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PCA outperforms popular hidden variable inference methods for molecular QTL map**
BackgroundEstimating and accounting for hidden variables is widely practiced as an important step in molecular quantitative trait locus (molecular...
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Flexible social inference facilitates targeted social learning when rewards are not observable
Groups coordinate more effectively when individuals are able to learn from others’ successes. But acquiring such knowledge is not always easy,...
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A Guide to Phylogenomic Inference
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes....
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A robust and accurate single-cell data trajectory inference method using ensemble pseudotime
BackgroundThe advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in...
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Name-based demographic inference and the unequal distribution of misrecognition
Academics and companies increasingly draw on large datasets to understand the social world, and name-based demographic ascription tools are...
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Integration of Boolean and Bayesian Networks
One great challenge in biological study is to identify the complex gene regulation networks. For decades, scientists have developed different methods...
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Forensic biogeographical ancestry inference: recent insights and current trends
BackgroundAs a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in...
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BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data
BackgroundGenome-wide association studies (GWASes) aim to identify single nucleotide polymorphisms (SNPs) associated with a given phenotype. A common...
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The covariance environment defines cellular niches for spatial inference
A key challenge of analyzing data from high-resolution spatial profiling technologies is to suitably represent the features of cellular neighborhoods...
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Species Tree Inference with SNP Data
While the inference of species trees from molecular sequences has become a common type of analysis in studies of species diversification, few...
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Bayesian approach for evaluation of lactation curve in cross bred cattle based on monthly and bimonthly test day milk yield
In field progeny testing program milk recording at monthly or bimonthly intervals and prediction of first lactation 305-day milk yield (FL305DMY)...
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Improved genomic prediction using machine learning with Variational Bayesian sparsity
BackgroundGenomic prediction has become a powerful modelling tool for assessing line performance in plant and livestock breeding programmes. Among...
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CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Finding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework, CoCoA-diff, that prioritizes disease...
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Characterization of Achromadora porosa sp. n. (Chromadorida: Achromadoridae) from the coal mines, with a detailed inference on the phylogeny of the group and the relationships between congeners
A new species, Achromadora porosa , is described and illustrated based on morphology, morphometric and molecular characterization supplemented with...
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Updated knowledge in the estimation of genetics parameters: a Bayesian approach in white oat (Avena sativa L.)
The present study aimed to implement a Bayesian framework for genetic analysis in crop species breeding and present different procedures for...
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Detecting social-ecological resilience thresholds of cultural landscapes along an urban–rural gradient: a methodological approach based on Bayesian Networks
ContextThe difficulty of analysing resilience and threshold responses to changing environmental drivers becomes evident in the social-ecological...
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Bayesian Cross-Validation Comparison of Amino Acid Replacement Models: Contrasting Profile Mixtures, Pairwise Exchangeabilities, and Gamma-Distributed Rates-Across-Sites
Models of amino acid replacement are central to modern phylogenetic inference, particularly so when dealing with deep evolutionary relationships....
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Bayesian analysis of dynamic phosphoproteomic data identifies protein kinases mediating GPCR responses
BackgroundA major goal in the discovery of cellular signaling networks is to identify regulated phosphorylation sites (“phosphosites”) and map them...
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On Bayesian modeling of censored data in JAGS
BackgroundJust Another Gibbs Sampling (JAGS) is a convenient tool to draw posterior samples using Markov Chain Monte Carlo for Bayesian modeling....
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Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM
BackgroundA cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an...
