Bayesian inference

How to reward animals based on their subjective percepts: A Bayesian approach to online estimation of perceptual biases.

The paper develops a Bayesian method to estimate perceptual biases in animals during task performance and adjusts rewards based on these estimates to minimize bias distortion.

Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival

The paper uses Bayesian inference to predict antibiotic survival in E. coli by integrating gene expression and growth rate data from single cells.

difFUBAR: Scalable Bayesian comparison of adaptive evolution

difFUBAR provides a scalable Bayesian method to compare adaptive evolution across different branch sets in phylogenetic trees, showing computational gains and moderate statistical benefits over existing methods.

Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations

The paper refines cryo-EM RNA structures using all-atom simulations and metainference to account for structural flexibility, revealing inaccuracies in single-structure approaches.

Autonomous adaptive optimization of NMR experimental conditions for precise inference of minor conformational states of proteins based on chemical exchange saturation transfer

The paper develops an adaptive optimization system for NMR CEST experiments to improve estimation of minor protein conformational states using Bayesian methods and MCMC.

Biophysical Modeling Uncovers Transcription Factor and Nucleosome Binding on Single DNA Molecules

The paper introduces HiddenFoot, a probabilistic model to infer TF, nucleosome, and Pol II occupancy from single-molecule data, revealing binding dynamics and heterogeneity in mouse, Drosophila, and human cells.

Bayesian Inference of Binding Kinetics from Fluorescence Time Series

This paper infers binding and unbinding rates from fluorescence time series while accounting for photobleaching using a two-stage Bayesian approach.

Transfer learning framework via Bayesian group factor analysis incorporating feature-wise dependencies

This paper introduces a Bayesian group factor analysis transfer learning framework that improves drug response prediction and tumor purity prediction across cancer datasets by modeling feature dependencies.

Incorporating gene expression and environment improves genomic prediction of wheat traits

This study improves genomic prediction of wheat traits by integrating gene expression and environmental data, showing that combining transcriptome and environment data enhances prediction accuracy.

Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty

BEASTIE improves allele-specific expression estimation by addressing phasing uncertainty and genotyping errors, enhancing accuracy in detecting rare variants.

Accurate tracking of lytic granules via simultaneous particle tracking, phase retrieval and point spread function reconstruction

This paper develops a framework for simultaneous particle tracking, phase retrieval, and PSF reconstruction to improve 3D tracking of lytic granules in T cells.

Bayesian phylodynamic inference of population dynamics with dormancy

This paper develops a Bayesian framework to infer population dynamics with dormancy using molecular sequence data under the strong seedbank coalescent model.

Sumatran orangutan mothers differ in the extent and trajectory of their expression of maternal behaviour

After controlling for confounders, 15 wild Sumatran orangutan mothers differed consistently in average expression of four of six maternal behaviours and in age-related plasticity for three.

I-SVVS: Integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data

I-SVVS improves clustering accuracy and reduces computation time for multi-omics microbiome data across soybean, mice, and human datasets.

Quantifying transcriptome turnover on phylogenies bymodeling gene expression as a binary trait

The paper develops Bayesian methods to quantify transcriptome turnover across species, finding accelerated gene expression changes in testes and accessory glands of Drosophila species.

AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks

AbBFN2 is a generative antibody foundation model that unifies diverse data sources and enables flexible conditional generation for multiple antibody design tasks.

Bridging Hearts and Muscles: Genetic Insights into Cardiac Structure and Sarcopenia

This study identifies genetic links between cardiac structure and sarcopenia using LDSC and MR, finding causal relationships and shared biological pathways.

An Eocene Origin of Passerine Birds Estimated Using Bayesian Tip Dating with Fossil Occurrences

This study estimates the origin of passerine birds in the Eocene using Bayesian tip-dating with fossil data, narrowing the gap between molecular and paleontological estimates.

BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data

BREADR estimates genetic relatedness from low-coverage genotype data using Bayesian methods and returns posterior probabilities for different degrees of relatedness.

Demonstrating the need for long inter-stimulus intervals when studying the post-movement beta rebound following a simple button press

This study shows that beta power returns to baseline levels 4-5 seconds after movement, advocating for longer inter-stimulus intervals in PMBR research.

Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing

This paper introduces SAVEMONEY, a computational method that enables cost-effective multiplex plasmid sequencing using nanopore sequencing and Bayesian analysis.

Excitability modulations of somatosensory perception do not depend on feedforward neuronal population spikes

The paper investigates whether somatosensory perception excitability depends on feedforward neuronal spikes, finding no evidence for such a link using HFO metrics and Bayesian analysis.

Robust Bayesian Integrative Modeling of Single Cell and Spatially Resolved Transcriptomics Data

This paper introduces iMOSCATO, a Bayesian model that integrates single-cell RNA-seq and spatial transcriptomics data to decompose cell-type compositions and detect spatial domains.

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model

The paper presents a Bayesian method for inferring pathogen migration history and population sizes using the structured coalescent model, validated on simulated and real datasets.

Phasing in and out of phytophagy: phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements

This study presents a molecular phylogeny of Eurytomidae wasps using Ultraconserved Elements, revealing multiple instances of secondary phytophagy evolution.

Bayesian Multi-Study Non-Negative Matrix Factorization for Mutational Signatures

This paper introduces a Bayesian multi-study NMF method to identify common and condition-specific mutational signatures across multiple datasets.

Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: a Bayesian analysis using logic-based network models.

This paper uses a Bayesian network model to analyze how mechanical loading and hormonal changes contribute to eccentric hypertrophy in volume overload, showing neurohormonal responses drive growth rather than initial stretch.

Robust Bayesian analysis of animal networks subject to biases in sampling intensity and censoring

This paper develops a Bayesian generative model to analyze animal social networks while accounting for sampling and censoring biases, showing improved performance over existing methods.

Inferring non-coding RNA regulatory network from transcriptomic data and curated databases

The paper introduces CAR-NET, a framework for inferring non-coding RNA regulatory networks using transcriptomic data and curated databases, showing its effectiveness in simulations and case studies.

Blood pressure, cardiometabolic traits and cardiovascular events in women with uterine fibroids: a genetic correlation and Mendelian randomization study

This study investigates genetic correlations and causal relationships between uterine fibroids and cardiometabolic traits using genetic data and Mendelian randomization.