2014
DOI: 10.1109/tcbb.2013.145
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HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

Abstract: This paper presents a new computational technique for the identification of HIV haplotypes. HIV tends to generate many potentially drug-resistant mutants within the HIV-infected patient and being able to identify these different mutants is important for efficient drug administration. With the view of identifying the mutants, we aim at analyzing short deep sequencing data called reads. From a statistical perspective, the analysis of such data can be regarded as a nonstandard clustering problem due to missing pa… Show more

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Cited by 100 publications
(158 citation statements)
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“…None of the other tools generated even only one such perfectly matching segment, possibly because they require much higher coverage. This improvement in terms of accuracy may be due to the probabilistic model that treats error Global haplotype assembly comparison of HaploClique with the software packages ShoRAH [33], PredictHaplo [14], and QuRe [16]. We report the estimated variant frequencies and, in parenthesis, the maximal length of the reconstructed haplotypes relative to the genome length, for each of the five variants.…”
Section: Discussionmentioning
confidence: 99%
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“…None of the other tools generated even only one such perfectly matching segment, possibly because they require much higher coverage. This improvement in terms of accuracy may be due to the probabilistic model that treats error Global haplotype assembly comparison of HaploClique with the software packages ShoRAH [33], PredictHaplo [14], and QuRe [16]. We report the estimated variant frequencies and, in parenthesis, the maximal length of the reconstructed haplotypes relative to the genome length, for each of the five variants.…”
Section: Discussionmentioning
confidence: 99%
“…Fourth, we evaluate the quality of the local and global haplotypes that HaploClique predicts. Lastly, we compare HaploClique to stateof-the-art tools ShoRAH [33], PredictHaplo [14], and QuRe [16] in quasispecies reconstruction of a simulated five virus mix of wellknown HIV-1 lab-strains.…”
Section: Simulation Studiesmentioning
confidence: 99%
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“…Optimizing its set of parameters is non-trivial. PredictHaplo [38] is also capable of performing full recoveries of the HIV-1 nonenv genes, but has been shown to recover conservatively outside of HIV-1. [39,40].…”
Section: Methodsological Comparison Of Our Approachmentioning
confidence: 99%