ArticleGenetics2007
Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Recombination plasticity in response to temperature variation in reptiles.PLoS genetics · 2025Article
- Recombination and phylogenetic inference.Evolutionary journal of the Linnean Society · 2025Article
- Revisiting the recombinant history of HIV-1 group M with dynamic network community detection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods.Genes · 2021Review
- A spatially varying change points model for monitoring glaucoma progression using visual field data.Spatial statistics · 2019Article
- Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation.Virus evolution · 2018Article
- Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2015Review
- Ecosystem simplification, biodiversity loss and plant virus emergence.Current opinion in virology · 2015Review
- Article
- Methodology and software to detect viral integration site hot-spots.BMC bioinformatics · 2011Article
- Conversion events in gene clusters.BMC evolutionary biology · 2011Article
- Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes--divide and conquer.PLoS computational biology · 2010Article
- A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.Evolutionary bioinformatics online · 2009Article
- Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.PLoS pathogens · 2009Article
- Accurate detection of recombinant breakpoints in whole-genome alignments.PLoS computational biology · 2009Article
- Bayesian modeling of recombination events in bacterial populations.BMC bioinformatics · 2008Article
- Article
- Phylogenetic detection of recombination with a Bayesian prior on the distance between trees.PloS one · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We present a Bayesian framework for inferring spatial preferences of recombination from multiple putative recombinant nucleotide sequences. Phylogenetic recombination detection has been an active area of research for the last 15 years. However, only recently attempts to summarize information from several instances of recombination have been made. We propose a hierarchical model that allows for simultaneous inference of recombination breakpoint locations and spatial variation in recombination frequency. The dual multiple change-point model for phylogenetic recombination detection resides at the lowest level of our hierarchy under the umbrella of a common prior on breakpoint locations. The hierarchical prior allows for information about spatial preferences of recombination to be shared among individual data sets. To overcome the sparseness of breakpoint data, dictated by the modest number of available recombinant sequences, we a priori impose a biologically relevant correlation structure on recombination location log odds via a Gaussian Markov random field hyperprior. To examine the capabilities of our model to recover spatial variation in recombination frequency, we simulate recombination from a predefined distribution of breakpoint locations. We then proceed with the analysis of 42 human immunodeficiency virus (HIV) intersubtype gag recombinants and identify a putative recombination hotspot.
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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.