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An Ensemble Algorithm for Bacterial Identification from Metagenomic Data
Başlık:
An Ensemble Algorithm for Bacterial Identification from Metagenomic Data
Yazar:
Fu, Shih-Chen, author.
ISBN:
9780355941883
Yazar Ek Girişi:
Fiziksel Tanımlama:
1 electronic resource (104 pages)
Genel Not:
Source: Dissertation Abstracts International, Volume: 79-10(E), Section: B.
Advisors: Jose C. Clemente.
Özet:
Identification of bacteria from metagenomic data is a fundamental problem in microbiome studies. Although numerous software tools exist to identify bacterial species and strains from shotgun metagenomic data, it is unclear whether these tools are concordant with each other, and how differences among the tools might affect our conclusions on what bacteria are associated with specific health outcomes. In this project, we first investigated the concordance of tools for bacterial identification in different metagenomic datasets derived from clinical samples. We found that the agreement between species predicted by different tools was extremely low across all datasets tested. This resulted in important biases when performing biomarker analysis, as different tools identified different sets of bacteria associated with the outcomes of each study. Importantly, this was not driven by the accuracy of each tool to identify bacterial species, and validation against in silico simulations, bacterial mock communities, and bacterial isolates showed moderate accuracy for all tools. Integrating the results of different tools using an ensemble algorithm improved the overall accuracy, and allowed the identification of bacteria associated with remission after fecal microbiota transplant in ulcerative colitis patients. Our results demonstrate the importance of ensemble approaches to identify bacterial species that are truly associated with clinical outcomes.
Notlar:
School code: 1734
Konu Başlığı:
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Yer Numarası | Demirbaş Numarası | Shelf Location | Lokasyon / Statüsü / İade Tarihi |
---|---|---|---|
XX(681438.1) | 681438-1001 | Proquest E-Tez Koleksiyonu | Arıyor... |
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