HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

Prabhakaran S.; Rey M.; Zagordi O.; Beerenwinkel N.; Roth V.

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HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

机译：HIV单倍型推断使用传播Dirichlet过程混合模型

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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 pairwise similarity measures between non-overlapping reads. To overcome this problem we propagate a Dirichlet Process Mixture Model by sequentially updating the prior information from successive local analyses. The model is verified using both simulated and real sequencing data.

机译：本文提出了一种新的计算技术，用于识别HIV单倍型。 HIV往往会在HIV感染的患者体内产生许多潜在的耐药突变体，因此能够识别出这些不同的突变体对于有效给药非常重要。为了识别突变体，我们旨在分析称为读取的短深测序数据。从统计角度来看，由于缺少非重叠读段之间的成对相似性度量，因此可以将此类数据的分析视为非标准聚类问题。为了克服这个问题，我们通过从连续的局部分析中顺序更新先验信息来传播Dirichlet过程混合模型。使用模拟和实际测序数据对模型进行验证。

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《Computational Biology and Bioinformatics, IEEE/ACM Transactions on》 |2014年第1期|182-191|共10页
作者
Prabhakaran S.; Rey M.; Zagordi O.; Beerenwinkel N.; Roth V.;
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Department of Mathematics and Computer Science, University of Basel, Bernoullistrasse 16, Switzerland|c|;

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正文语种 eng
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454 sequencing reads; HIV; MCMC; haplotype inference;

机译：454测序;HIV;MCMC;单体型推断;

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专利

1. Dirichlet process model for joint haplotype inference and GWAS [J] . Avinash Das Sahu, Sridhar Hannenhalli BMC proceedings. . 2012,第S6期

机译：联合单倍型推断和GWAS的Dirichlet过程模型
2. Prior selection method using likelihood confidence region and Dirichlet process Gaussian mixture model for Bayesian inference of building energy models [J] . Yi Dong Hyuk, Kim Deuk Woo, Park Cheol Soo Energy and Buildings . 2020,第Octa期

机译：使用似然置信区和Dirichlet工艺Gaussian推理的Dirichlet工艺Gaussian混合模型的先前选择方法
3. Fast bayesian inference in dirichlet process mixture models [J] . Wang, L., Dunson, D.B. Journal of computational and graphical statistics: A joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America . 2011,第1期

机译：Dirichlet过程混合模型中的快速贝叶斯推断
4. Bayesian multi-population haplotype inference via a hierarchical dirichlet process mixture [C] . Eric P. Xing, Kyung-Ah Sohn, Michael I. Jordan, International conference on Machine learning . 2006

机译：通过分层狄利克雷混合过程进行贝叶斯多种群单倍型推断
5. Dirichlet process mixture modeling: Hidden Markov mixture models and multi-task compressive sensing [D] . Qi, Yuting 2009

机译：Dirichlet过程混合物建模：隐马尔可夫混合物模型和多任务压缩感测
6. Fast Bayesian Inference in Dirichlet Process Mixture Models [O] . Lianming Wang, David B. Dunson -1

机译：Dirichlet Process混合模型的快速贝叶斯推断
7. Bayesian multi-population haplotype inference via a hierarchical dirichlet process mixture [O] . Xing EP, Sohn K-A, Jordan MI, 2006

机译：通过分层狄利克雷混合过程进行贝叶斯多种群单倍型推断
8. Memoized Online Variational Inference for Dirichlet Process Mixture Models. [R] . Hughes, M. C., Sudderth, E. B. 2014

机译：Dirichlet过程混合模型的memoized在线变分推断。

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

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