learned avoidance biorxiv.org 2026-06-28 Adaptive avoidance depends on a delicate balance: animals must act rapidly when a cue predicts danger, but suppress the same action when the cue no lo
Literacy acquisition and functional connectivity drive the emergence and continued development of the VWFA biorxiv.org 2026-06-28 The visual word form area (VWFA) is a hallmark of literacy in the human brain.
mTOR drives cerebrovascular dysfunction and blood-brain barrier breakdown in a model of Alzheimers disease with cerebral amyloid angiopathy biorxiv.org 2026-06-28 Cerebral amyloid angiopathy (CAA) is characterized by the deposition of amyloid {beta} fibrils (A{beta}) within walls of the cerebrovasculature and co
Dissociation between hemodynamic and neurochemical responses during chemogenetic modulation of cortical circuits in rats biorxiv.org 2026-06-28 Introduction: Chemogenetic tools such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) provide a powerful means to causally man
A reduced multicompartment network model of CA1 theta-gamma oscillations under extracellular stimulation biorxiv.org 2026-06-28 Deep brain stimulation has demonstrated its therapeutic potential in modulating pathological oscillations associated with Parkinson's disease and epil
Frontotemporal cortex flexibly adapts latent structural representations biorxiv.org 2026-06-28 Humans excel at navigating complex environments by forming abstract structural representations that can be flexibly updated when environments change.
A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance biorxiv.org 2026-06-28 Cortical expansion in the human lineage was accompanied by alterations in cortical circuit architecture, including an elaboration of cortico-cortical
Brain Structure Shapes Function through higher-order Functional Interactions biorxiv.org 2026-06-28 Brain function is deeply embedded within multiscale structural architecture.
Hierarchical Predictive Processing during Natural Reading biorxiv.org 2026-06-28 Key neural mechanisms underlying reading, especially in the context of sentences and texts, remain elusive.
Appetitive Pavlovian goal-tracking memory reconsolidation is reduced by both adrenergic and NMDA receptor antagonism biorxiv.org 2026-06-28 Rationale Appetitive Pavlovian cues can drive maladaptive reward seeking via stimulus-reward memories.
Dissociating the behavioral and computational features of implicit motor learning and explicit perturbation detection biorxiv.org 2026-06-28 The human sensorimotor system is remarkably effective at automatically parsing total movement error into its constituent parts, the error component du
TRPML1 positions lysosomes and regulates actin-membrane linkers in astrocyte processes biorxiv.org 2026-06-28 Lysosomes are critical for neuronal physiology and synaptic function, but their organization and roles within astrocytes, an integral component of the
Preserved geometry during representational drift enables stable perception and memory biorxiv.org 2026-06-28 In many brain regions, the stimulus tuning of neurons is stable on a timescale of hours but not on a timescale of weeks, a phenomenon often called 're
The genetic signature of memory encoding along the human hippocampal axis biorxiv.org 2026-06-28 Episodic memory formation engages hippocampal oscillations that vary along the anterior-posterior axis, but the molecular programs supporting this phy
Brain Connectivity Modelling Through Joint Estimation of Parcels and Gradients biorxiv.org 2026-06-28 This paper presents a framework for modelling the topography of whole-brain connectivity in resting-state functional MRI.
The Importance of Synchrony in the Neural Control of Movement biorxiv.org 2026-06-28 Throughout the mammalian cortex, populations of neurons must work together to enact behaviors.