Using phylogenetic summary statistics for epidemiological inference

Summary statistics provide a straightforward way of extracting information from a phylogenetic tree, but the relationship between these ...

Branch lengths (patristic distances) denote the amount of evolutionary change or time between two nodes. Tree depth or tree height refers to the ...

Using phylogenetic summary statistics for epidemiological inference ...

... use of phylogenetic analysis to get valuable epidemiological insights. We conducted a simulation study to evaluate 74 phylogenetic summary statistics and ...

Deep learning from phylogenies to uncover the epidemiological ...

This scheme relies on the definition of a set of summary statistics aimed at representing a phylogeny and on a distance measure between trees.

Using an Epidemiological Model for Phylogenetic Inference Reveals ...

The chain of transmission can in principle be reconstructed with phylogenetic methods which analyze the evolutionary history using pathogen sequence data. The ...

bxv_genetics on X: "Using phylogenetic summary statistics for ...

Using phylogenetic summary statistics for epidemiological inference https://t.co/VKzwkVb3xo.

Estimating Epidemic Incidence and Prevalence from Genomic Data

Here, we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model ...

[PDF] Using an Epidemiological Model for Phylogenetic Inference ...

This article presents the first fully stochastic implementation of a classical epidemiological model for phylogenetic inference and thereby addresses a key ...

Using an Epidemiological Model for Phylogenetic Inference Reveals ...

analyze the evolutionary history using pathogen sequence data. The ... explain the data equally well (recall that our data are essentially a LTT plot).

Inferring epidemiological parameters from phylogenies using ...

Overall, ABC based on a large variety of summary statistics and a regression method able to perform variable selection and avoid overfitting is a promising ...

Phylogenetic and phylodynamic approaches to understanding and ...

Phylodynamic studies have provided other parameter estimates that are useful for understanding virus biology and transmission, or for use as ...

[PDF] Inferring epidemiological parameters from phylogenies using ...

A new regression-based Approximate Bayesian Computation (ABC) approach, which is based on a large variety of summary statistics intended to capture the ...

Approaches and challenges to inferring the geographical source of ...

Phylogeographic methods that use epidemiological and genomic data obtained from surveillance enable us to infer the history of spatial ...

Employing phylogenetic tree shape statistics to resolve the ...

Determining whether a population is structured or not is useful in informing the type of phylogenetic methods to be used in a given study. We ...

Using phylogenetics to infer HIV-1 transmission direction ... - PNAS

With epidemiological and clinical information typically unavailable to infer transmission direction, phylogenetic analysis of pathogen sequence data offers an ...

Phylogenetic interpretation during outbreaks requires caution - Nature

How viruses are related, and how they have evolved and spread over time, can be investigated using phylogenetics.

31st International Dynamics & Evolution of Human Viruses

USING PHYLOGENETIC TREE SUMMARY STATISTICS FOR EPIDEMIOLOGICAL INFERENCE AND CALIBRATION · Speaker · Primary authors · Presentation materials.

Phylogenetic and epidemic modeling of rapidly evolving infectious ...

We survey the Bayesian phylogenetic approach to epidemic modeling of infection diseases and describe the contrasts it provides to mathematical epidemiology.

Genomic Epidemiology Archives - IDMOD

Genomic Epidemiology. Using phylogenetic summary statistics for epidemiological inference. Since the coining of the term phylodynamics, the use of phylogenies ...

Genomic Epidemiology Analysis of Infectious Disease Outbreaks ...

In order to draw epidemiological interpretations, it is especially useful to consider a dated phylogeny (Biek, Pybus, Lloyd-Smith, & Didelot, ...