ArticleNature communications2011
A novel methodology for large-scale phylogeny partition.
Article in Nature communications, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 1 of them a synthesis that pooled it.
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Who cites it
86 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Comprehensive Mapping of the Virus and Host Factors that Guide the Paths of HIV-1 Escape from a Therapeutic.bioRxiv : the preprint server for biology · 2025Article
- Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.PLoS computational biology · 2025Article
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- Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus.Virologica Sinica · 2024Article
- Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic.Journal of virology · 2024Article
- Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics.Bioinformatics advances · 2024Article
- Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China.Emerging microbes & infections · 2023Article
- SMRT-AgRenSeq-d in potato (Horticulture research · 2023Article
- The Evolution and Global Spatiotemporal Dynamics of Senecavirus A.Microbiology spectrum · 2022Article
- Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications.PLoS computational biology · 2022Article
- Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution.Cell systems · 2022Article
- Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013-2019.Viruses · 2022Article
- SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets.International journal of molecular sciences · 2022Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics.
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