Bayesian inference

Unravelling genomic and environmental contributions to nitrogen-use efficiency in tropical maize through Bayesian causal forests

This paper uses Bayesian causal forests to estimate the causal effect of nitrogen levels on maize traits, finding that environmental factors largely drive trait variation while genomic background influences baseline levels.

Efficient approximate Bayesian inference for large, heterogeneous biological datasets

The paper introduces an adaptive minibatch approach for approximate Bayesian inference, improving speed-precision tradeoffs for large, heterogeneous biological datasets.

Application of Bayesian-Derived Gene Interaction Network and Subnetwork for Classification of Idiopathic Parkinson Disease with Biomarkers

The paper develops a Bayesian gene interaction network to identify 13 genes for PD classification, achieving high AUC in a blood-based transcriptomic analysis of the PPMI cohort.

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.

Multi-Trajectory Pseudotime Inference via Permutation Factorizations

Factorizing multiple monotone pseudotimes into one shared donor permutation plus cluster-specific warps (HiP-BIND) yields Alzheimer's donor orderings agreeing better with Braak, ADNC and CERAD staging than single-trajectory B-BIND.

Prion Protein Deficiency Results in Synaptic, Neural Network and Behavioral Alterations

Lifelong prion protein (PrP) loss in mice lowers excitatory synaptic proteins, makes network bursts in mature cortical cultures rarer and neuronal activity more correlated, and increases adult dimming-disk escapes.

Estimating protein isoform abundances with PAQu

PAQu estimates protein isoform abundances using multiomic data, outperforming existing methods and revealing increased C4A isoform levels in schizophrenia.

Bayesian Inference of Gene Regulatory Networks at Stochastic Steady State

This paper introduces a Bayesian method for inferring gene regulatory networks using a Chemical Langevin Equation model, enabling structure identification and kinetic parameter estimation without observing transient dynamics.

GLORB: Robust Bayesian inference for differential expression underglobal expression shifts

GLORB improves differential expression analysis by accounting for global expression shifts, outperforming existing methods in scenarios with widespread upregulation or downregulation.

Transcriptomic and proteomic Mendelian randomization identifies putative therapeutic targets for thoracic aortic disease

This study uses Mendelian randomization to identify 28 putative causal genes for thoracic aortic disease, highlighting potential therapeutic targets.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

Bayesian model discovery for reverse-engineering biochemical networks from data

This paper introduces a Bayesian sparse likelihood-free inference method to reverse-engineer biochemical networks from single-cell data, showing high accuracy and outperforming correlation-based methods.

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.

Behavioral metabolic suppression confounds thermal performance estimates and climate vulnerability assessments in a marine ectotherm

In an undescribed intertidal Urticina anemone, heat-induced closure suppresses measured respiration, and fitted thermal performance curves place the critical thermal maximum far above the 25-30°C lethal range.

Systematic Integration of genomics with transcriptomics for the Study of Coronary Artery Disease and Subclinical Atherosclerosis

This study integrates CAD GWAS with transcriptomic data to identify genes and networks associated with CAD and subclinical atherosclerosis.

A hyperspherical deep Bayesian model for interpretable clustering and relationship prediction in microbiome multi-omics integration

DBayesCM integrates multi-omics microbiome data using a deep Bayesian model to enable interpretable clustering and relationship prediction across diseases.

Bayesian Network Analysis Identifies PREX1 as a Master Regulator of Cytoskeletal Disruption in Inflammatory Bowel Disease

A Bayesian Network-Based Framework for Causal Cancer Drug Target Discovery Integrating Patient and Cell Line Data

BayesTx identifies causal cancer drug targets by integrating patient and cell line data using Bayesian networks, ranking 47 transcription factors and validating them with survival and drug response data.

SimMapNet: A Bayesian Framework for Gene Regulatory Network Inference Using Gene Ontology Similarities as External Hint

SimMapNet improves gene regulatory network inference by integrating Gene Ontology similarities, outperforming existing methods on bacterial and fly datasets.

A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders

This paper introduces FGMB, a multi-context regulome-wide association atlas, and applies it to Alzheimer's disease to identify 327 regulatory associations and resolve 86 gene-molecular-trait pairs.

Unraveling the Genetic Overlap Between Parkinson's Disease and Schizophrenia Through Genome-wide Association and Cell-Type Specific Transcriptomic Analysis

This study identifies shared genetic loci between Parkinson's disease and schizophrenia using GWAS and scRNA-seq, highlighting RAI1's role in mitochondrial dysfunction and non-motor symptoms.

Temporally overlapping mechanisms diversify clonal B cell responses in vivo.

Single-cell RNA and BCR sequencing of infected mouse spleens shows class switching overlaps clonal expansion, GC-seeding clones also form plasmablasts, and SHM proceeds at constant rate.

Overweight status drives early tumor microenvironment reprogramming in pancreatic ductal adenocarcinoma: a cell-type-resolved Bayesian hierarchical modeling and interactome analysis

This study identifies how overweight status reprograms the pancreatic tumor microenvironment through cell-type-specific changes using Bayesian modeling and interactome analysis.

Evolutionary transitions to self-fertilization influence the inference of introgression history

This study shows that transitions to self-fertilization can mislead introgression inferences, and coalescent statistics help correct these biases in demographic models.

Bayesian Estimation of Mosaic Loss of Chromosome Y from Bulk RNA Sequencing Data

This paper develops a Bayesian method to estimate mosaic loss of chromosome Y from bulk RNA-seq data, showing it can detect large LOY events with moderate accuracy.

A Bayesian approach for identifying similar transcript dynamics using curve registration

This paper introduces a Bayesian method to align transcript dynamics across different time scales and species, enabling comparative analysis of gene expression patterns.

Leveraging cell-type specificity and similarity improves single-cell eQTL fine-mapping

The paper introduces CASE, a Bayesian framework for cell-type-specific and shared eQTL fine-mapping, showing improved performance over existing methods in simulations and real data.

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.

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.

Integrating 730,947 exome sequences with clinical literature improves gene discovery

gnomAD v4 (730,947 exomes) brings LOFTEE-2 loss-of-function annotation (0.90 precision, strict mode), missense-aware constraint, and LLM-mined literature evidence combined with constraint to rank disease genes.