Sampling and summarizing transmission trees with multi-strain infections
Sampling and summarizing transmission trees with multi-strain infections
复制标题
多菌株感染传播树的采样和总结
DOI：
10.1093/bioinformatics/btaa438
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发表时间：
2020
期刊：
影响因子：
5.8
通讯作者：
El-Kebir, Mohammed
中科院分区：
文献类型：
--
作者：
Sashittal, Palash;El-Kebir, Mohammed
动机基因组和流行病学数据的结合有可能使准确的病原体传播历史推断成为可能。然而，由于宿主内病原体多样性和多菌株感染等各种因素，对暴发传播历史的推断仍然具有挑战性。目前的计算方法忽略了宿主内的多样性和/或多菌株感染，往往无法准确推断传播历史。因此，需要高效的传播树推理计算方法，以适应实际数据的复杂性。结果我们建立了直接传播推理(DTI)问题，用于在给定时间的系统发育和额外的流行病学数据的情况下，推断支持多毒株感染的传播树。我们建立了DTI问题的决策版和计数版的难度。介绍了一种利用可满足性对传输树空间进行几乎一致采样的方法--传输树统一采样器(TITURS)。我们引入了对简约传输树进行优先排序的标准，随后使用一种新的共识树方法对其进行了总结。我们展示了TITUS在模拟数据和记录的艾滋病毒传播链上准确重建传播树的能力。可用性和implementationhttps://github.com/elkebir-group/TiTUS.Supplementary信息补充数据可在BioInformation在线获得。
MotivationThe combination of genomic and epidemiological data holds the potential to enable accurate pathogen transmission history inference. However, the inference of outbreak transmission histories remains challenging due to various factors such as within-host pathogen diversity and multi-strain infections. Current computational methods ignore within-host diversity and/or multi-strain infections, often failing to accurately infer the transmission history. Thus, there is a need for efficient computational methods for transmission tree inference that accommodate the complexities of real data.ResultsWe formulate the direct transmission inference (DTI) problem for inferring transmission trees that support multi-strain infections given a timed phylogeny and additional epidemiological data. We establish hardness for the decision and counting version of the DTI problem. We introduceTransmissionTreeUniformSampler (TiTUS), a method that uses SATISFIABILITY to almost uniformly sample from the space of transmission trees. We introduce criteria that prioritize parsimonious transmission trees that we subsequently summarize using a novel consensus tree approach. We demonstrate TiTUS’s ability to accurately reconstruct transmission trees on simulated data as well as a documented HIV transmission chain.Availability and implementationhttps://github.com/elkebir-group/TiTUS.Supplementary informationSupplementary data are available atBioinformaticsonline.
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影响因子：
5.8
作者：
Aguse, Nuraini;Qi, Yuanyuan;El-Kebir, Mohammed
通讯作者：
El-Kebir, Mohammed
SharpTNI：弱瓶颈下简约传输网络的计数和采样
DOI：
--
发表时间：
2019
期刊：
bioRxiv
影响因子：
--
作者：
P. Sashittal;M. El
通讯作者：
M. El
瓶颈
DOI：
--
发表时间：
2021
期刊：
International Encyclopedia of Transportation
影响因子：
--
作者：
Kentaro Wada;Toru Seo;Yasuhiro Shiomi
通讯作者：
Yasuhiro Shiomi
DOI：
10.1073/pnas.93.20.10864
发表时间：
1996-10-01
影响因子：
11.1
作者：
Leitner, T;Escanilla, D;Albert, J
通讯作者：
Albert, J
影响因子：
5.4
作者：
Lemey, P;Derdelinckx, I;Vandamme, AM
通讯作者：
Vandamme, AM