Developing Statistical and Algorithmic Methods for Shotgun Metagenomics and Time Series Analysis

Authors: Li Charlie Xia

Recent developments in experimental molecular techniques, such as microarray, next generation sequencing technologies, have led molecular biology into a high-throughput era with emergent omics research areas, including metagenomics and transcriptomics. Massive-size omics datasets generated and being generated from the experimental laboratories put new challenges to computational biologists to develop fast and accurate quantitative analysis tools. We have developed two statistical and algorithmic methods, GRAMMy and eLSA, for metagenomics and microbial community time series analysis. GRAMMy provides a unied probabilistic framework for shotgun metagenomics, in which maximum likelihood method is employed to accurately compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy). We extended the Local Similarity Analysis technique (eLSA) to time series data with replicates, capturing statistically signicant local and potentially time-delayed associations. Both methods are validated through simulation studies and their capability to reveal new biology is also demonstrated through applications to real datasets. We implemented GRAMMy and eLSA as C++ extensions to Python, with both superior computational eciency and easy-to-integrate programming interfaces. GRAMMy and eLSA methods will be increasingly useful tools as new omics researches accelerating their pace.

Comments: 127 Pages.

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Submission history

[v1] 2013-04-11 17:27:00

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