ArticleThe annals of applied statistics2016
Reconstructing transmission trees for communicable diseases using densely sampled genetic data.
Article in The annals of applied statistics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Investigating pathways of vancomycin-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.Molecular biology and evolution · 2024Article
- A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms.PLoS computational biology · 2023Article
- Molecular source attribution.PLoS computational biology · 2022Article
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 2022Article
- Reconstruction of the Transmission Chain of COVID-19 Outbreak in Beijing's Xinfadi Market, China.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Probabilistic modelling of effects of antibiotics and calendar time on transmission of healthcare-associated infection.Scientific reports · 2021Article
- Article
- Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.PLoS computational biology · 2021Article
- nosoi: A stochastic agent-based transmission chain simulation framework in r.Methods in ecology and evolution · 2020Article
- Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data.Journal of the Royal Society, Interface · 2020Article
- Estimating the relative probability of direct transmission between infectious disease patients.International journal of epidemiology · 2020Article
- Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data.Statistics in medicine · 2020Article
- Long-distance transmission patterns modelled from SNP barcodes of Plasmodium falciparum infections in The Gambia.Scientific reports · 2019Article
- Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Inferring who-infected-whom-where in the 2016 Zika outbreak in Singapore-a spatio-temporal model.Journal of the Royal Society, Interface · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measures. We considered disease outbreaks in a setting with dense genomic sampling, and formulated stochastic epidemic models to investigate person-to-person transmission, based on observed genomic and epidemiological data. We constructed models in which the genetic distance between sampled genotypes depends on the epidemiological relationship between the hosts. A data augmented Markov chain Monte Carlo algorithm was used to sample over the transmission trees, providing a posterior probability for any given transmission route. We investigated the predictive performance of our methodology using simulated data, demonstrating high sensitivity and specificity, particularly for rapidly mutating pathogens with low transmissibility. We then analyzed data collected during an outbreak of methicillin-resistant
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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.