{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/112387"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/112387","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Identification of reassortant influenza viruses at scale : algorithm and applications","abstract":"Reassortment is a reticulate evolutionary process that results in genome shuffling; the most prominent virus known to reassort is the influenza A virus. Methods to identify reassortant influenza viruses do not scale well beyond hundreds of isolates at a time, because they rely on phylogenetic reconstruction, a computationally expensive method. This thus hampers our ability to test systematically whether reassortment is associated with host switching events. In this thesis, I use phylogenetic heuristics to develop a new reassortment detection algorithm capable of finding reassortant viruses in tens of thousands viral isolates. Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence.","abstract_html":"Reassortment is a reticulate evolutionary process that results in genome shuffling; the most prominent virus known to reassort is the influenza A virus. Methods to identify reassortant influenza viruses do not scale well beyond hundreds of isolates at a time, because they rely on phylogenetic reconstruction, a computationally expensive method. This thus hampers our ability to test systematically whether reassortment is associated with host switching events. In this thesis, I use phylogenetic heuristics to develop a new reassortment detection algorithm capable of finding reassortant viruses in tens of thousands viral isolates. Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence.","abstract_has_math":false,"creators":["Ma, Eric J. (Eric Jinglong)"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Biological Engineering.","school":null,"contributors":[],"advisors":["Jonathan A. 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Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Sc. D."]},{"key":"dc:title","label":"Title","values":["Identification of reassortant influenza viruses at scale : algorithm and applications"]}]}],"canonical_facts":{"dc:contributor.advisor":["Jonathan A. Runstadler."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Biological Engineering."],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Biological Engineering."],"dc:creator":["Ma, Eric J. (Eric Jinglong)"],"dc:date.accessioned":["2017-12-05T16:25:42Z"],"dc:date.available":["2017-12-05T16:25:42Z"],"dc:date.issued":["2017"],"dc:description":["Thesis: Sc. 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