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  • Thesis

  • Authors: Walker, Megon Jarmaine (2006)

  • Understanding molecular interactions is at the core of computational biology and includes problems such as characterizing protein-protein, protein-small molecule, protein-DNA, and Protein-RNA binding events. These interactions are often elucidated by expensive and time-consuming assays during which candidate binders are screened against a target. The main aim of this dissertation is to improve the speed, cost, and overall efficiency of screening assays in the context of drug design and molecular systems biology. Sequential screening is an iterative process of experimentation and model refinement. Target binding activity is determined for samples of putative binders, results are used to update a classification model, and subsequent binding experiments are performed based on knowledg...

  • Thesis

  • Authors: Reck, Gregory M. (2006)

  • While most proteins in biological systems are inherently stable as a prerequisite to performing their functions, a small number of normally well-behaved proteins can engage in a process of aggregation that eventually leads to the formation of an insoluble material identified as an amyloid. Details of the aggregation process are not fully known, but for some model proteins the process can be initiated with known destabilizing conditions. While no sequence or structural similarities have been observed among the proteins, structural instability associated with a characteristic motif in the protein could be a common thread. The proposed strategy to search for such a feature employs a knowledge-based tool that examines the sequence-structure relationship in a specific target protein base...

  • Thesis

  • Authors: Gu, Zhenmei (2006)

  • As text-based resources available online continue to grow explosively, there is ever-increasing need for automatically extracting useful information from these textual data. Information Extraction (IE) is the problem of extracting specific information from textual documents for generating structured summaries. The research in IE has evolved from the IE systems that were manually built with hand-crafted rules, to more recent ones that obtain extraction knowledge automatically from annotated texts. The advantage of using machine learning is that it is easier to adapt an IE system to different extraction tasks. Such adapt-ability is a key requirement for practical IE systems. In view of these, in this thesis we focus our work on the IE systems that can learn extraction knowledge from d...

  • Thesis

  • Authors: Laine, Tei (2006)

  • Human-initiated land-use and land-cover change is the most significant single factor behind global climate change. Since climate change affects human, animal and plant populations alike, and the effects are potentially disastrous and irreversible, it is equally important to understand the reasons behind land-use decisions as it is to understand their consequences. Empirical observations and con-trolled experimentation are not usually feasible methods for studying this change. Therefore, scientists have resorted to computer modeling, and use other complementary approaches, such as household surveys and field experiments, to add depth to their models. The computer models are not only used in the design and evaluation of environmental programs and policies, but they can be used to edu...

  • Thesis

  • Authors: Kim, Namhoon (2006)

  • The notion of local quantum algebras that encode the "algebra" aspects of quantum field theories is introduced. This setup provides a foundation on which we can define precisely what an operator product expansion is, and we describe the relationships between local quantum algebras, operator product expansion, conformal field theories and some generalizations of vertex algebras that are introduced by various authors including Borcherds, Nikolov, and Huang and Kong. Traditional approaches to vertex algebras are characterized by vertex operators and the formal calculus which lead to useful formal operator identities. We introduce the notion of factorization, and study local quantum algebras that satisfy factorization property in a general setting. Such a structure can be formulated ab...

  • Thesis

  • Authors: Eriksson, Nicholas Karl (2006)

  • Algebraic statistics is the study of the algebraic varieties that correspond to discrete statistical models, Such statistical models are used throughout computational biology, for example to describe the evolution of DNA sequences. This perspective on statistics allows us to bring mathematical techniques to bear and also provides a source of new problems in mathematics, The central focus of this thesis is the use of the language of algebraic statistics to translate between biological and statistical problems and algebraic and combinato¬rial mathematics. The wide range of biological and statistical problems addressed in this work come from phylogenetics, comparative genomics, virology, and the analysis of ranked data. While these problems are varied, the mathematical techniques used...

  • Thesis

  • Authors: He, Jingwu (2006)

  • The most intriguing problems in genetics epidemiology are to predict genetic disease susceptibility and to associate single nucleotide polymorphisms (SNPs) with diseases. In such these studies, it is necessary to resolve the ambiguities in genetic data. The primary obstacle for ambiguity resolution is that the physical methods for separating two haplotypes from an individual genotype (phasing) are too expensive. Although computational haplotype inference is a well-explored problem, high error rates continue to deteriorate association accuracy. Secondly, it is essential to use a small subset of informative SNPs (tag SNPs) accurately representing the rest of the SNPs (tagging). Tagging can achieve budget savings by genotyping only a limited number of SNPs and computationally inferring...

  • Thesis

  • Authors: Cicco, Tracey Martine Westbrook (2006)

  • Algorithms for Computing Restricted Root Systems and Weyl Groups. (Under the direction of Dr. Aloysius Helminck.) While the computational packages LiE, Gap4, Chevie, and Magma are sufficient for work with Lie Groups and their corresponding Lie Algebras, no such packages exist for computing the k-structure of a group or the structure of symmetric spaces. My goal is to examine the k-structure of groups and the structure of symmetric spaces and arrive at various algorithms for computing in these spaces.

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  • Authors: Zaslavsky, Elena (2006)

  • A major objective in molecular biology is to understand how a genome encodes the information that speci es when and where a gene will be transcribed into its protein product. Mediating proteins, known as transcription factors, facilitate this process by interacting with the cell 's sDNA and the transcription machinery. It is of central importance to identify all sequence-speci c DNA binding sites of transcription factors. In this thesis, we consider two relevant computational problems. The first problem is to develop a representation for a group of known binding sites of a particular transcription factor, in order to facilitate recognition of other binding sites of the same protein. We evaluate the e ectiveness of several approaches commonly used for this problem, and show that the...