ArticleBMC bioinformatics2018
outbreaker2: a modular platform for outbreak reconstruction.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Probing Genomic Diversity ofFoods (Basel, Switzerland) · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population.Equine veterinary journal · 2026Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.Nature communications · 2025Article
- ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.PLoS computational biology · 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
- Multiple incursions of foot-and-mouth disease virus serotype O into the Republic of Korea between 2010 and 2019.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2024Article
- Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.PLoS computational biology · 2024Article
- Approaches forAmerican journal of respiratory and critical care medicine · 2024Article
- Article
- Expanding the use of mathematical modeling in healthcare epidemiology and infection prevention and control.Infection control and hospital epidemiology · 2024Review
- Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.Microbial genomics · 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
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Authors and funding
6 authors.
Funding
Abstract
backgroundReconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of methodologies for reconstructing transmission chains using both epidemiological and genetic data. However, only a few of these methods have been implemented in software packages, and with little consideration for customisability and interoperability. Users are therefore limited to a small number of alternatives, incompatible tools with fixed functionality, or forced to develop their own algorithms at considerable personal effort.
resultsHere we present outbreaker2, a flexible framework for outbreak reconstruction. This R package re-implements and extends the original model introduced with outbreaker, but most importantly also provides a modular platform allowing users to specify custom models within an optimised inferential framework. As a proof of concept, we implement the within-host evolutionary model introduced with TransPhylo, which is very distinct from the original genetic model in outbreaker, and demonstrate how even complex model results can be successfully included with minimal effort.
conclusionsoutbreaker2 provides a valuable starting point for future outbreak reconstruction tools, and represents a unifying platform that promotes customisability and interoperability. Implemented in the R software, outbreaker2 joins a growing body of tools for outbreak analysis.
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Registered trials
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.