Bayesian inference

Multiobjective design of growth media with genome-scale metabolic models and Bayesian optimization

This paper introduces gsMOBO, a computational method that uses genome-scale metabolic models and Bayesian optimization to design cost-effective and productive culture media by optimizing nutrient combinations across high-dimensional spaces.

Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations

This paper introduces BASIL, a Bayesian method to estimate fitness effects of beneficial mutations from BLT data, showing it is more accurate and robust than existing methods.

Quantifying annotation-stratified pleiotropy and co-polygenicity between complex traits

This paper introduces SBayesAPP, a Bayesian model that estimates annotation-stratified pleiotropy and co-polygenicity between complex traits using GWAS summary statistics, revealing cell-type-specific genetic correlations.

Bayesian Inference Framework to Identify Skin Material Properties \textit{in vivo} from Active Membranes

This paper introduces a Bayesian framework using active membranes to infer skin biomechanical properties from strain fields without direct force measurements.

Live-cell imaging and lipidomics of low density lipoprotein containing intrinsically fluorescent cholesteryl esters

This study uses live-cell imaging and lipidomics to track LDL-derived cholesteryl esters in cells, revealing their transport and metabolism kinetics.

PhyMapNet: A Phylogeny-Guided Bayesian Framework for Reliable Microbiome Network Inference

PhyMapNet infers microbiome networks using a phylogeny-guided Bayesian framework, showing improved robustness and reproducibility compared to existing methods.

BayesR3AD: Joint analysis of additive and dominance in Bayesian mixture models

BayesR3AD extends Bayesian mixture models to jointly estimate additive and dominance genetic effects, improving prediction accuracy for fertility and longevity in Holstein cattle.

What microbes want: exploring microbial substrate preferences with the Web of Microbes Agent

The paper introduces a Bayesian Personalized Ranking model to predict microbial substrate preferences and develops an agent that integrates this model with a growth model and LLM for autonomous microbial analysis.

DemuxHMM: Large-Scale Single-Cell Embryo Profiling via Recombination Barcoding

The paper introduces DemuxHMM, a recombination-aware demultiplexing method that improves scalability and performance for large-scale single-cell embryo profiling.

A case-control neuroimaging investigation of chronic Zika virus-infected adults

This study investigates chronic ZIKV infection in adults using neuroimaging, finding no significant brain changes associated with long-term infection.

Sensitive detection of copy number alterations in low-pass liquid biopsy sequencing data

This paper introduces BayesCNA, a Bayesian method for detecting copy number alterations in low-pass liquid biopsy sequencing data, showing improved sensitivity in low-quality cases.

A Systems-Level Framework Integrating Geometry-Controlled Plasmonics, AI-Driven Molecular Kinetics, and Organoid Validation for Next-Generation Biosensing

This paper introduces a systems-level framework combining plasmonic nanosensors, AI-driven molecular kinetics, and organoid validation to enhance biosensing capabilities.

Efficient Gaussian Process-based Motor Hotspot Hunting with Concurrent Optimization of TMS Coil Location and Orientation

This paper presents a Gaussian process-based method for optimizing TMS coil location and orientation to improve motor hotspot identification efficiency and precision.

Crossmodal Interaction of Flashes and Beeps Across Time and Number Follows Bayesian Causal Inference

This study extends Bayesian Causal Inference (BCI) to multidimensional sensory processing, showing it accurately predicts multisensory perception outcomes across varying temporal and numerical disparities.

Functional response predicts invasiveness but not trophic impact

Across 269 functional responses from 45 freshwater fish species, invasive species exceed non-invasive species only when sampled in their native range; introduced populations match non-invasive species.

Validation of Dynamic Bayesian Optimization for a Non-Stationary Human-in-the-Loop Optimization Problem

This study compares dynamic Bayesian optimization (DBO) and Bayesian optimization (BO) in a human-in-the-loop system, finding DBO better handles non-stationary behavior in later training stages.

Bayesian analysis of longitudinal RB-TnSeq resolves the fitness seascape in fluctuating environments

The paper develops a Bayesian framework for longitudinal RB-TnSeq to analyze fitness dynamics in fluctuating environments and identifies a 'fitness seascape' model that predicts mutational targets.

Beyond thresholds: a fully Bayesian framework for quantifying allele count evidence for variant pathogenicity

This paper introduces a Bayesian framework to quantify allele count evidence for variant pathogenicity using Bayes factors, showing compatibility with existing criteria while allowing tunable parameters.

PhyloSOLID: Robust phylogeny reconstruction from single-cell data despite inherent error and sparsity

PhyloSOLID improves phylogenetic reconstruction from single-cell data by addressing error and sparsity, achieving better accuracy than existing methods.

Atomic resolution ensembles of intrinsically disordered proteins with Alphafold

This paper introduces bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of intrinsically disordered proteins using AlphaFold2 and molecular mechanics, showing improved accuracy over existing methods.

bayesReact: Expression-coupled regulatory motif analysis detects microRNA activity in cancer and at the single cell level

bayesReact infers microRNA regulatory activities from single-cell and bulk data, showing strong correlation with expression and improved performance over existing methods.

BESTish: A Diffusion-Approximation Framework for Inferring Selection and Mutation in Clonal Hematopoiesis

BESTish infers mutation fitness, mutation rate, and environmental strength in clonal hematopoiesis using a diffusion-approximation framework applied to VAF datasets.

Integrating fossils samples with heterogeneous diversification rates: a combined Multi-Type Fossilized Birth-Death model

This paper introduces a multi-type fossilized birth-death model to jointly infer phylogenies and diversification rates with fossils and extant species, showing improved accuracy when morphological data are available.

Bayesian neural networks enable inference of complex phylodynamic processes

This paper introduces BELLA, a Bayesian neural network framework for modeling complex phylodynamic processes, showing improved accuracy over linear models in capturing nonlinear relationships between predictors and evolutionary rates.

Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja

D-BPP detects ghost introgression in Panthera and Thuja by combining heuristic D-statistic with Bayesian phylogenomic inference.

Braess' Paradox in Enzyme Kinetics: Asymmetry from Population Balance without Direct Cooperativity

The paper uses Bayesian Markov models to explain asymmetric ATP hydrolysis kinetics in ABCE1 without requiring direct cooperativity between nucleotide-binding sites.

Investigating high pathogenicity avian influenza virus incursions to remote islands: Detection of H5N1 on Gough Island in the South Atlantic Ocean

Whole-genome sequencing and geolocation tracking indicate that high pathogenicity avian influenza H5N1 reached Tristan skuas on remote Gough Island via sub-Antarctic marine networks linked to South Georgia rather than Africa.

An Integrative Phylogenomic Framework Quantifies the Dominant Role of Introgression in Phylogenetic Discordance among Diploid Oryza Species

This study quantifies introgression's role in phylogenetic discordance among diploid Oryza species, finding it explains most gene tree-species tree conflict.

Molecular phylogenetics of Neotropical chrysomeline beetles: Evidence for a constrained history of host plant use

This study reconstructs the phylogeny of Neotropical leaf beetles and reveals a complex history of host plant switches among restricted plant families.

Natural scene segmentation dynamics reveal iterative Bayesian inference

This study reveals that iterative Bayesian inference explains the spatiotemporal dynamics of natural scene segmentation by integrating visual inputs with spatial priors.