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Filtering by: Creator O'Gorman, David Remove constraint Creator: O'Gorman, David Degree Field Computer Science Remove constraint Degree Field: Computer Science

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  • Position-Dependent Codon Usage Bias in the Human Transcriptome

    Creator:
    Subramanian, Kaavya
    Abstract:
    All life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate position-dependent...
    Resource Type:
    Honors College Thesis
    Full Text:
    :_____________________________________________________ David Hendrix All life depends on the reliable translation of RNA to protein according

  • 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...
    Resource Type:
    Dissertation
    Full Text:
    Abstract approved: David A. Hendrix Our goal is to build a system to model the RNA sequences that reveals

  • New Strategies to Develop Hidden Markov Models Combining KEGG and Pfam

    Creator:
    Gupta, Sonica
    Abstract:
    Profile Hidden Markov Models utilize the information stored in a multiple sequence alignment such as its residues and conserved regions to assign probabilities at each column. This indicates areas in the sequences where similar functionality is observed. These probability weights are then combined to assign a sequence score, which is...
    Resource Type:
    Honors College Thesis
    Full Text:
    . Abstract approved:_____________________________________________________ Maude David Profile

  • Tracing the Pacific Islander Diaspora in the Pacific Northwest

    Creator:
    Yarbrough, Nicole
    Abstract:
    The Pacific Islander diaspora in the Pacific Northwest United States is a unique community characterized by diverse cultures, experiences, and motivations for migration. This study aimed to explore the narratives of individuals from different Pacific Islander backgrounds residing in Oregon, shedding light on their reasons for migration and the impact...
    Resource Type:
    Honors College Thesis
    Full Text:
    Abstract approved: _____________________________________________________ David G. Lewis The

  • Determining free energies of hard sphere fluids via Monte Carlo simulation

    Creator:
    Valeskea, Austin
    Abstract:
    Free energy is a fundamental property of a thermodynamic system, from which pressure, entropy, and other interesting properties can be derived. It is useful, then, to be able to accurately compute the free energy at various densities and temperatures in a way that can serve as the basis for further...
    Resource Type:
    Honors College Thesis
    Full Text:
    . Abstract approved: David Roundy Free energy is a fundamental property of a thermodynamic system, from

  • An enhanced version of Caesar supporting 45° geometries

    Creator:
    Lanfri, Ann R.
    Abstract:
    Caesar is an interactive graphic editor that is used to generate layouts for VLSI circuits. It runs on a VAX-11 /780 under the UNIX operating system with Berkeley extensions. Caesar has a unique and simple user interface. Phled is an enhanced version of Caesar that runs on a M68000-based engineering...
    Resource Type:
    Capstone Project

  • Shape Modeling and GPU Based Image Warping

    Creator:
    Burri, David
    Abstract:
    This project addresses the problems of manually placing facial landmarks on a portrait and finding a fast way to warp the annotated image of a face. While there are many approaches to automatically find facial landmarks, most of them provide insufficient results in uncontrolled environments. Thus I introduce a method...
    Resource Type:
    Capstone Project
    Full Text:
    AN ABSTRACT OF THE PROJECT REPORT OF David Burri for the

  • Deep Learning for Human and Biological Languages

    Creator:
    Hong, Junki
    Abstract:
    We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
    Resource Type:
    Dissertation
    Full Text:
    Human and Biological Languages Abstract approved: David Hendrix and Liang Huang We explore the

  • The role of documentation in program modification tasks

    Creator:
    Tolman, David M.
    Abstract:
    This paper reports the findings of two studies conducted at Oregon State University. The first set of studies compares use of header comments versus mnemonic procedure and function names by programmers performing tasks relating to modification tasks. The second study compares the use of header comments versus in-line comments when...
    Resource Type:
    Capstone Project
    Full Text:
    Submitted by David M. Tolman · in partial fulfillment of the requirements for ·the degree ·~ Master of

  • Implementation of a Java Graphical User Interface for the Visual Programming Language Forms/3

    Creator:
    Hackenyos, David P.
    Abstract:
    The visual programming language Forms/3 currently uses a graphical user interface implemented in Garnet. Garnet was developed by the User Interface Software Group in the Human Computer Interaction Institute at Carnegie Mellon University, but is no longer supported. This paper presents an implementation of a user interface for Forms/3 written...
    Resource Type:
    Capstone Project
    Full Text:
    for the Visual Programming Language Forms/3 by David P. Hackenyos B.S., University of Utah, 1989