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University of Washington

1. Jones, Daniel Caleb. The analysis of RNA-Seq experiments using approximate likelihood.

Degree: PhD, 2021, University of Washington

The analysis of mRNA transcript abundance with RNA-Seq is a central tool in molecular biology research, but often analyses fail to account for the uncertainty in these estimates, which can be significant, especially when trying to disentangle isoforms or duplicated genes. Preserving uncertainty necessitates a full probabilistic model of the all the sequencing reads which quickly becomes intractable, as experiments can consist of billions of reads. To overcome these limitations, we propose a new method of approximating the likelihood function of a sparse mixture model, using a technique we call the Polya tree transformation. We demonstrate that substituting this approximation for the real thing achieves most of the benefits with a fraction of the computational costs, leading to more accurate detection of differential transcript expression. Advisors/Committee Members: Ruzzo, Walter L. (advisor).

Subjects/Keywords: likelihood approximation; RNA-Seq; variational inference; Computer science; Bioinformatics; Computer science and engineering

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Jones, D. C. (2021). The analysis of RNA-Seq experiments using approximate likelihood. (Doctoral Dissertation). University of Washington. Retrieved from http://hdl.handle.net/1773/46770

Chicago Manual of Style (16th Edition):

Jones, Daniel Caleb. “The analysis of RNA-Seq experiments using approximate likelihood.” 2021. Doctoral Dissertation, University of Washington. Accessed April 22, 2021. http://hdl.handle.net/1773/46770.

MLA Handbook (7th Edition):

Jones, Daniel Caleb. “The analysis of RNA-Seq experiments using approximate likelihood.” 2021. Web. 22 Apr 2021.

Vancouver:

Jones DC. The analysis of RNA-Seq experiments using approximate likelihood. [Internet] [Doctoral dissertation]. University of Washington; 2021. [cited 2021 Apr 22]. Available from: http://hdl.handle.net/1773/46770.

Council of Science Editors:

Jones DC. The analysis of RNA-Seq experiments using approximate likelihood. [Doctoral Dissertation]. University of Washington; 2021. Available from: http://hdl.handle.net/1773/46770

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