Bayesian inference

The conquest and diversification of leafy spurges across the Holarctic and beyond: biogeography and evolution of life-history of Euphorbia subgenus Esula

This study investigates the biogeography and evolution of life-history traits in Euphorbia subgenus Esula, showing that perenniality and range expansion are linked to diversification.

Genetic and Proteomic Investigation of the Smoking-Parkinson Disease Association

This study investigates the causal relationship between smoking and Parkinson's disease using genetic and proteomic data, identifying shared biological pathways and potential therapeutic targets.

Zero-inflated Bayesian factor analysis model with skew-normal priors for modeling microbiome data

The paper introduces a Bayesian factor analysis model with skew-normal priors to improve microbiome data analysis by addressing zero inflation and skewness.

Polygenic risk scores enhance the identification of carriers of monogenic forms of idiopathic pulmonary fibrosis

This study shows that polygenic risk scores improve the identification of IPF patients carrying rare variants associated with monogenic pulmonary fibrosis.

Efficient Bayesian Phylogenetics under the Infinite Sites Model

The paper introduces inPhynite, an efficient Bayesian phylogenetics algorithm under the infinite sites model, achieving 225x speedup without accuracy loss on large datasets.

Reconstructing intra-tumor fitness landscapes from scSeq CNA genotypes via simulation-based Bayesian inference and Deep Learning

This paper infers intra-tumor selection coefficients from clonal CNA profiles using a simulation-based Bayesian framework and deep learning, achieving better performance than baseline methods.

Convergent and selective representations of pain, appetitive processes, aversive processes, and cognitive control in the insula

The paper identifies convergent and selective functional zones in the insula using fMRI data, revealing a hierarchical convergence architecture across pain, appetitive, aversive, and cognitive control domains.

Sex-Stratified Multi-Omics Identifies Sexually Dimorphic Molecular Targets in Parkinsons Disease

This study identifies sex-specific molecular targets in Parkinson's disease through multi-omic integration, revealing sexually dimorphic pathways and gene associations.

IEKB: a comprehensive knowledge base for inner ear genetics integrating curated associations, cochlear interactions, Bayesian candidate prioritisation, explainable dark-gene support relations, and a scientific entity network

IEKB is a database that integrates curated gene-phenotype-disease associations, cochlear gene interactions, and a scientific network for inner-ear genetics research.

A joint Bayesian framework for modeling Plasmodium vivax transmission

This paper develops a joint Bayesian model to analyze P. vivax parasite density, gametocyte density, and mosquito infectivity, showing gametocyte density has the strongest association with infectivity.

Shared Genetic Architecture Between Kidney Function and Alzheimer Disease Across Ancestries

This paper identifies shared genetic loci between kidney function and Alzheimer disease across ancestries, revealing both horizontal and vertical pleiotropy with APOE as the only shared locus.

Spatially Varying Graphical Models for Cell-Cell Interaction Networks in Multiplexed Tissue Imaging

This paper introduces GP-GHS, a Bayesian method for inferring spatially varying cell-cell interaction networks from multiplexed tissue imaging data, identifying differentially active edges in colorectal cancer.

DenMark: A Bayesian Hierarchical Model for Identifying Cell-Density Correlated Genes from Spatial Transcriptomics

DenMark identifies genes correlated with cell density in spatial transcriptomics data using a Bayesian hierarchical model, revealing density-related biological programs across tissues.

Cross-species transmission of human hepatitis B virus to wild Neotropical primates

Sequenced HBV from wild Amazonian primates in a deforested, densely settled region matched human genotypes A and D, while pristine-forest monkeys were all negative, consistent with human-to-primate spillover.

Isoform-Resolved Genetic Architecture of Epilepsy and SUDEP Reveals Divergent Brain and Heart Channelopathy Signatures

The paper identifies tissue- and isoform-level genetic regulation differences between epilepsy and SUDEP, revealing distinct cardiac and neuronal gene expression patterns.

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

This paper introduces a Bayesian Varying Coefficient Model to analyze time-related phenotypic plasticity across species, revealing dynamic QTLs and improving phenotypic variance explanation.

Functionality-Informed Fine-Mapping Dissects Common Variant Contributions to Coronary Artery Disease and Identifies Causal Variants and Pathways

This study uses functionality-informed fine mapping to identify causal variants and pathways contributing to coronary artery disease risk using GWAS summary statistics from over a million individuals.

Limitations of Variational Laplace-based Dynamic Causal Modelling for Multistable Cortical Circuits

This study shows that variational Laplace-based DCM struggles to accurately estimate connectivity parameters in multistable neural systems with complex dynamics.

AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network

ROCKET refines AlphaFold2 predictions against crystallographic, cryo-EM and cryo-ET data by gradient descent on MSA cluster profiles, capturing loop flips and domain shifts without retraining.

Mixture Models Unveil the Origin of the Enigmatic Satyrine Butterfly Genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae).

The paper uses genomic data and phylogenetic methods to resolve the origins of two Satyrinae butterfly genera, finding Calisto originated from Old World ancestors and Llorenteana split early in Euptychiina.

Estimating Bayesian phylogenetic information content using geodesic distances

The paper introduces a Bayesian measure of phylogenetic information content using geodesic distances and demonstrates its application with simulated and empirical examples.

Noise Correlation Length Distinguishes Neurometabolic Protection from Vulnerability Across HIV Infection Phases

The paper identifies noise correlation length as a marker distinguishing neurometabolic protection from vulnerability in HIV infection phases using Bayesian inference and enzyme kinetics modeling.

Multi-trait colocalisation using MystraColoc: improved performance, deeper insights

The paper introduces MystraColoc, a Bayesian algorithm for multi-trait colocalisation, showing improved performance in clustering genetic association signals across GWAS datasets.

Modeling Rotational Fluoroquinolone Therapy as a Novel Treatment for Ophthalmic MRSA Infections

The paper evaluates rotational fluoroquinolone therapy for ophthalmic MRSA infections, showing it improves bacterial clearance compared to monotherapy by leveraging resistance profiles and pharmacokinetics.

Explaining attractive and repulsive biases in the subjective visual vertical

The paper explains both attractive and repulsive biases in the subjective visual vertical using a Bayesian model, resolving a long-standing question in perceptual psychology.

Bayesian marker-based principal component ridgeregression - a flexible multipurpose framework forquantitative genetics in wild study systems

This paper introduces a Bayesian marker-based principal component ridge regression framework for estimating quantitative genetic parameters in wild study systems, showing efficient estimation of additive genetic variance and accurate breeding value prediction.

GraphBG: Fast Bayesian Domain Detection via Spectral Graph Convolutions for Multi-slice and Multi-modal Spatial Transcriptomics

GraphBG detects spatial domains in multi-slice and multi-modal spatial transcriptomics data using spectral graph convolutions and Bayesian modeling, achieving high accuracy and scalability.

Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference

The paper develops a Bayesian method to infer inheritance patterns of allelic imbalance across trios, improving ASE estimation and linking it to chromatin state and causal variants.

A Neural Population Code for Value in Human Orbitofrontal Cortex.

The paper investigates the neural code for value in the human orbitofrontal cortex and finds that a probabilistic, non-linear population code represents both value and its uncertainty.

Biallelic variants in RNU2-2 cause the most prevalent known recessive neurodevelopmental disorder

The paper identifies biallelic variants in RNU2-2 as a common cause of recessive neurodevelopmental disorders, showing higher prevalence than the dominant form in England.