ArticleCurrent protocols2021
Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo.
Article in Current protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed.
- Comparing subsampling strategies for efficient pairwise analysis of large pathogen genomic and spatial datasets: An application to Mycobacterium tuberculosis transmission.PLoS computational biology · 2026Article
- Mapping the resistance landscape: A large-scale study of polymyxin-resistant pathogens circulating in low-and middle-income countries.Research square · 2026Article
- Clinical utility and limitations of whole-genome sequencing via nanopore technology and Bayesian modeling for outbreak transmission inference.Antimicrobial resistance and infection control · 2026Article
- A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease.Journal of molecular evolution · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Genomic inference of sites of transmission during regional spread of blaNature communications · 2026Article
- Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population.Equine veterinary journal · 2026Article
- Transmission Dynamics of Torque Teno Sus Virus 1 (TTSuV1) Between Wild and Farmed Pigs: A Molecular Tool for Monitoring Cross-Population Spillover in Swine.Microorganisms · 2025Article
- Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.Nature communications · 2025Article
- The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission.PLoS computational biology · 2025Article
- Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.PLoS computational biology · 2025Article
- Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.Molecular biology and evolution · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.Research square · 2025Article
- JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.medRxiv : the preprint server for health sciences · 2025Article
- Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.bioRxiv : the preprint server for biology · 2024Article
- Sustained transmission over two decades of a previously unrecognised MPT64 negativeThe Lancet regional health. Western Pacific · 2024Article
- Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State.BMC public health · 2024Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.