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Assessing the accuracy of Approximate Bayesian Computation approaches to infer epidemiological parameters from phylogenies

https://doi.org/10.1101/050211
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Random Forests
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Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups
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Sequential Monte Carlo without likelihoods
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Mammalian phylogeny reveals recent diversification rate shifts
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Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
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Reliable ABC model choice via random forests
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Phylogenetic tree shapes resolve disease transmission patterns
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Inferring Coalescence Times From DNA Sequence Data
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An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies
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Approximate Bayesian Computation in Population Genetics
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Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
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Estimating the Basic Reproductive Number from Viral Sequence Data
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A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
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Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission
inferredcites →https://doi.org/10.1093/molbev/msv123openalex-snapshot
Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology
inferredcites →https://doi.org/10.1093/oso/9780198545996.001.0001openalex-snapshot
Infectious Diseases of Humans
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Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot
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The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history
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"Good" and "Bad" Phenograms
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Mathematical and Computational Evolutionary Biology (2013)
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Fast Dating Using Least-Squares Criteria and Algorithms
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Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
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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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Revealing the history of infectious disease epidemics through phylogenetic trees
inferredcites →https://doi.org/10.1098/rstb.2012.0208openalex-snapshot
Modelling tree shape and structure in viral phylodynamics
inferredcites →https://doi.org/10.1111/2041-210x.12350openalex-snapshot
Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
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PHYLOGENIES WITHOUT FOSSILS
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00179.xopenalex-snapshot
abc: an R package for approximate Bayesian computation (ABC)
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Regression Shrinkage and Selection Via the Lasso
inferredcites →https://doi.org/10.1117/1.2819119openalex-snapshot
Book Review: Pattern Recognition and Machine Learning
inferredcites →https://doi.org/10.1126/science.1058321openalex-snapshot
The Epidemic Behavior of the Hepatitis C Virus
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-102209-144621openalex-snapshot
Approximate Bayesian Computation in Evolution and Ecology
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
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.1002136openalex-snapshot
Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series
inferredcites →https://doi.org/10.1371/journal.pcbi.1002616openalex-snapshot
Digital Epidemiology
inferredcites →https://doi.org/10.1371/journal.pcbi.1002803openalex-snapshot
Approximate Bayesian Computation
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.1002947openalex-snapshot
Viral Phylodynamics
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.1003570openalex-snapshot
Phylodynamic Inference for Structured Epidemiological Models
inferredcites →https://doi.org/10.1515/9781400841035openalex-snapshot
Modeling Infectious Diseases in Humans and Animals
inferredcites →https://doi.org/10.1534/genetics.109.102509openalex-snapshot
Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood
inferredcites →https://doi.org/10.1534/genetics.109.106021openalex-snapshot
Phylodynamics of Infectious Disease Epidemics
inferredcites →https://doi.org/10.1534/genetics.111.134627openalex-snapshot
Complex Population Dynamics and the Coalescent Under Neutrality
inferredcites →https://doi.org/10.1534/genetics.112.143164openalex-snapshot
A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation
inferredcites →https://doi.org/10.1534/genetics.113.158808openalex-snapshot
Exact vs. Approximate Computation: Reconciling Different Estimates of Mycobacterium tuberculosis Epidemiological Parameters
inferredcites →https://doi.org/10.18637/jss.v033.i01openalex-snapshot
Regularization Paths for Generalized Linear Models via Coordinate Descent
inferredcites →https://doi.org/10.2202/1544-6115.1389openalex-snapshot
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inferredcites →https://doi.org/10.2307/j.ctvcm4gk0openalex-snapshot
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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
inferredcites →https://doi.org/10.4137/ebo.s9738openalex-snapshot
PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences
inferredcites →https://doi.org/10.48550/arxiv.1601.04096openalex-snapshot
Goodness-of-fit statistics for approximate Bayesian computation
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Pattern recognition and machine learning
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00285-020-01488-9openalex-snapshot
On the minimum value of the Colless index and the bifurcating trees that achieve it
inferred← citeshttps://doi.org/10.1093/sysbio/syy048openalex-snapshot
Phylodynamic Model Adequacy Using Posterior Predictive Simulations
inferred← citeshttps://doi.org/10.1101/2023.10.13.562305openalex-snapshot
Identifying summary statistics for approximate Bayesian computation in a phylogenetic island biogeography model
inferred← citeshttps://doi.org/10.1186/s12862-018-1210-5openalex-snapshot
Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
inferred← citeshttps://doi.org/10.48550/arxiv.2007.14731openalex-snapshot
Squaring within the Colless index yields a better balance index
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.