From the Origins of Life to Epidemics: Bayesian Inference, Stochastic Simulation, and Dynamics of Bioinformatic Systems

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dc.contributor.advisor Wills, P en
dc.contributor.advisor Steel, M en
dc.contributor.author Popinga, Alexandra en
dc.date.accessioned 2019-11-26T01:56:40Z en
dc.date.issued 2019 en
dc.identifier.uri http://hdl.handle.net/2292/49212 en
dc.description.abstract With the advent of DNA and protein sequencing, X-ray crystallography, and other methods of analysis, researchers interested in biological questions have been presented with a wealth of data to parse and interpret. Additionally, some hypotheses, such as those pertaining to the origin of life, are difficult to test experimentally using real molecules and/or systems. Computational and statistical models have therefore become essential tools to understanding the natural world. Such models can be applied to questions ranging from the origin of life on Earth to the spread of infectious diseases. This work provides background and descriptions of novel computational methods pertaining to: (a) a simulation study of sets of catalytic molecules that carry a minimal amount of genetic information for replication, (b) a new substitution method for phylogenetic inference on the aminoacyl-tRNA synthetase enzymes, which are responsible for attaching amino acids to tRNA molecules and are thereby instrumental to the functioning of the genetic code, and (c) the development, testing, and implementation of, and results generated by, a new model for joint phylogenetic and epidemiological inference from the sequences of rapidly evolving, infectious agents, and the comparison of two of these types of models with differing ways of describing branching processes. en
dc.publisher ResearchSpace@Auckland en
dc.relation.ispartof PhD Thesis - University of Auckland en
dc.relation.isreferencedby UoA99265191012302091 en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/nz/ en
dc.title From the Origins of Life to Epidemics: Bayesian Inference, Stochastic Simulation, and Dynamics of Bioinformatic Systems en
dc.type Thesis en
thesis.degree.discipline Computer Science en
thesis.degree.grantor The University of Auckland en
thesis.degree.level Doctoral en
thesis.degree.name PhD en
dc.rights.holder Copyright: The author en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.elements-id 786851 en
pubs.org-id Science en
pubs.org-id Biological Sciences en
pubs.record-created-at-source-date 2019-11-26 en


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http://creativecommons.org/licenses/by-nc-sa/3.0/nz/ Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc-sa/3.0/nz/

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