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A Comparative Analysis Of Machine Learning Algorithms For Genome Wide Association Studies, Neha Singh

Theses

Variations present in human genome play a vital role in the emergence of genetic disorders and abnormal traits. Single Nucleotide Polymorphism (SNP) is considered as the most common source of genetic variations. Genome Wide Association Studies (GWAS) probe these variations present in human population and find their association with complex genetic disorders. Now these days, recent advances in technology and drastic reduction in costs of Genome Wide Association Studies provide the opportunity to have a plethora of genomic data that delivers huge information of these variations to analyze. In fact, there is significant difference in pace of data generation and …

Phenotype Prediction And Feature Selection In Genome-Wide Association Studies, Andrew Roberts

Theses

Genome wide association studies (GWAS) search for correlations between single nucleotide polymorphisms (SNPs) in a subject genome and an observed phenotype. GWAS can be used to generate models for predicting phenotype based on genotype, as well as aiding in identification of specific genes affecting the biological mechanism underlying the phenotype.

In this investigation, phenotype prediction models are constructed from GWAS training data and are evaluated for performance on test data. Three methods are used to rank SNPs by their correlation with the phenotype: the univariate Wald test, a multivariate, support vector machine (SVM) based technique, and a hybrid method where …

The Functional Effects Of Barium And Hypoxia On The In Vitro Respiratory Activity, Gaofeng Xu

Theses

The hypoxic respiratory response in mammals consists of a transit increase in the respiratory frequency (augmentation phase) followed by a decrease in frequency (depression phase). To understand how the central respiratory system contributes to this response, the in vitro transverse brainstem slice model is used, which contains the pre-Bötzinger Complex, which is responsible for respiratory rhythm generation. The in vitro experiments performed for this thesis provide evidence that external barium exposure alters respiratory activity and significantly increases (P<0.00 1) the voltage of tonic activity under control oxygen conditions (95% FO2). During severe hypoxia (0% FO2), respiratory tonic activity is significantly elevatedduring the depression phase (from 0.55 to 0.95, n=6, P<0.001) by external barium, presumablydue to the closing of K+ channels and a reduction in K+ conductance.

Data Mining Of Tetraloop-Tetraloop Receptors In Rna Xml Files, Sinan Ramazanoglu

Theses

RNA (Ribonucleic acid) Motifs are tertiary structures that play an important role in the folding mechanism of the RNA molecule. The overall function of a RNA Motif depends on its specific bp (base pairs) sequence that constitutes the secondary structure. Data mining is a novel method in both discovering potential tertiary structures within DNA (Deoxyribonucleic acid), RNA, and protein molecules and storing the information in databases. The RNA Motif of interest is the tetraloop-tetraloop receptor, which is composed of a highly conserved 11 nt (nucleotide) sequence and a tetraloop with the generic form of GNRA (where N = any base …

The Effects Of Theophylline On The In Vitro Respiratory Response To Hypoxia, Ke Geng

Theses

The isolated transverse brainstem slice preparation of neonatal mice is employed to investigate the function of theophylline, a competitive nonselective phophodiesterase inhibitor and adenosine receptor antagonist, on the hypoxic ventilatory response. Brainstem slices are isolated from neonatal mice (4-8 days old) and superfused with artificial cerebrospinal fluid (aCSF), equilibrated with a hyperoxic gas mixture (95% O₂, 5% CO₂) as a control, and anoxic mixture (0% O₂, 5% CO₂, 95% N₂) to create severe hypoxia at the tissue level. Using suction electrodes, extracellular population activities of respiratory neurons is recorded from …