Physical Sciences and Mathematics Commons^™

Disk Diffusion Breakpoint Determination Using A Bayesian Nonparametric Variation Of The Errors-In-Variables Model, Glen Richard Depalma

Open Access Dissertations

Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility tests used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Both tests use breakpoints to classify the pathogen as either susceptible, indeterminant, or resistant to each drug under consideration. While the determination of these drug-specific MIC classification breakpoints is straightforward, determination of comparable DIA breakpoints is not. It is this issue that motivates this research.

Traditionally, the error-rate bounded (ERB) method has been used to calibrate the two tests. This procedure involves determining DIA breakpoints which minimize the observed discrepancies between …

Non-Parametric Spatial Models, Cheng Liu

Open Access Dissertations

Covariance functions play a central role in spatial statistics. Parametric covariance functions have been used in most of the existing works on the analysis of spatial data. The primary reason for this is that the classes of parametric covariance functions guarantee that the fitted covariance function is positive definite. In this dissertation, I undertake two non-parametric approaches to modelling the covariance functions.

Our approach is motivated by problems that arise in spatial data analysis in recent years. First, it is nontrivial to choose a parametric family among many parametric families of covariance function. A non-parametric covariance function circumvents this problem. …

Estimation Of Variation For High-Throughput Molecular Biological Experiments With Small Sample Size, Danni Yu

Open Access Dissertations

Motivation: In the quantification of molecular components, a large variation can affect and even potentially mislead the biological conclusions. Meanwhile, the high-throughput experiments often involve a small number of samples due to the limitation of cost and time. In such cases, the stochastic information may dominate the outcome of an experiment because there may not be enough samples to present the true biological information. It is challenging to distinguish the changes in phenotype from the stochastic variation.

Methods: Since the biological molecules have been quantified with different technologies, different statistical methods are required. Focusing on three types of important high-throughput …

Statistical Models For Gene And Transcripts Quantification And Identification Using Rna-Seq Technology, Han Wu

Open Access Dissertations

RNA-Seq has emerged as a powerful technique for transcriptome study. As much as the improved sensitivity and coverage, RNA-Seq also brings challenges for data analysis. The massive amount of sequence reads data, excessive variability, uncertainties, and bias and noises stemming from multiple sources all make the analysis of RAN-Seq data difficult. Despite much progress, RNA-Seq data analysis still has much room for improvement, especially on the quantification of gene and transcript expression levels. The quantification of gene expression level is a direct inference problem, whereas the quantification of the transcript expression level is an indirect problem, because the label of …

A Jackknife Empirical Likelihood Approach To Goodness Of Fit U-Statistic Testing With Side Information, Qun Lin

Open Access Dissertations

Motivated by applications to goodness of fit U-statistics testing, the jackknife empirical likelihood of Jing, et al. (2009) is justified with an alternative approach, and the Wilks theorem for vector U-statistics is proved. This generalizes Owen's empirical likelihood theorem for a vector mean to a vector U-statistics-based mean and includes the jackknife empirical likelihood of U-statistics with side information as a special case. The results are generalized to allow for the constraints to use estimated criteria functions and for the number of constraints to grow with the sample size. The latter is needed to handle naturally occurring nuisance parameters in …

Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach, Nicholas Fico

Open Access Dissertations

Generation of active protein chimeras is a valuable tool to probe the functional space of proteins. Statistical modeling is the next logical step, allowing us to build a model of gene fragment replaceability between species. In this thesis I begin to develop the statistical tools that are needed to systematically describe combinatorial protein libraries. I present three sets of diverse chimeric protein libraries developed using sequence information. The statistical model of the human N-Ras and human K-Ras-4B genes reveal a set previously unidetifed surface residues on the N-Ras G-Domain that may be involved in cellular localization. Statistical modeling of a …