A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data

DOI10.1093/BIOSTATISTICS/KXJ033zbMATH Open1170.62368arXivq-bio/0603031OpenAlexW2149958386WikidataQ31035308 ScholiaQ31035308MaRDI QIDQ3434182FDOQ3434182

Authors: Niko Beerenwinkel, Mathias Drton 

Publication date: 23 April 2007

Published in: Biostatistics (Search for Journal in Brave)

Abstract: RNA viruses provide prominent examples of measurably evolving populations. In HIV infection, the development of drug resistance is of particular interest, because precise predictions of the outcome of this evolutionary process are a prerequisite for the rational design of antiretroviral treatment protocols. We present a mutagenetic tree hidden Markov model for the analysis of longitudinal clonal sequence data. Using HIV mutation data from clinical trials, we estimate the order and rate of occurrence of seven amino acid changes that are associated with resistance to the reverse transcriptase inhibitor efavirenz.

Full work available at URL: https://arxiv.org/abs/q-bio/0603031

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zbMATH Keywords

EM algorithmGraphical modelHIV drug resistanceLongitudinal dataHidden Markov modelMeasurably evolving populationsMutagenetic tree

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50) Markov processes (60J99)

Cited In (21)

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• A Hierarchical Semiparametric Regression Model for Combining HIV‐1 Phylogenetic Analyses Using Iterative Reweighting Algorithms
• Modeling sequence evolution in HIV-1 infection with recombination
• Estimation of the HIV-1 backward mutation rate from transmitted drug-resistant strains
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• Combining Genotype Groups and Recursive Partitioning: An Application to Human Immunodeficiency Virus Type 1 Genetics Data
• Combining Cross‐Sectional and Prospective Data Methods to Improve Transition Parameter Estimation for Characterizing the Accumulation of HIV‐1 Drug Resistance Mutations
• Mixed hidden Markov models for longitudinal data: an overview
• Learning monotonic genotype-phenotype maps
• Improving hidden Markov models for classification of human immunodeficiency virus-1 subtypes through linear classifier learning
• Summary statistics of neutral mutations in longitudinal DNA samples
• Log-linear models for mutations in the HIV genome
• Modeling sequence evolution in acute HIV-1 infection
• Model Selection for Mixtures of Mutagenetic Trees
• Multiple testing and error control in Gaussian graphical model selection
• Characterizing the relationship between HIV-1 genotype and phenotype: prediction-based classification
• Title not available (Why is that?)
• Learning robust multi-label sample specific distances for identifying HIV-1 drug resistance
• Conjunctive Bayesian networks
• Accommodating uncertainty in a tree set for function estimation

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