A novel methodology for large-scale phylogeny partition.
A novel methodology for large-scale phylogeny partition.
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DOI：
10.1038/ncomms1325
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发表时间：
2011
影响因子：
16.6
通讯作者：
ARCA collaborative group
中科院分区：
文献类型：
--
作者：
Prosperi MC;Ciccozzi M;Fanti I;Saladini F;Pecorari M;Borghi V;Di Giambenedetto S;Bruzzone B;Capetti A;Vivarelli A;Rusconi S;Re MC;Gismondo MR;Sighinolfi L;Gray RR;Salemi M;Zazzi M;De Luca A;ARCA collaborative group
系统发生分析用于确定传播链，但没有软件可用于自动划分大型系统发生。Prosperiet等人应用一种新的搜索算法来识别HIV-1基因序列同源性内的传播簇，该序列将分子和流行病学数据联系起来。本文的在线版本（doi：10.1038/ncomms 1325）包含补充材料，授权用户可以使用。了解病毒传播的决定因素是有效设计控制病毒流行的筛查和干预策略的基本步骤。系统发生分析可以是识别传播链的有效方法，并且可以通过并行计算分析非常大的数据集。在这里，我们提出并验证了一个新的方法来划分大规模的遗传和推断的传输集群。该方法在深度优先搜索算法的基础上，结合了节点可靠性评估、树拓扑和父权距离分析。该方法已被应用于确定从一个大的意大利队列的11，541人免疫缺陷病毒-1亚型B pol基因序列的同源性的传输集群。分子传播链的特点是通过不同的临床/人口因素，如男性同性恋者和男性异性恋者之间的相互作用。我们的方法利用了一个灵活的概念，传输集群，可以成为一个通用的框架来分析其他流行病。本文的在线版本（doi：10.1038/ncomms 1325）包含补充材料，授权用户可以使用。
Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data. The online version of this article (doi:10.1038/ncomms1325) contains supplementary material, which is available to authorized users. Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics. The online version of this article (doi:10.1038/ncomms1325) contains supplementary material, which is available to authorized users.
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影响因子：
3.8
作者：
Gray, Rebecca R.;Tatem, Andrew J.;Salemi, Marco
通讯作者：
Salemi, Marco
DOI：
10.1097/qad.0b013e3283121c90
发表时间：
2008-11-30
期刊：
AIDS (London, England)
影响因子：
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作者：
Brenner BG;Roger M;Moisi DD;Oliveira M;Hardy I;Turgel R;Charest H;Routy JP;Wainberg MA;Montreal PHI Cohort and HIV Prevention Study Groups
通讯作者：
Montreal PHI Cohort and HIV Prevention Study Groups
影响因子：
5.8
作者：
Li, KB
通讯作者：
Li, KB
DOI：
10.1084/jem.20082831
发表时间：
2009-05-11
期刊：
The Journal of experimental medicine
影响因子：
--
作者：
Keele BF;Li H;Learn GH;Hraber P;Giorgi EE;Grayson T;Sun C;Chen Y;Yeh WW;Letvin NL;Mascola JR;Nabel GJ;Haynes BF;Bhattacharya T;Perelson AS;Korber BT;Hahn BH;Shaw GM
通讯作者：
Shaw GM
DOI：
10.1097/qad.0b013e328340fdaf
发表时间：
2011-01-14
期刊：
AIDS (London, England)
影响因子：
--
作者：
Gray RR;Salemi M;Lowe A;Nakamura KJ;Decker WD;Sinkala M;Kankasa C;Mulligan CJ;Thea DM;Kuhn L;Aldrovandi G;Goodenow MM
通讯作者：
Goodenow MM