Using phylogenetic summary statistics for epidemiological inference

Genomic Epidemiology Analysis of Infectious Disease Outbreaks ...

Phylogenetic inference using RevBayes. Cur- rent Protocols in Bioinformatics ... Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Genomic epidemiology of superspreading events in Austria reveals ...

... epidemiological clusters. Integration of the phylogenetic analysis of Austrian SARS-CoV-2 sequences with epidemiological data resulted in strong overlap of ...

What is Phylogenetic Analysis? - News-Medical

A more accurate estimation of the evolutionary relationship among species is now possible in a molecular phylogenetic analysis using gene sequencing data. Also, ...

Evolutionary Dynamics and Molecular Epidemiology of Viruses

The most popular way to do so is by using phylogenetic and phylodynamic methods. These allow us to reconstruct how individual pathogens isolated from different ...

A scalable analytical approach from bacterial genomes to ... - Journals

Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which ...

Epidemiological and phylogenetic analyses of COVID-19 in Africa ...

Phylogenetic reconstruction of genomic data can provide epidemiological inferences about time of pathogen introduction, epidemic growth rate ...

Genomic epidemiology of the first two waves of SARS-CoV-2 ... - eLife

Although in an earlier pre-print version of this analysis using data downloaded in ... phylogenetic inference in the genomic era. Molecular ...

Explaining the geographic spread of emerging epidemics: a ...

Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance ...

Inferring epidemiological parameters from phylogenies using ...

Here, we present a new regression-based Approximate Bayesian Computation (ABC) approach, which we base on a large variety of summary statistics ...

Phylogenetic inference of pneumococcal... | Wellcome Open Research

Therefore, we conducted a pilot study to test the ability to infer who infected whom from cross-sectional pneumococcal sequences using ...

Phylogenetic analysis of SARS-CoV-2 in Boston highlights ... - Science

Using ancestral trait inference, the authors identified several importation events, further investigated the context and contribution of particular ...

Chapter 7 Tools and methods | An applied genomic epidemiological ...

Selecting appropriate contextual data to include in a phylogenetic analysis can be a bit of an art, although as you do it more frequently you will begin to ...

[1306.3427] Phylogenetic analysis accounting for age-dependent ...

The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework ...

Structural modeling and phylogenetic analysis for infectious disease ...

2019). In infectious disease epidemiology, genetic sequences of pathogens are an increasingly important source of information. The pathogenic ...

Phylogenetic analysis of SARS-CoV-2 - Imperial College London

Genetic data can give insights into the evolving epidemic which are not always apparent from the epidemiological data alone. As a virus is ...

Philosophical Transactions of the Royal Society B: Biological Sciences

Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic ...

Available CRAN Packages By Name

... Inference for Mediation Analysis with Enhanced Statistical Power. abind ... using B-Splines. abstr, R Interface to the A/B Street Transport System ...

Expasy: SIB Swiss Institute of Bioinformatics

ISA. Finding modules in gene expression data ... Phylogeny. Software tool. REALPHY. Inference of phylogenetic trees from genome data. Proteins & Proteomes.

Epidemiological inference for emerging viruses using segregating ...

Our approach presented here indicates that inference approaches that rely on simple population genetic summary statistics can be informative of epidemiological ...

Theo Sanderson

I am an Assistant Professor at the London School of Hygiene and Tropical Medicine where I lead a research group working on large-scale viral genomics.