Bayesian inference

The Segmentome: a novel representation of the DNA methylome identified by a Bayesian HMM framework

The paper introduces the segmentome, a DNA methylome representation using a Bayesian HMM, and shows it can group cell types and identify cell-of-origin in DNA samples.

Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech

The paper identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

Gene-level evolutionary conservation and human constraint decline at comparable rates across the age of onset of Mendelian disease

The paper compares the rate of decline in gene-level evolutionary conservation and human constraint scores with disease onset age across Mendelian diseases.

Empirical Bayes Estimation of Sample-Specific Correlation Networks for Cross-Sectional and Longitudinal Omics Data

PRISM estimates sample-specific correlation networks for cross-sectional and longitudinal omics data, improving accuracy and uncertainty quantification over existing methods.

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

The limits of Bayesian estimates of divergence times in measurably evolving populations

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

The prevalence of protein misfolding as a mechanism for hereditary deafness

The paper evaluates computational frameworks to prioritize pathogenic variants in deafness-associated genes, identifying 28,866 VUSs with high pathogenicity probability and improving diagnoses for 12 patients.

SMORE: joint dimension reduction and cell population discovery on single-cell methylome data

SMORE performs joint dimensionality reduction and cell population discovery on single-cell methylome data, accurately recovering population structures in human datasets.

decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylomes

The paper introduces decemedip, a Bayesian hierarchical model for cell type deconvolution of MeDIP-seq data, showing its accuracy and utility in identifying methylation signatures.

Probabilistic mapping of sub-genic intolerance reveals functional and disease-critical protein regions

PRIME is a Bayesian model that improves estimation of sub-genic intolerance by sharing information across regions, identifying disease-critical protein regions and enhancing variant interpretation.

Holocene North Asian gene flow and cryptic substructure in the genome history of Nilgiri tribes

This study analyzes the genomic history of Nilgiri tribes, revealing fine-scale substructure and complex Holocene gene flow patterns.

Activity-level evaluation of DNA transfer to stockings: comparisonof HaloGen with simplified contributor-based approaches

This paper evaluates DNA transfer to stockings using HaloGen, showing its ability to distinguish active contact from social contact, while simplified methods lose important information.

Synchronizing speciation, extinction, and dispersal to island paleodynamics through Bayesian phylogenetics in a Hawaiian plant radiation

The paper introduces a Bayesian phylogenetic framework to infer divergence times, ancestral ranges, and diversification rates in Hawaiian plants without fossil calibration.

A Bayesian Multi-Species Approach Infers Gene Regulatory Networks Across Non-Model Organisms

This paper introduces GRN-BMuSeR, a Bayesian multi-species method for gene regulatory network inference, showing improved performance in bacteria and novel predictions in archaea.

Genetically nominated cardiovascular-kidney-metabolic features are not consistently more responsive to weight-loss and cardiometabolic interventions

This study shows that molecular features genetically linked to cardiovascular-kidney-metabolic diseases do not consistently show greater response to weight-loss and cardiometabolic interventions compared to other features.

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

This study reconstructs the evolution of multicellularity and reproductive strategies in Xanthophyceae using phylogenomic data, showing multiple transitions to multicellularity linked to changes in propagule types.

Compartment-dependent selection regimes maintain the G-quadruplex paradox across the eukaryotic kingdoms

The paper investigates the G4 paradox across eukaryotic genomes, finding compartment-dependent selection regimes that maintain G4 structures in regulatory regions and suppress them in coding sequences.

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multi-Layered Constraints on the Evolution of Viral and Mammalian Genomes

This paper introduces B-STILL, a Bayesian framework to detect functional constraints in genomes by analyzing evolutionary stasis, identifying significant clusters of invariant sites in viral and mammalian genomes.

A hierarchical clock-mixture model for Bayesian phylogenetic dating

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

Ancient Rapid Radiation Underlies Persistent Phylogenomic Conflict in Early Collembola Diversification

This study resolves phylogenetic conflicts in Collembola by showing ancient rapid radiation and incomplete lineage sorting, supporting Poduromorpha as the earliest-diverging lineage.

Indirect genomic effects shape cancer risk across species

This study identifies genes linked to cancer risk variation across species, showing indirect effects on body size dominate cancer suppression, while direct effects increase tumour prevalence.

The phylodynamic threshold of measurably evolving populations

This study shows that determining if a population is measurably evolving or has reached the phylodynamic threshold depends on model assumptions and sampling strategies, not just data, and emphasizes prior sensitivity over tests of temporal signal.

Bayesian optimisation and graph-based rheology enable sequence-dependent modelling of DNA materials

This paper uses Bayesian optimisation and graph-based rheology to model DNA materials by linking sequence design to material properties.

A modular Bayesian framework for inferring transmission networks from polyclonal infections, with application to Plasmodium falciparum

This paper introduces a Bayesian framework for inferring transmission networks from polyclonal infections, demonstrating its application to Plasmodium falciparum with high precision and recall in simulations.

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

PHYFUM reconstructs the evolutionary history of normal and pre-malignant tissues using methylation data, revealing early gland divergence in the gut and later divergence in the endometrium.

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.

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.

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.

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

This study reconstructs the evolutionary history of trematode parasitic strategies using mitogenomic and nuclear genomic data, finding that ancestral trematodes had direct life cycles with no intermediate hosts.

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.