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Biomedical Engineering and Bioengineering Commons

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Theses/Dissertations

Life Sciences

University of Colorado, Boulder

Chemical & Biological Engineering Graduate Theses & Dissertations

Antibiotic Resistance

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Improved Methods For Understanding Sparse, Multi-Dimensional, High Throughput Sequencing Data, Sophie J. Weiss Jan 2015

Improved Methods For Understanding Sparse, Multi-Dimensional, High Throughput Sequencing Data, Sophie J. Weiss

Chemical & Biological Engineering Graduate Theses & Dissertations

Tremendous advances in genetic and sequencing technology are enabling unprecedented insight into human disease, forensics, and cellular mechanisms, to name a few. Conclusions drawn from these studies are strongly influenced by the interpretation of their associated massive data sets. The goal of this thesis is to understand, develop, and apply algorithms to help overcome common ecological and biological sequencing study challenges: contamination, differences in sampling efforts, a very large amount of zeroes, and compositionality.

We use simulations and experimental data to understand how different matrix normalization strategies mitigate the effects of the aforementioned challenges on downstream analyses, particularly principal coordinate ...