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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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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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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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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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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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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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Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking

Proceedings of the National Academy of Sciences - PNAS, 2017-07, Vol.114 (29), p.E5854-E5863

2017

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Birth/birth-death processes and their computable transition probabilities with biological applications

Journal of mathematical biology, 2018-03, Vol.76 (4), p.911-944

2018

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Estimation for General Birth-Death Processes

Journal of the American Statistical Association, 2014-06, Vol.109 (506), p.730-747

2014

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Fitting and interpreting continuous-time latent Markov models for panel data

Statistics in medicine, 2013-11, Vol.32 (26), p.4581-4595

2013

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Optimal experimental design for mathematical models of haematopoiesis

Journal of the Royal Society interface, 2021-01, Vol.18 (174), p.20200729

2021

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Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

Molecular biology and evolution, 2009-04, Vol.26 (4), p.801-814

2009

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joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data

Biometrics, 2015-03, Vol.71 (1), p.90-101

2015

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

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

Estimating effective population size changes from preferentially sampled genetic sequences

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

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

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

Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking

Birth/birth-death processes and their computable transition probabilities with biological applications

Estimation for General Birth-Death Processes

Fitting and interpreting continuous-time latent Markov models for panel data

Optimal experimental design for mathematical models of haematopoiesis

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data

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