ArticleMolecular biology and evolution2019
Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic.Communications medicine · 2025Article
- Phylodynamics unveils invading and diffusing patterns of dengue virus serotype-1 in Guangdong, China from 1990 to 2019 under a global genotyping framework.Infectious diseases of poverty · 2024Article
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 2022Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- The need for linked genomic surveillance of SARS-CoV-2.Canada communicable disease report = Releve des maladies transmissibles au Canada · 2022Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Sampling and summarizing transmission trees with multi-strain infections.Bioinformatics (Oxford, England) · 2020Article
- Phylogenetic interpretation during outbreaks requires caution.Nature microbiology · 2020Article
- Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Evolving COVID-19 conundrum and its impact.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One approach to the reconstruction of infectious disease transmission trees from pathogen genomic data has been to use a phylogenetic tree, reconstructed from pathogen sequences, and annotate its internal nodes to provide a reconstruction of which host each lineage was in at each point in time. If only one pathogen lineage can be transmitted to a new host (i.e., the transmission bottleneck is complete), this corresponds to partitioning the nodes of the phylogeny into connected regions, each of which represents evolution in an individual host. These partitions define the possible transmission trees that are consistent with a given phylogenetic tree. However, the mathematical properties of the transmission trees given a phylogeny remain largely unexplored. Here, we describe a procedure to calculate the number of possible transmission trees for a given phylogeny, and we then show how to uniformly sample from these transmission trees. The procedure is outlined for situations where one sample is available from each host and trees do not have branch lengths, and we also provide extensions for incomplete sampling, multiple sampling, and the application to time trees in a situation where limits on the period during which each host could have been infected and infectious are known. The sampling algorithm is available as an R package (STraTUS).
Indexed as
Identifiers
What OpenQuestion holds
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.