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Topological Data Analysis of DNA sequence data in human gut microbiome

  • Author / Creator
    Petrov, Pavel
  • Persistent Homology broadly refers to tracking the topological features of a geometric object. This study aims to use persistent homology to explore the effect of Human Biotherapy on patients suffering from Clotridium Difficile Infection. The data is presented in the form of several distance matrices and these are analyzed applying summary statistics of persistent homology, namely barcodes, persistence diagrams and persistence landscapes. It is found that there is a difference in the area under the persistence landscapes before and after treatment in dimensions zero and one. These differences are explored using projection onto lower dimensions using isometric mapping. It is found that there are differences in the number of clusters in dimension zero and the number and length of loops in dimension one.

  • Subjects / Keywords
  • Graduation date
    2014-11
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/R3XW4831V
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Master's
  • Department
    • Department of Mathematical and Statistical Sciences
  • Specialization
    • Statistics
  • Supervisor / co-supervisor and their department(s)
    • Heo, Giseon (Mathematical and Statistical Sciences)
  • Examining committee members and their departments
    • Mizera, Ivan (Mathematical and Statistical Sciences)
    • Cho, Eung (Mathematics)
    • Kong, Linglong (Mathematical and Statistical Sciences)