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Filtering by: Creator Klaine, Stephen J. Remove constraint Creator: Klaine, Stephen J. Degree Field Computer Science Remove constraint Degree Field: Computer Science

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  • Exploration of regression models for cancer noncoding mutation recurrence

    Creator:
    Xu, Tanjin
    Abstract:
    An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Integrated with current well-studied massive knowledge and findings about the role of protein-coding mutations in cancer, demystifying the functional...
    Resource Type:
    Masters Thesis
    Full Text:
    for Cancer Noncoding Mutation Recurrence Abstract approved: Stephen A. Ramsey An important impact

  • Variant Annotation

    Creator:
    He, Jun
    Abstract:
    With the development of technologies in genome sequencing and variant detection, a huge number of variants are detected. To further analyze the variants, it requires an efficient tool to annotate the functional effect of variants. This project managed to develop an efficient program to annotate the functional effect of variants...
    Resource Type:
    Capstone Project
    Full Text:
    approved: Stephen Ramsey With the development of technologies in genome sequencing and variant detection

  • Analytical Methods for Improving Causal Inference

    Creator:
    Sinha, Meghamala
    Abstract:
    Causal inference is an important analytical tool to bridge the gap between prediction and decision-making. However, learning a causal network solely from data is a challenging task. In this work, various techniques have been explored for a better and improved causal network learning from data. Firstly, the problem of learning...
    Resource Type:
    Dissertation
    Full Text:
    : Analytical Methods for Improving Causal Inference Abstract approved: Stephen A. Ramsey Causal inference is

  • 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...
    Resource Type:
    Dissertation
    Full Text:
    Elucidation of the Regulatory SNPs in the Non-Coding Regions of the Human Genome Abstract approved: Stephen

  • Machine Learning for Precision Medicine: Application to Cancer Chemotherapy Response Prediction and Wound Healing Status Assessment

    Creator:
    Wei, Qi
    Abstract:
    Ph.D. candidate Qi Wei's thesis consists of two projects: Chemotherapy Project: a study based on the research paper "Predicting chemotherapy response of various cancer types using a variational auto-encoder approach" submitted to the bioRxiv preprint archive and accepted by the BMC bioinformatics; and Wound Monitor Project: implementing and assessing analytics...
    Resource Type:
    Dissertation
    Full Text:
    Assessment Abstract approved: Stephen A. Ramsey Ph.D. candidate Qi Wei’s thesis consists of two projects

  • On asymmetric error-correcting codes

    Creator:
    Cunningham, Robert Stephen
    Abstract:
    Historically, coding theory has dealt with binary codes correcting symmetric errors, in which errors are made in both 0 and 1 bits with equal likelihood. Within the past ten years, some study has been made of asymmetric codes, under the assumption that the only errors which occur are errors in...
    Resource Type:
    Masters Thesis
    Full Text:
    THESIS OF Robert Stephen Cunningham for the degree of Master of Science in Computer Science presented

  • A fast division algorithm

    Creator:
    Dum, Stephen Anthony
    Abstract:
    A radix 2n non-restoring division algorithm is described. The algorithm is designed to be compatible with hardware multiprecision multiplication methods currectly used in high speed digital computers. This enables the use of the same hardware, with only changes in control logic, to be used to implement both multiplication and division....
    Resource Type:
    Dissertation
    Full Text:
    A fast division algorithm STEPHEN ANTHONY DUM (Name

  • AOPS : an abstraction oriented programming system for literate programming

    Creator:
    Shum, Stephen M.
    Abstract:
    The practice of literate programming is not widespread because existing literate programming systems have some undesirable characteristics such as programming language and text processor dependence and lack of flexible tools for viewing and manipulation of the source file. This dissertation describes the literate programming system AOPS (Abstraction Oriented Programming System)...
    Resource Type:
    Dissertation
    Full Text:
    literate programming AN ABSTRACT OF THE THESIS OF Stephen M. Shum for the degree of Doctor of Philosophy

  • Transformers for representing microbiome data: an empirical evaluation

    Creator:
    Varma, Rohan
    Abstract:
    As the link between human microbiomes and health has become more established, the interest in applying statistical approaches to microbiome data to understand the mechanisms behind these links has grown. However, microbiome data is often of unmanageable size, and consequently, producing quality lower dimensional representations of samples is a significant...
    Resource Type:
    Honors College Thesis
    Full Text:
    , representing Microbiology Stephen Ramsey, Committee Member, representing Electrical Engineering and Computer

  • 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:
    _____________________________________________________________________ Stephen Ramsey, Committee Member, representing Electrical Engineering and Computer Science