Nested sampling for physical scientists

G Ashton, N Bernstein, J Buchner, X Chen… - Nature Reviews …, 2022 - nature.com
Abstract This Primer examines Skilling's nested sampling algorithm for Bayesian inference
and, more broadly, multidimensional integration. The principles of nested sampling are …

Bayesian model averaging: A systematic review and conceptual classification

TM Fragoso, W Bertoli… - International Statistical …, 2018 - Wiley Online Library
Bayesian model averaging (BMA) provides a coherent and systematic mechanism for
accounting for model uncertainty. It can be regarded as an direct application of Bayesian …

[HTML][HTML] The NANOGrav 15 yr data set: Evidence for a gravitational-wave background

G Agazie, A Anumarlapudi, AM Archibald… - The Astrophysical …, 2023 - iopscience.iop.org
We report multiple lines of evidence for a stochastic signal that is correlated among 67
pulsars from the 15 yr pulsar timing data set collected by the North American Nanohertz …

[PDF][PDF] Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

MA Suchard, P Lemey, G Baele, DL Ayres… - Virus …, 2018 - academic.oup.com
Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package
has become a primary tool for Bayesian phylogenetic and phylodynamic inference from …

The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the substitution rate

JH Tay, AF Porter, W Wirth… - Molecular Biology and …, 2022 - academic.oup.com
The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly
generated genome data. These data have revealed the emergence of lineages with …

Model selection may not be a mandatory step for phylogeny reconstruction

S Abadi, D Azouri, T Pupko, I Mayrose - Nature communications, 2019 - nature.com
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …

The early spread and epidemic ignition of HIV-1 in human populations

NR Faria, A Rambaut, MA Suchard, G Baele, T Bedford… - science, 2014 - science.org
Thirty years after the discovery of HIV-1, the early transmission, dissemination, and
establishment of the virus in human populations remain unclear. Using statistical …

Markov chain Monte Carlo simulation using the DREAM software package: Theory, concepts, and MATLAB implementation

JA Vrugt - Environmental Modelling & Software, 2016 - Elsevier
Bayesian inference has found widespread application and use in science and engineering
to reconcile Earth system models with data, including prediction in space (interpolation) …

BayesWave analysis pipeline in the era of gravitational wave observations

NJ Cornish, TB Littenberg, B Bécsy, K Chatziioannou… - Physical Review D, 2021 - APS
We describe updates and improvements to the BayesWave gravitational wave transient
analysis pipeline, and provide examples of how the algorithm is used to analyze data from …

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

ND Grubaugh, JT Ladner, MUG Kraemer, G Dudas… - Nature, 2017 - nature.com
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital
abnormalities,. In July 2016, mosquito-borne ZIKV transmission was reported in the …