simulation

Lipopolysaccharide chain length and coat assembly keep guanylate-binding proteins upright on bacterial membranes

This study uses molecular dynamics simulations to show that open-state GBP1 and GBP2 require specific membrane environments to remain stable on bacterial membranes.

Integrating Genetic Domestication and Model-Guided Kill-Switch Engineering in a Non-Model Bacterial Therapeutic

Host-measured parts and inducible systems for Brucella melitensis ΔvjbR guided a modeled Cas9 kill-switch, which cut mouse liver bacterial burden by about 91% at 30 mg/kg doxycycline.

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

This study examines how localized evolutionary changes affect ancestral state reconstruction and shows that tree partitioning can reduce errors in these reconstructions.

Mapping the Trade-Offs That Shape Mammalian Brain Network Architecture

Across 25,000 generative-model networks scored on 29 properties, 635 human and 224 mammalian connectomes cluster in one narrow niche, trading wiring economy for computational capability and robustness.

Gradients of local circuit architecture shape stability and information integration across the cortical hierarchy

This study uses biologically realistic simulations to show that cortical circuit stability and information integration increase with hierarchy, linked to increased connectivity and SST cell proportion.

Mechanistic simulation identifies predictive dose-dependent biomarkers of propofol anesthesia

The paper uses a mechanistic model to simulate propofol's effects on brain circuits, identifying a dose-dependent biomarker confirmed in empirical data.

Rapid simulation of organ-scale oxygen transport for tissue ischemia prediction

The paper introduces a computational toolkit to simulate organ-scale oxygen transport and predict tissue ischemia by analyzing vessel networks and physiological conditions.

Thalamocortical credit routing from the basal ganglia and cerebellum: anatomical constraints and circuit principles

The paper investigates how thalamocortical pathways from the basal ganglia and cerebellum route credit signals to cortical circuits, revealing anatomical segregation and plasticity mechanisms that enhance learning.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Loss of Cerebral Autoregulation After Stroke Drives Abnormal Perfusion Patterns

This study develops an in silico model to simulate cerebral blood flow in mice with and without leptomeningeal collaterals, showing that myogenic reactivity, not collateral extent, drives hyperperfusion after stroke.

Mice adapt their learning rate to stochasticity and volatility through a simple heuristic

The paper shows mice adjust their learning rate based on environmental volatility and stochasticity in a probabilistic reversal task, using a meta-learning rule that captures these dependencies.

Rapid spatial cognition in mice, with and without neocortex and hippocampus

Naive mice learn a 9-turn route in a reconfigurable 3D maze within about 20 rewards; mutants lacking neocortex and hippocampus also learn, remember and generalize, though early exploration is inefficient.

Experiment-anchored abundance-coverage frontiers define conditional RHSVV exposure requirements in TP53-missense tumors

Experiment-anchored sweep of p53 abundance thresholds in CPTAC TP53-missense tumors maps how much RHSVV exposure contrast is needed as target coverage falls.

Prion Protein Deficiency Results in Synaptic, Neural Network and Behavioral Alterations

Lifelong prion protein (PrP) loss in mice lowers excitatory synaptic proteins, makes network bursts in mature cortical cultures rarer and neuronal activity more correlated, and increases adult dimming-disk escapes.

AnnoAudit: a marker-based protocol for auditing single-cell atlas annotations reveals systematic, state-dependent annotation failure in a widely used traumatic brain injury resource

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

Rewiring Oncogenic Transcriptional Complexes with Domain-ALTerAtion Chimeras (DALTACs) in Prostate Cancer

A bifunctional AR–p300/CBP molecule, DALTAC-1, forces a non-native contact between AR and p300 domains, silences AR enhancers and regresses AR-driven prostate tumors in mice while sparing AR-negative lines.

Dynamic Pocketome of Trace Amine-Associated Receptors

The paper presents a dynamic pocketome analysis of TAAR receptors using simulations, revealing receptor-specific ligand-receptor interplay and plasticity in binding sites.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Sex differences in exploration-exploitation strategies during home-cage decision making

In 136 mice on FED3 tasks, males showed slightly higher win-stay in all three choice tasks, with higher accuracy in a deterministic bandit but not a probabilistic one.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

Fast-ripples are emergent properties of neuronal networks

Most fast-ripples (250-500 Hz) in rat and human recordings are consistent with chance clustering of action potentials; in awake patients, distinct events make up an estimated 37.5% of detections.

The Cerebellar Engine: Multiscale Digital Brain Co-simulations Reveal How Cerebellar Spiking Architecture Shapes Cortical Coherence

In a mouse whole-brain co-simulation with a spiking olivocerebellar network, cutting mossy-fiber input to cerebellar nuclei lowers M1-S1 gamma coherence, while removing Purkinje inhibition raises it.

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

PhysiCelldFBA links single-cell metabolism to multicellular spatial dynamics by integrating genome-scale metabolic models with agent-based simulations.

Evolutionary rise of a synaptic mechanism for creating and diversifying key reinforcement signals

The paper shows that GABA co-release in the lateral habenula produces TD-like computations linked to decision-making, and that this mechanism evolved across vertebrates.

Granule cells reorient cortical trajectories to separate contexts

In mice learning two tasks, cerebellar granule cells kept the low-rank geometry of premotor cortical output within each task but rotated their population trajectories apart between tasks, while cortex generalized.

Sensory experience drives glutamate spillover, presynaptic LTP and functional connectome remodeling in the barrel cortex

The paper shows that sensory experience increases glutamate release and strengthens synaptic connections in the barrel cortex, leading to changes in the functional connectome.

Transcription-specific synaptic plasticity mediates engram computations

The paper shows that transcription-specific synaptic plasticity in distinct neuronal ensembles drives memory computations in mice.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.

Multiplexing of functionally distinct inputs by intrinsic modulation of spike timing in a monoaminergic nucleus

The paper investigates how 5-HT neurons in the DRN encode and distinguish two excitatory inputs using spike timing and intrinsic cellular mechanisms.

Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates

Autocorrelation-aware bivariate Moran's I, bivariate Gaussian process tests and generalized additive models (R package sbivar) test cross-modality colocalisation on disjoint coordinates; many existing permutation tests inflate false positives.