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19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology

Systematic biology, 2020-03, Vol.69 (2), p.209

2020

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A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

PLoS computational biology, 2020-08, Vol.16 (8), p.e1008030

2020

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Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007999-e1007999

2020

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Fast, accurate and simulation-free stochastic mapping

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2008-12, Vol.363 (1512), p.3985

2008

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Estimating effective population size changes from preferentially sampled genetic sequences

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007774-e1007774

2020

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Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004789-e1004789

2016

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Predictors of Test Positivity, Mortality, and Seropositivity during the Early Coronavirus Disease Epidemic, Orange County, California, USA

Emerging infectious diseases, 2021-10, Vol.27 (10), p.2604-2618

2021

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Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

Proceedings of the National Academy of Sciences - PNAS, 2014-11, Vol.111 (44), p.E4736-E4742

2014

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Predicting B cell receptor substitution profiles using public repertoire data

PLoS computational biology, 2018-10, Vol.14 (10), p.e1006388-e1006388

2018

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Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Emerging infectious diseases, 2023-05, Vol.29 (5), p.977-987

2023

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Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori

BMC genomics, 2018-11, Vol.19 (1), p.835-835, Article 835

2018

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A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts

Biometrics, 2022-12, Vol.78 (4), p.1530-1541

2022

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High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

Proceedings of the National Academy of Sciences - PNAS, 2009-07, Vol.106 (30), p.12412-12417

2009

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Species Delimitation using Genome-Wide SNP Data

Systematic biology, 2014-07, Vol.63 (4), p.534-542

2014

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Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

Molecular biology and evolution, 2008-07, Vol.25 (7), p.1459-1471

2008

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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae)

Systematic biology, 2016-05, Vol.65 (3), p.465-477

2016

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Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors

Bayesian analysis, 2018-03, Vol.13 (1), p.225-252

2018

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phylodyn: an R package for phylodynamic simulation and inference

Molecular ecology resources, 2017-01, Vol.17 (1), p.96-100

2017

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Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications

Systematic biology, 2019-09, Vol.68 (5), p.681

2019

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Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Biometrics, 2020-09, Vol.76 (3), p.677-690

2020

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Counting labeled transitions in continuous-time Markov models of evolution

Journal of mathematical biology, 2008-03, Vol.56 (3), p.391-412

2008

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Using Genotype Abundance to Improve Phylogenetic Inference

Molecular biology and evolution, 2018-05, Vol.35 (5), p.1253-1265

2018

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An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Bioinformatics, 2015-10, Vol.31 (20), p.3282-3289

2015

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Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data

Journal of computational and graphical statistics, 2017-01, Vol.26 (4), p.918-929

2017

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Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”

Biometrics, 2020-09, Vol.76 (3), p.695-699

2020

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19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

Fast, accurate and simulation-free stochastic mapping

Estimating effective population size changes from preferentially sampled genetic sequences

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

Predictors of Test Positivity, Mortality, and Seropositivity during the Early Coronavirus Disease Epidemic, Orange County, California, USA

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

Predicting B cell receptor substitution profiles using public repertoire data

Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori

A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

Species Delimitation using Genome-Wide SNP Data

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae)

Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors

phylodyn: an R package for phylodynamic simulation and inference

Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications

Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Counting labeled transitions in continuous-time Markov models of evolution

Using Genotype Abundance to Improve Phylogenetic Inference

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data

Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”

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