simulation

fastQpick: scalable bootstrap and subsampling of FASTQ reads

fastQpick generates bootstrap replicates of FASTQ reads for uncertainty quantification in sequencing data.

Intrinsic representational drift from predictive excitatory-inhibitory plasticity

This study shows that representational drift in neural networks arises from predictive excitatory-inhibitory plasticity, with changes in neuron preferences and stable ensemble coding.

Mechanistic Insights into the inhibition of Plasmodium falciparum DNA gyrase A by withanolides derivatives through integrated computational analysis

This study uses computational methods to analyze the binding of three withanolide derivatives to Plasmodium falciparum DNA gyrase, showing their potential as antimalarial drug candidates.

A Neural Mass Modelling Framework for Evaluating EEG Source Localisation of Seizure Activity

This paper presents a simulation framework to evaluate EEG source localisation methods by generating biologically plausible seizure dynamics and EEG signals with known ground truth.

Modelling and Inferring Large-scale Demographic Fluctuations in Structured Populations Through Simulations and PSMC-based Methods.

This study simulates structured populations to assess PSMC's ability to infer demographic history, finding it fails to recover older fluctuations but works better for recent periods.

Parallel connectivity and genomic divergence but heterogeneous demographic history in sympatric Mediterranean clingfishes

This study examines connectivity and genomic divergence in sympatric Mediterranean clingfishes, finding concordant connectivity patterns but heterogeneous demographic histories.

Inhibitory Gain and Hub Architecture Confer Dynamic Resilience to Microcircuit Degeneration

The paper investigates how inhibitory gain and hub architecture contribute to neural circuit resilience against degeneration by analyzing spiking networks with controlled pruning strategies.

Habitat restoration promotes recolonisation by extirpated species in model meta food webs

This study uses model food webs to show that habitat restoration affects species recolonization based on dispersal ability, proximity to source patches, and landscape connectivity.

Conformational dynamics of the membrane-anchored foldase LipH from Pseudomonas aeruginosa governs recognition and release of its client lipase

This study investigates the conformational dynamics of the membrane-anchored foldase LipH and shows how it recognizes, folds, and releases its client lipase LipA.

Comparative pangenomics of Trypanosoma brucei reveal host specialization is driven by targeted or segmental genome streamlining in human and equine-restricted lineages

This paper investigates how Trypanosoma brucei adapts its genome during host specialization, revealing two distinct structural evolution pathways in human and equine-restricted lineages.

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

Temporal structure of task engagement reorganizes infra-slow BOLD dynamics

This paper shows that task engagement in fMRI reorganizes infra-slow BOLD dynamics by redistributing power across frequencies rather than just adding to ongoing activity.

Crowder induced conformational fluctuations modulate the phase separation of yeast SUP35 NM domain

This study shows that crowder shape affects Sup35NM conformation and phase separation, with rod-like crowders promoting phase separation while spherical ones do not.

Role of stereochemistry on electron transport in peptides

This study examines how stereochemistry affects electron transport in peptides through experiments and simulations, showing that stereochemical modifications alter conductance via aromatic interactions or secondary structure effects.

Simulating Neutron Protein Crystallography Experiments: Applications to the Development of the NMX Instrument at ESS

The paper uses Monte Carlo simulations to model neutron protein crystallography experiments for the NMX instrument at ESS, improving event formation and analyzing scattering effects.

Stochastic colonization and host-to-host transmission shape gut bacterial variability

This study shows that stochastic colonization and host-to-host transmission significantly influence gut bacterial variability in C. elegans using E. coli under different diets.

Dynamic single-molecule binding of carbamazepine explains diffuse cryo-EM density in the SUR1 drug-binding pocket

The paper investigates the diffuse cryo-EM density of carbamazepine in the SUR1 drug-binding pocket and finds it results from dynamic single-molecule binding rather than dimerization.

From Proteome Mining to Structural Validation: Phosphopyruvate Hydratase as a Structurally Tractable Drug Target in Kinetoplastid Parasites

The paper identifies phosphopyruvate hydratase (PPH) as a drug target in kinetoplastid parasites through proteome mining, structural modeling, and experimental validation, and identifies hinokinin as a promising antiparasitic compound.

Multiscale Modeling Identifies Cardiovascular Risk from Common Chemical Exposures

This study uses multiscale modeling to identify cardiovascular risks from common chemicals by integrating in vitro data, human exposure estimates, and animal studies.

Unified comparison of spinal locomotion control architectures in neuromechanical simulations

This paper compares four spinal locomotion control architectures in neuromechanical simulations, finding that reflex-based and CPG-reflex-synergy-based controllers best reproduce human-like gait and show the greatest versatility across speed-slope conditions.

Effects of Left Atrial Wall Thickness on Myocardial Mechanics and Blood Dynamics using Multiscale Modeling

This study uses multiscale modeling to show that left atrial wall thickness significantly affects myocardial stresses and oscillatory shear, more than other factors like cavity volume or displacement.

Spatial Organization of Lipids Drives GPCR Conformational Equilibria

The paper investigates how lipid organization in nanodiscs affects GPCR conformational states, finding that anionic lipid concentration thresholds vary between POPS and POPG.

seekrflow: Towards end-to-end automated simulation pipeline with machine-learned force fields for accelerated drug-target kinetic and thermodynamic predictions

seekrflow automates drug-target kinetic and thermodynamic predictions using a multiscale milestoning simulation pipeline, achieving accurate results with reduced manual intervention and computational cost.

Forward Modelling for Magnetospinography: Systematic Comparison of Boundary Element and Finite Element Methods

This study compares boundary element and finite element methods for forward modelling in magnetospinography, finding consistent results between methods but significant differences based on bone geometry representations.

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Population-scale detection of methylation outliers from long-read genome sequencing

METAFORA calls depth-aware, covariate-adjusted methylation outlier regions from PacBio and Nanopore long reads; in 551 rare-disease genomes, outliers tracked structural variants, repeat expansions, and imprinting defects.

Between Friends and Foes: Evolutionary Diversification in Mutualistic-Antagonistic Networks

The paper uses an eco-evolutionary model to show how mutualism and antagonism interact to influence diversification in ecological networks, finding that trait correlation affects diversification rates across guilds.

Cortical E-fields of deep brain stimulation in Parkinson's disease patients exceed typical E-field magnitudes of transcranial electrical stimulation

This study quantifies whole-brain E-field distributions from STN-DBS in Parkinson's patients, finding cortical peak magnitudes exceeding typical transcranial stimulation values.

Structural Characterization of the Type IV Secretion System in Brucella melitensis for Virtual Screening-Based Therapeutic Targeting

This study models the T4SS structure of Brucella melitensis and identifies three FDA-approved drugs that could target the system for anti-virulence therapy.