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  • Machine Learning Methods for the Discovery and Analysis of MicroRNAs

    Creator:
    Bell, Jimmy D.
    Abstract:
    MicroRNAs are a highly conserved class of small endogenous RNA, about ~22nt in length, involved in post-transcriptional gene silencing and have prominent roles in disease and development. Though the process of microRNA discovery was once an arduous task, the advent of high throughput sequencing technology has resulted in novel microRNAs...
    Resource Type:
    Masters Thesis
    Full Text:
    : ______________________________________________________ David A. Hendrix MicroRNAs are a highly conserved class of small endogenous RNA, about

  • 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...
    Resource Type:
    Dissertation
    Full Text:
    Machine Learning: Applications in Biology and Genomics Abstract approved: David A. Hendrix Machine

  • The cloze procedure : a proposal for a measure of program comprehension

    Creator:
    Foote, David A.
    Resource Type:
    Capstone Project
    Full Text:
    10th day of August, 1Sl82 TYfed by David A. Foote for David A. Foote ------------------- The Cloze

  • 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:
    I J j J Table 2C shows a comparison of variants from the experiment. The data again showed

  • The Pursuit of Hoppiness : Propelling Hop into the Genomic Era

    Creator:
    Hill, Steven T.
    Abstract:
    Hop (Humulus lupulus L. var lupulus) is a plant of great cultural significance, used as a medicinal herb for thousands of years, and for flavor and as a preservative in brewing beer. Studies of the medicinal effects of the unique compounds produced by hop have led to interest from the...
    Resource Type:
    Masters Thesis
    Full Text:
    David A. Hendrix John A. Henning Hop (Humulus lupulus L. var

  • Type-correct changes — a safe approach to version control implementation

    Creator:
    Dagit, Jason
    Abstract:
    Ensuring correctness of real-world software applications is a challenging task. Testing can be used to find many bugs, but is typically not sufficient for proving correctness or even eliminating entire classes of bugs. However, formal proof and verification techniques tend to be very heavy weight and are simply not available...
    Resource Type:
    Masters Thesis
    Full Text:
    for his continued patience, guidance, and generous nature. Without David this work would not be a

  • A computer-simulated Stern-Gerlach laboratory

    Creator:
    Jia, Lichun
    Abstract:
    This project aims at building a Java application and a Java applet that would simulate a Stern-Gerlach laboratory in Quantum Mechanics. The project provides a tool for allowing the student to quickly design and run on the computer screen a number of experiments involving spin systems. This application could be...
    Resource Type:
    Capstone Project
    Full Text:
    A computer-simulated Stern-Gerlach laboratory Major

  • 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:
    A THESIS submitted to Oregon State University Honors College in partial

  • 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
    Full Text:
    _ J The attached paper describes a project I completed on a graphic editor Phled45. The work was done