{"623812":{"#nid":"623812","#data":{"type":"event","title":"PhD Defense by Shashidhar Ravishankar","body":[{"value":"\u003Cp\u003EIn partial fulfillment of the requirements for the degree of\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDoctor of Philosophy in Bioinformatics\u003C\/p\u003E\r\n\r\n\u003Cp\u003Ein the School of Biological Sciences\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EShashidhar Ravishankar\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDefends his thesis:\u003Cbr \/\u003E\r\n\u003Cstrong\u003EGenetic epidemiology algorithms for tracking drug resistance variants and Genomic clustering of \u003Cem\u003EPlasmodium\u003C\/em\u003E species\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EMonday, August 12, 2019\u003C\/p\u003E\r\n\r\n\u003Cp\u003E10:00 AM Eastern Time\u003C\/p\u003E\r\n\r\n\u003Cp\u003EMolecular Sciences and Engineering Building, (MoSE) Room 1201A\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EThesis Advisor:\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. Fredrik O. Vannberg\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Biological Sciences\u003C\/p\u003E\r\n\r\n\u003Cp\u003EGeorgia Institute of Technology\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003ECommittee\u003C\/strong\u003E \u003Cstrong\u003Emembers\u003C\/strong\u003E:\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. King I. Jordan\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Biological Sciences\u003C\/p\u003E\r\n\r\n\u003Cp\u003EGeorgia Institute of Technology\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. Eberhard O. Voit\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Biomedical Engineering\u003C\/p\u003E\r\n\r\n\u003Cp\u003EGeorgia Institute of Technology\/Emory University\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. John F. McDonald\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Biological Sciences\u003C\/p\u003E\r\n\r\n\u003Cp\u003EGeorgia Institute of Technology\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. Venkatachalam Udhayakumar\u003C\/p\u003E\r\n\r\n\u003Cp\u003EMalaria Branch\u003C\/p\u003E\r\n\r\n\u003Cp\u003ECenters for Disease Control and Prevention\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EAbstract\u003C\/strong\u003E:\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe goal of this thesis is to develop algorithms for the analysis of \u003Cem\u003EP. falciparum\u003C\/em\u003E, \u003Cem\u003EP. brasilianum\u003C\/em\u003E, and \u003Cem\u003EP. malariae\u003C\/em\u003E. Malaria is endemic in many parts of the world including regions of central Africa, South America and South East Asia. Currently there are five known species that cause malaria in humans:\u0026nbsp; \u003Cem\u003EP. falciparum\u003C\/em\u003E, \u003Cem\u003EP. vivax\u003C\/em\u003E, \u003Cem\u003EP. malariae\u003C\/em\u003E, \u003Cem\u003EP. ovale\u003C\/em\u003E and \u003Cem\u003EP. knowlesi\u003C\/em\u003E. According to a World Health Organization (WHO) report from 2018, these five species were responsible for nearly 219 million infections, resulting in an estimated 435,000 deaths related to malaria in 2017. In this work, we highlight algorithms that can identify relatedness of the \u003Cem\u003EPlasmodium\u003C\/em\u003E species and detect drug resistant \u003Cem\u003EP. falciparum\u003C\/em\u003E parasites. The two specific aims in this proposal are designed towards improving the genetic epidemiology of \u003Cem\u003EPlasmodium\u003C\/em\u003E species using novel algorithmic approaches. First, we describe a consensus based variant identification framework to identify SNPs with high confidence. We highlight its applicability in malaria surveillance by using the framework to track known markers associated with drug resistance in \u003Cem\u003EP. falciparum\u003C\/em\u003E. Our results show that consensus based variant calling framework can be used to overcome the inherent bias of different variant calling algorithms as well as providing a metric to assess the confidence associated within any variant detected from NGS data. In the second aim, we describe a k-mer based alignment free algorithm to identify the relatedness of isolates from raw NGS data. Using a weighted Jaccard distance, we describe an exact method for estimation of distance between isolates from k-mer count data. The memory efficiency, scalability and accuracy of the algorithm was demonstrated using in-silico datasets generated from genomes of 12 \u003Cem\u003EPlasmodium \u003C\/em\u003Especies, as well as real-world isolates from an outbreak of \u003Cem\u003EC. auris\u003C\/em\u003E in Colombia. The improved accuracy and scalability offered by the methods described in this work can have significant impact on the use of NGS towards understanding the genetic epidemiology of malaria and enable standardization of NGS analysis across public health laboratories.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":"","field_summary_sentence":[{"value":"Genetic epidemiology algorithms for tracking drug resistance variants and Genomic clustering of Plasmodium species"}],"uid":"27707","created_gmt":"2019-07-30 14:54:14","changed_gmt":"2019-07-30 14:54:14","author":"Tatianna Richardson","boilerplate_text":"","field_publication":"","field_article_url":"","field_event_time":{"event_time_start":"2019-08-12T11:00:00-04:00","event_time_end":"2019-08-12T13:00:00-04:00","event_time_end_last":"2019-08-12T13:00:00-04:00","gmt_time_start":"2019-08-12 15:00:00","gmt_time_end":"2019-08-12 17:00:00","gmt_time_end_last":"2019-08-12 17:00:00","rrule":null,"timezone":"America\/New_York"},"extras":[],"groups":[{"id":"221981","name":"Graduate Studies"}],"categories":[],"keywords":[{"id":"100811","name":"Phd Defense"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[{"id":"1788","name":"Other\/Miscellaneous"}],"invited_audience":[{"id":"78761","name":"Faculty\/Staff"},{"id":"78771","name":"Public"},{"id":"174045","name":"Graduate students"},{"id":"78751","name":"Undergraduate students"}],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[],"email":[],"slides":[],"orientation":[],"userdata":""}}}