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  • Computational Approaches for Understanding Combinatorial Gene Regulation

    Creator:
    Ansariola, Mitra
    Abstract:
    Gene regulation is a complex mechanism that controls the spatial and temporal expression of genes in a living cell. My dissertation studies focus on two problems. First, tissue-specific gene expression prediction from DNA sequence and chromatin state, and second, the accurate discovery of small over-represented regulatory circuits in gene regulatory...
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    Dissertation
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    computational biology community in studying these fundamental scientific questions. 9 Chapter 2: Chromatin

  • Computational methods for protein-protein interface prediction

    Creator:
    Tribelhorn, Benjamin
    Abstract:
    Protein-protein interactions underlie all biological processes and are a field of study that has wide implications throughout many other fields including medicine, genetics, biology, and ecology. Proteins are the building blocks and primary actors of life. They work together to accomplish virtually every task within a cell, including, metabolism, signal...
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    Dissertation
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    degree of Doctor of Philosophy in Computer Science presented on August 14, 2013. Title: Computational

  • Algorithms for massive biological datasets

    Creator:
    Bryant, Douglas W. (Douglas Wesley)
    Abstract:
    Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...
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    Dissertation
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    techniques. We examine these issues through the lens of computational biology. ©Copyright by Douglas W

  • Elucidating Computational Narratives to Facilitate Code Comprehension

    Creator:
    Chattopadhyay, Souti
    Abstract:
    Programming is integrated across the workflow of multiple domains where end-user programmers, those who need to program as a means to an end, regularly need to code. In the modern setting of collaborative development, end-user programmers have to interpret the intentions behind existing code to contribute and build solutions to...
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    Dissertation
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    : Elucidating Computational Narratives to Facilitate Code Comprehension Abstract approved: Anita Sarma

  • Plant-Pollinator Interactions in a Changing World: Cryptic Specialization, Pollinator Movement, and Landscape Genetics of Pollinator-Dependent Plants

    Creator:
    Gannon, Dustin G.
    Abstract:
    Plant-pollinator mutualisms are one of the most prevalent and economically important mutualisms in nature. Like many other ecological systems, plant-pollinator communities are threatened by anthropogenic activity, both directly (e.g., habitat conversion and fragmentation) and indirectly (e.g., climate change). While we are aware of many of the activities that adversely impact...
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    Dissertation
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    Jirka for creating such a fun and loving space in which to learn biology and chemistry. I likely would

  • Candidate Causes, Consequences, and Estimation of Individual Diet Specialization

    Creator:
    Coblentz, Kyle E.
    Abstract:
    Diet variation among individuals within populations is widespread. Often diet differences among individuals are attributable to obvious differences among individuals such as age, sex, or morphology. However, growing evidence suggests that individual diet variation is also common among seemingly identical individuals within populations. This phenomenon has been termed individual diet...
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    Dissertation
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    . APPROVED: Major Professor, representing Zoology Acting Chair of the Department of Integrative Biology

  • Computational Elucidation of the Regulatory SNPs in the Non-Coding Regions of the Human Genome

    Creator:
    Yao, Yao
    Abstract:
    We describe a series of novel computational models, CERENKOV (Computational Elucidation of the REgulatory NonKOding Variome) and its successors CERENKOV2, CERENKOV3, and Convolutional CERENKOV3, for discriminating regulatory single nucleotide polymorphisms (rSNPs) from non-regulatory SNPs within non-coding genetic loci. The CERENKOV models are designed for recognizing rSNPs in the context of...
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    Dissertation
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    , how- ever, this task remains a fundamental challenge in computational biology. To address the

  • Computational Approaches for RNA Structure Prediction with Dynamic Programming and Deep Neural Networks

    Creator:
    Deng, Dezhong
    Abstract:
    Our goal is to build a system to model the RNA sequences that reveals their structural information by using efficient dynamic programming algorithms and deep learning approaches. We aim to 1) achieve linear-time for RNA secondary structure prediction based on existing minimum free energy models; 2) utilize deep neural networks...
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    Dissertation
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    for RNA biology have emerged and be- come an important part of computational biology. While

  • A Computational Framework for Resilience-Informed Design

    Creator:
    Hulse, Daniel E.
    Abstract:
    It is desirable for complex engineered systems to perform missions efficiently and economically, even when these missions' complex, variable, long-term operational profiles make it likely for hazards to arise. It is thus important to design these systems to be resilient so that they will actively prevent and recover from hazards...
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    Dissertation
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    Computational Framework for Resilience-Informed Design Abstract approved: Irem Y. Tumer Christopher Hoyle It

  • Interpretable Machine Learning: Applications in Biology and Genomics

    Creator:
    Danaee, Padideh
    Abstract:
    Machine learning (ML) and deep learning (DL) models impact our daily lives with applications in natural language modeling, image analysis, healthcare, genomics, and bioinformatics. The exponential growth of biological sequence data necessitates accompanying advances in computational methods. Although deep learning is highly effective for detecting and classifying biological sequences, challenges...
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    Machine Learning: Applications in Biology and Genomics Abstract approved: David A. Hendrix Machine