Thesiss

A atresia biliar é a causa mais comum de colangiopatia obstrutiva infantil e a indicação mais frequente para transplante hepático na população pediátrica. É uma patologia que se inicia exclusivamente na infância e que se caracteriza por uma obstrução de parte ou da totalidade da…

Sarcophagidae, commonly known as the flesh flies, comprises one of the more behaviorally diverse families among the insects. In addition to carrion feeding, sarcophagids have evolved life history strategies that include predation, parasitism, and kleptoparasitism. Most kleptopar…

Reconstructing evolutionary trees, also known as phylogenies, from molecular sequence data is a fundamental problem in computational biology. Classically, evolutionary trees have been estimated over a set of species, where leaves correspond to extant species and internal nodes c…

The understanding of the genetic architecture of a desirable trait is vital in enabling sustainable increased yields of a root crop such as cassava, especially in a low-input agricultural system. The understanding of desirable trait architecture is also vital for the sustained a…

Production of soft red winter wheat ( Triticum aestivum ), the type of wheat used for baking cookies, crackers, and cakes, is known to be reduced by several biotic diseases; however, the impact of virus diseases on wheat health is widely underestimated in Ohio. This is partially…

Reptiles inhabiting shrub-steppe ecosystems of the Intermountain West have adapted to harsh, unpredictable desert conditions, yet recent changes in disturbance regimes may put species at risk. In southwest Idaho, cheatgrass ( Bromus tectorum ) has altered the fire regime resulti…

Subsistence strategy—the method by which a population obtains its food—has likely exerted strong selective pressure on humans for much of our evolutionary history. The genomes of 929 individuals from 54 populations in the HDGP-CEPH dataset were analyzed to characterize populatio…

The classical Duplication-Loss-Coalescence parsimony model (DLC-model) is a powerful tool when studying the complex evolutionary scenarios of simultaneous duplication-loss and deep coalescence events in evolutionary histories of gene families. However, inferring such scenarios i…

Proteins are known to interact with each other to perform specific living organism functions by forming functional modules or protein complexes. Many community detection methods have been devised for the discovery of functional modules or protein complexes in protein interaction…

Genome assembly is the process of merging fragments of DNA sequences produced by shotgun sequencing in order to reconstruct the original genome. It is complicated by repeated regions in genomes, sequencing errors, and experimental biases. Here we focus on our efforts to confront…

Current high-throughput gene expression experiments have a straightforward design of examining the gene expression of one group or condition relative to that of another. The data is typically analyzed as if they represent strictly intracellular events, and often treats genes as …

From the discovery of nucleic acids, their significance as an information carrier in the cell, and with the development of high-throughput sequencing (HTS) techniques, molecular biology has seen ever-increasing developments in our understanding of the mechanisms of life. Here we…

Capturing the changes between two biological phenotypes is a crucial task in understanding the mechanisms of various diseases. Most of the existing computational approaches depend on testing the changes in the expression levels of each single gene individually. In this work, we …

With the advent of modern computing technology, there is increased reliance on biometric to provide stronger personal authentication. Among the variety of biometric solutions in the markets, hand-based system is the oldest and most successful form of biometric technology. This t…

This thesis consists of two studies pertaining to the evolution and genomic signatures of viruses. Viruses are obligate intracellular parasites that have a great impact on human, animal and plant health. The first study involves the human infecting Influenza A H5N1 viruses. H5N1…

Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although su…

In systems biology study, biological networks were used to gain insights into biological systems. While the traditional approach to studying biological networks is based on the identification of interactions among genes or the identification of a gene set ranking according to di…

This study explores healthcare coverage disparity using a quantitative analysis on a large dataset from the United States. One of the objectives is to build supervised models including decision tree and neural network to study the efficient factors in healthcare coverage. We als…