Bayesian inference

Sex differences in the pleiotropy of hearing difficulty with imaging-derived phenotypes: a brain-wide investigation.

This study investigates sex differences in the genetic pleiotropy between hearing difficulty and brain imaging-derived phenotypes using large-scale GWAS data and multiple analytical methods.

Tracking subjects' strategies in behavioural choice experiments at trial resolution

This paper introduces a probabilistic method to track choice strategies in decision-making tasks at trial resolution, showing it identifies learning and exploratory strategies across species and synthetic agents.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

The paper reconstructs the evolutionary history of Betula pubescens, showing it originated from an autoploid event and later hybridized with multiple species, with introgressed alleles contributing to climate adaptation and meiotic stability.

Force, angle, and velocity parameters of finger movements are reflected in corticospinal excitability

The paper investigates which movement parameters are reflected in corticospinal excitability using MEP amplitude and finds that force, angle, and velocity are all reflected when EMG is considered.

Learning Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning

The paper develops a Bayesian method using Gaussian Processes to map diffusion coefficients continuously across membranes from particle trajectories without data binning.

Resistance Gene Association and Inference Network (ReGAIN): A Bioinformatics Pipeline for Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens

ReGAIN identifies and maps resistance gene networks in bacterial pathogens using Bayesian networks, providing insights into co-occurrence patterns and antimicrobial resistance dynamics.

Blood-based DNA methylation study of alcohol consumption

This paper develops an epigenetic score to objectively measure alcohol consumption using blood-based DNA methylation and validates it across multiple cohorts, finding associations with brain health metrics.

Power analysis for human melatonin suppression experiments

This paper presents a Bayesian framework and Shiny app for power analysis in melatonin suppression experiments, accounting for individual variability and experimental parameters.

SHARE-Topic: Bayesian Inerpretable Modelling of Single-Cell Multi-Omic Data

SHARE-Topic is a Bayesian model for multi-omic single-cell data that identifies interpretable patterns of co-variation between gene expression and epigenomic layers, demonstrating its utility in B-cell lymphoma analysis.

Optimizing representations for integrative structural modeling using Bayesian model selection

This paper introduces NestOR, a Bayesian method to automatically select optimal coarse-grained representations for integrative structural modeling, improving accuracy and efficiency.

PeakPerformance - a tool for Bayesian inference-based fitting of LC-MS/MS peaks

PeakPerformance automates LC-MS/MS peak fitting using Bayesian inference, providing uncertainty quantification and reducing false positives/negatives.

Signaling pathway evaluation of leading ATRi, PARPi and CDK7i cancer compounds targeting the DNA Damage Response using Causal Inference

This paper uses causal inference to evaluate resistance mechanisms of DDR inhibitors in cancer, identifying pathway-specific resistance drivers and potential combination therapies.

SAFE-OPT: A Bayesian optimization algorithm for learning optimal deep brain stimulation parameters with safety constraints

SAFE-OPT is a Bayesian optimization algorithm that incorporates safety constraints to find optimal deep brain stimulation parameters without harmful side-effects, validated in rodent studies.

Bayesian Modelling Approaches for Breath-Hold Induced Cerebrovascular Reactivity

This paper introduces a variational Bayesian approach for cerebrovascular reactivity mapping using fMRI data and compares it to a standard GLM method, showing improved computational efficiency and handling of noisy voxels.

Exploring muscle recruitment by Bayesian methods during motion

This paper uses Bayesian methods to model muscle activation patterns during motion, comparing prior models with observed data to understand how the musculoskeletal system selects activation strategies.

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

The paper introduces an R package called chronospace to visualize and quantify the sensitivity of divergence time estimates to methodological choices in phylogenetic analysis.

BayVarC: an ultra-sensitive ctDNA variant caller using Bayesian approach

BayVarC is a Bayesian variant caller for liquid biopsy that detects low-frequency variants with high sensitivity and low false positive rate.

A hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data

Perceptual error based on Bayesian cue combination drives implicit motor adaptation

This paper proposes a perceptual error framework based on Bayesian cue combination to explain implicit motor adaptation, showing it outperforms sensory error-based models.

Linking phenotypic and genotypic variation: a relaxed phylogenetic approach using the probabilistic programming language Stan

The paper introduces a Bayesian method to link sequence evolution and phenotypic variation using Stan, showing that faster sequence evolution correlates with faster phenotypic evolution.

A Bayesian overhaul of thermal tolerance landscape models: Predicting ectotherm lethality buildup and survival amid heatwaves

This study improves thermal tolerance models using Bayesian methods to predict ectotherm survival during heatwaves, showing better alignment with experimental data.

Comprehensive epitope mutational scan database enables accurate T cell receptor cross-reactivity prediction

The paper introduces a database of TCR-peptide mutational assays and a Bayesian model to predict TCR cross-reactivity, showing improved performance over existing methods.

Bayesian Estimation of Cooccurrence Affinity with Dyadic Regression

This paper improves co-occurrence affinity estimation using Bayesian dyadic regression and presents a software package for ecological analysis.

"Bayesian anchoring" and the fourfold pattern of risk attitudes

This paper models decision-making under uncertainty using Bayesian anchoring to explain the fourfold pattern of risk attitudes and related effects observed in experiments.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

BeXY is a Bayesian method that jointly infers sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data, outperforming existing methods in accuracy and power.

A novel Bayesian fine-mapping model using a continuous global-local shrinkage prior with applications in prostate cancer analysis

This paper introduces a Bayesian fine-mapping model, h2-D2, which outperforms existing methods in identifying causal variants and applies it to prostate cancer, discovering new variants and associated genes and pathways.

Bayesian modeling disentangles language versus executive control disruption in stroke

This study uses Bayesian modeling to analyze stroke patient data and identifies distinct brain regions associated with language and executive control impairments.

MetaNorm: Incorporating Meta-analytic Priors into Normalization of NanoString nCounter Data

MetaNorm improves normalization of NanoString nCounter data by incorporating meta-analytic priors, enhancing stability and computational efficiency.

Complex Reticulation in Backbone Subfamily Relationships in Leguminosae

The paper resolves conflicting phylogenetic relationships in legumes by identifying independent whole genome duplications in six subfamilies, with evidence of ancient hybridization in three.