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Phylodynamic Model Adequacy Using Posterior Predictive Simulations
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Simple diagnostic statistical tests of models for DNA substitution
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Approximate Bayesian Computation (ABC) in practice
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Measurably evolving populations
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Lack of confidence in approximate Bayesian computation model choice
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Impact of the tree prior on estimating clock rates during epidemic outbreaks
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Modeling Compositional Heterogeneity
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Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies
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Phylogenetic Signal, Evolutionary Process, and Rate
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MASCOT: parameter and state inference under the marginal structured coalescent approximation
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Molecular Investigation of Human Immunodeficiency Virus (HIV) Infection in a Patient of an HIV-Infected Surgeon
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Bayesian Phylogenetic Model Selection Using Reversible Jump Markov Chain Monte Carlo
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Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods
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Estimating the Basic Reproductive Number from Viral Sequence Data
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Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics
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Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty
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Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics
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A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
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Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology
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Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
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Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
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Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
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The Structured Coalescent and Its Approximations
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Infectious Diseases of Humans
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Bayesian Model Adequacy and Choice in Phylogenetics
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Posterior Predictive Bayesian Phylogenetic Model Selection
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Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit
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Predictive Approaches to Assessing the Fit of Evolutionary Models
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Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty
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The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling
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The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic
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Real-time characterization of the molecular epidemiology of an influenza pandemic
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Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model
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Viral phylodynamics and the search for an ‘effective number of infections’
inferredcites →https://doi.org/10.1101/050211openalex-snapshot
Assessing the accuracy of Approximate Bayesian Computation approaches to infer epidemiological parameters from phylogenies
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Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA
inferredcites →https://doi.org/10.1111/j.2044-8317.2011.02037.xopenalex-snapshot
Philosophy and the practice of Bayesian statistics
inferredcites →https://doi.org/10.1111/mec.13586openalex-snapshot
Inferences from tip‐calibrated phylogenies: a review and a practical guide
inferredcites →https://doi.org/10.1111/mec.13590openalex-snapshot
Assessing the performance of DNA barcoding using posterior predictive simulations
inferredcites →https://doi.org/10.1126/science.1065889openalex-snapshot
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
inferredcites →https://doi.org/10.1126/science.1090727openalex-snapshot
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
inferredcites →https://doi.org/10.1126/science.1259657openalex-snapshot
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110411-160331openalex-snapshot
Evolutionary Inferences from Phylogenies: A Review of Methods
inferredcites →https://doi.org/10.1186/1471-2156-9-68openalex-snapshot
Fully Bayesian tests of neutrality using genealogical summary statistics
inferredcites →https://doi.org/10.1186/1471-2350-9-68openalex-snapshot
Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1) gene is not associated with preeclampsia
inferredcites →https://doi.org/10.1186/s12862-017-0890-6openalex-snapshot
bModelTest: Bayesian phylogenetic site model averaging and model comparison
inferredcites →https://doi.org/10.1214/aos/1176346785openalex-snapshot
Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician
inferredcites →https://doi.org/10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25fopenalex-snapshot
Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data
inferredcites →https://doi.org/10.1371/currents.outbreaks.6f7025f1271821d4c815385b08f5f80eopenalex-snapshot
Phylodynamic Analysis of Ebola Virus in the 2014 Sierra Leone Epidemic
inferredcites →https://doi.org/10.1371/journal.pcbi.1002835openalex-snapshot
Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1005416openalex-snapshot
Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
inferredcites →https://doi.org/10.1371/journal.pcbi.1006546openalex-snapshot
Bayesian phylodynamic inference with complex models
inferredcites →https://doi.org/10.3102/10769986006004377openalex-snapshot
Estimation in Parallel Randomized Experiments
inferredcites →https://doi.org/10.3389/fmicb.2016.00067openalex-snapshot
Applications of Bayesian Phylodynamic Methods in a Recent U.S. Porcine Reproductive and Respiratory Syndrome Virus Outbreak
inferredcites →https://doi.org/10.3929/ethz-b-000081901openalex-snapshot
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
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Infectious Diseases of Humans: Dynamics and Control
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
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Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
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Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
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Estimating Evolutionary Rates and Timescales from Time-Stamped Data
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When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis
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Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves
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Squaring within the Colless index yields a better balance index
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Prediction on influenza-like virus pathogen and its effects on prognosis of patients with community acquired pneumonia under long and short term memory neural network model
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Assessing model adequacy leads to more robust phylogeographic inference
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The build-up of the present-day tropical diversity of tetrapods
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ReMASTER: improved phylodynamic simulation for BEAST 2.7
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Bayesian phylogenetic analysis of linguistic data using BEAST
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Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families
inferred← citeshttps://doi.org/10.1093/molbev/msae073openalex-snapshot
Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories
inferred← citeshttps://doi.org/10.1093/molbev/msag133openalex-snapshot
The Phylodynamic Threshold of Measurably Evolving Populations
inferred← citeshttps://doi.org/10.1093/sysbio/syad010openalex-snapshot
Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools
inferred← citeshttps://doi.org/10.1093/sysbio/syad075openalex-snapshot
The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference
inferred← citeshttps://doi.org/10.1093/ve/veac045openalex-snapshot
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications
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Model design for nonparametric phylodynamic inference and applications to pathogen surveillance
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TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data
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A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites
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Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus)
inferred← citeshttps://doi.org/10.1101/2023.03.06.531416openalex-snapshot
adequaSSE: Model Adequacy Testing for Trait-Dependent Diversification Models
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Bayesian phylodynamics of early vertebrate development in BEAST 2
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Skeletons in the Forest: Using Entropy-Based Rogue Detection on Bayesian Phylogenetic Tree Distributions
inferred← citeshttps://doi.org/10.1111/2041-210x.13514openalex-snapshot
Quantifying the impact of an inference model in Bayesian phylogenetics
inferred← citeshttps://doi.org/10.1144/sp549-2023-174openalex-snapshot
Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth–death skyline model
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Testing adequacy for DNA substitution models
inferred← citeshttps://doi.org/10.1186/s12859-020-3405-1openalex-snapshot
On Sackin’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
inferred← citeshttps://doi.org/10.12688/openreseurope.16679.4openalex-snapshot
Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
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The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand
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Speciation and the error we make in phylogenetic inference
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The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic
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Computational Approaches and Challenges to Developing Universal Influenza Vaccines
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Squaring within the Colless index yields a better balance index
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Additional file 1 of On Sackin’s original proposal: the variance of the leaves’ depths as a phylogenetic balance index
inferred← citeshttps://doi.org/10.7287/peerj.13910v0.1/reviews/1openalex-snapshot
Peer Review #1 of "A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.13910v0.1/reviews/2openalex-snapshot
Peer Review #2 of "A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.13910v0.2/reviews/1openalex-snapshot
Peer Review #1 of "A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.13910openalex-snapshot
A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree
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Posterior simulation-based calibration tests of phylogenetic dating methods
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