simulation

Optimiser Repairs for Living-Cell Self-Driving Laboratories: Performance and Redundancy under Experimental Constraints

This paper evaluates optimiser repairs in living-cell self-driving labs, showing when they improve performance and when constraints make them redundant.

Steering Before Selection: Energy-Limited Developmental Control as a Phenotypic Capacitor, a Pre-Specified Simulation Study

This paper uses simulations to show that developmental control conceals genetic variation from selection, acting as an energy-dependent phenotypic capacitor that can be beneficial if harmful mutations are reversed.

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Eco-evolutionary Dynamics of Colonization: When Does Source Selection Matter?

This study uses simulations to show balancing selection in source populations increases colonization success in new habitats when founder populations are small, regardless of environmental conditions.

mock-fastq-generator: A synthetic FASTQ generator

mock-fastq-generator creates synthetic FASTQ files for testing bioinformatics pipelines without using biological data.

Degeneracy in neuronal bifurcation landscapes: equivalent bifurcation sequences across distinct parameter sets

The paper shows that different biophysical parameters can produce equivalent bifurcation sequences in neuronal models, revealing degeneracy in neuronal dynamics.

Coordinated Drift of Image Representations in Human EEG

The paper investigates drift in human EEG responses to images across sessions, finding coordinated drift along image identity dimensions and preserved global structure.

Predictive adequacy and measurement dependence of metabolic representations in controlled synthetic systems

The paper evaluates metabolic representations in synthetic systems, finding that adequacy, compactness, and responsiveness are distinct properties, and adequacy certification does not guarantee predictive accuracy.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

A NEST-based framework unlocks massively parallel simulation of networks of multicompartment neurons with customizable subcellular dynamics.

The paper introduces a framework for simulating multicompartment neurons with customizable subcellular dynamics using NEST and NESTML, enabling efficient and scalable network simulations.

Optimizing Cognitive Phenotyping for Genetic Discovery in Alzheimer's Disease: A Simulation-Based Evaluation of Mini-Mental State Examination-Based Decline Measures

The paper evaluates cognitive decline measures for genetic studies in Alzheimer's disease using simulations, finding that simpler measures like Slope and dMMSE/dt are more powerful.

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

The impact of strain heterogeneity on genomic profiling accuracy in mixed-strain Escherichia coli metagenomes

The paper evaluates how strain heterogeneity affects the accuracy of genomic profiling in mixed-strain Escherichia coli metagenomes using simulated data and various bioinformatic tools.

Optimal MR-ARFI encoding parameters for a range of contemporary magnetic field gradient systems

The paper optimizes MR-ARFI gradient parameters and provides a simulation tool to enhance sensitivity under various hardware conditions.

Strain resolution and wide relative abundance quantification of bacterial microbiomes with nanopore sequencing of the ribosomal RNA operon

This paper demonstrates strain-level resolution and quantification of bacterial microbiomes using nanopore sequencing of the ribosomal RNA operon, showing accurate relative abundance quantification over multiple orders of magnitude.

Hemodynamic-Structural Multi-Fidelity Assessment of Endovascular Flow Diversion Strategies for Cerebral Aneurysm Treatment: An Integrated Computational and Experimental Framework

The paper evaluates hemodynamic and structural outcomes of endovascular flow diversion strategies for cerebral aneurysms using computational models and experimental tests.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination

The paper presents DeFluorX, a pipeline using Boltz-2 to identify FAcD variants for PFAS defluorination by analyzing geometric and energetic factors in enzyme-PFAS complexes.

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.

ALBIS: simulation of multi-resolution and multi-dimensional spatial transcriptomics data

ALBIS generates synthetic spatial transcriptomics data across multiple resolutions and dimensions to enable benchmarking of computational methods.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

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.

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.

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Measurement-Induced Decision Loss: A feasible-set theory of microbiome intervention under observation loss

Measurement-induced decision loss (MIDL), host benefit forgone versus perfect observation, grows linearly with microbiome information loss in a binary model, then plateaus once the optimal policy becomes signal-independent.

Learning source weights for target-position estimation: comparing fixed weights and an input-dependent rule

In simulation, under reduced accuracy or temporally correlated errors, recalibration or fixed-weight learning captured most gains; a disagreement-dependent rule beat fixed weights mainly under occasional large errors (4.05% lower MSE).