ArticleVirus evolution2020
Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection.
Article in Virus evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- From giant components to communities: community-level insights for prioritizing interventions within large clusters of HIV-1 transmission networks.Infectious Disease Modelling · 2027Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.PLoS computational biology · 2024Article
- AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS.bioRxiv : the preprint server for biology · 2024Article
- High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA.Virus evolution · 2024Article
- Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics.Bioinformatics advances · 2024Article
- AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters.Frontiers in bioinformatics · 2024Article
- Modeling homophily in dynamic networks with application to HIV molecular surveillance.BMC infectious diseases · 2023Article
- From components to communities: bringing network science to clustering for molecular epidemiology.Virus evolution · 2023Article
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.PLoS computational biology · 2022Article
- Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020.Journal of the International AIDS Society · 2021Article
- Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering.Evolution, medicine, and public health · 2021Article
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Authors and funding
3 authors.
Funding
Abstract
Genetic clustering is a popular method for characterizing variation in transmission rates for rapidly evolving viruses, and could potentially be used to detect outbreaks in 'near real time'. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here, we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analysed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B
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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.