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Integrated Genomics Of Susceptiblity To Therapy-Related Leukemia, Patrick Cahan
Integrated Genomics Of Susceptiblity To Therapy-Related Leukemia, Patrick Cahan
All Theses and Dissertations (ETDs)
Therapy-related acute myeloid leukemia t-AML is a secondary, generally incurable, malignancy attributable to the chemotherapeutic treatment of an initial disease. Although there is a genetic component to susceptibility to therapy-related leukemias in mice, little is understood either about the contributing loci, or the mechanisms by which susceptibility factors mediate their effect. An improved understanding of susceptibility factors and the biological processes in which they act may lead to the development of t-AML prevention strategies. In this thesis work, we identified expression networks that are associated with t-AML susceptibility in mice. These networks are robust in that they emerge from distinct …
Accurate Docking Is Achieved By Decoupling Systematic Sampling From Scoring, Jianwen Feng
Accurate Docking Is Achieved By Decoupling Systematic Sampling From Scoring, Jianwen Feng
All Theses and Dissertations (ETDs)
This dissertation discusses two main projects from my thesis work. The first project focuses on the development of a small molecule docking program, SKATE, for drug discovery. The second project focuses on the critical analysis of the thermal stability of a mini-protein, FSD-1. SKATE is a novel approach to small molecule docking. It removes any inter-dependence between sampling and scoring to improve docking accuracy. SKATE systematically and exhaustively samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. A total of 266 ligands were re-docked to their respective receptors …
Modeling And Identification Of Differentially Regulated Genes Using Transcriptomics And Proteomics Data, Thanura Elvitigala
Modeling And Identification Of Differentially Regulated Genes Using Transcriptomics And Proteomics Data, Thanura Elvitigala
All Theses and Dissertations (ETDs)
Photosynthetic organisms are complex dynamical systems, showing a remarkable ability to adapt to different environmental conditions for their survival. Mechanisms underlying the coordination between different cellular processes in these organisms are still poorly understood. In this dissertation we utilize various computational and modeling techniques to analyze transcriptomics and proteomics data sets from several photosynthetic organisms. We try to use changes in expression levels of genes to study responses of these organisms to various environmental conditions such as availability of nutrients, concentrations of chemicals in growth media, and temperature. Three specific problems studied here are transcriptomics modifications in photosynthetic organisms under …
Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki
Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki
All Theses and Dissertations (ETDs)
Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due …