{"647008":{"#nid":"647008","#data":{"type":"event","title":"PhD Defense by Ashwath Kumar","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\u003Cbr \/\u003E\r\n\u003Cstrong\u003EAshwath Kumar\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDefends his thesis:\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EQUANTITATIVE ANALYSIS OF CHIP-SEQ SIGNALS AND TRANSCRIPTOMES\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003ETuesday, May 4\u003Csup\u003Eth\u003C\/sup\u003E, 2021\u003C\/p\u003E\r\n\r\n\u003Cp\u003E10:00 AM Eastern Time\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Ca href=\u0022https:\/\/bluejeans.com\/106700132\u0022\u003Ehttps:\/\/bluejeans.com\/106700132\u003C\/a\u003E\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. Yuhong Fan\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 Members:\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. Yajun Mei\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Industrial and Systems Engineering\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. King 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\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EDr. Shuyi Nie\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\u003Cbr \/\u003E\r\nDr. Kaixiang Cao\u003C\/p\u003E\r\n\r\n\u003Cp\u003ESchool of Medicine\u003C\/p\u003E\r\n\r\n\u003Cp\u003ECase Western Reserve University\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\u003E\u003Ca name=\u0022_Toc439062360\u0022\u003E\u003C\/a\u003E\u003Ca name=\u0022_Hlk70462586\u0022\u003EChromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is commonly used to analyze the in vivo interactions between proteins and DNA across the genome. Analysis of ChIP-seq data has largely focused on detection of presence of peaks that represent DNA regions enriched by chromatin immunoprecipitation, i.e. the DNA loci bound by the immunoprecipitated proteins. To properly interpret ChIP-seq data, capturing its quantitative features is imperative. In this dissertation, we develop a statistically robust pipeline, named as ChIP-seq Signal Quantifier (CSSQ), that provides normalized ChIP-seq data, enabling detection and quantification of differential binding (DBs) across the genome, allowing calculable comparisons among multiple ChIP-seq datasets on predefined regions. Using both experimental datasets and computational simulations, we demonstrate the superior performance of CSSQ against existing tools as evidenced by its high sensitivity and specificity, and low false discovery rate. CSSQ is applicable to ChIP-seq datasets with varied signal to noise ratio, significantly improving the accuracy of comparison of ChIP-seq datasets from different experiments, serving as a powerful pipeline suited to garner quantitative information from ChIP-seq datasets for deciphering epigenomes. \u003C\/a\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003ERNA-seq has become the leading choice for transcriptome analysis.\u0026nbsp; Using RNA-seq and bioinformatics analysis, we characterize gene expression profiles and key cellular processes during stem cell differentiation and cell responses upon nanoparticle exposure. Collectively, these studies show that transcriptome analysis is a powerful tool for characterization and understanding cellular mechanisms.\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":"QUANTITATIVE ANALYSIS OF CHIP-SEQ SIGNALS AND TRANSCRIPTOMES"}],"uid":"27707","created_gmt":"2021-04-28 19:36:27","changed_gmt":"2021-04-28 19:36:27","author":"Tatianna Richardson","boilerplate_text":"","field_publication":"","field_article_url":"","field_event_time":{"event_time_start":"2021-05-04T11:00:00-04:00","event_time_end":"2021-05-04T13:00:00-04:00","event_time_end_last":"2021-05-04T13:00:00-04:00","gmt_time_start":"2021-05-04 15:00:00","gmt_time_end":"2021-05-04 17:00:00","gmt_time_end_last":"2021-05-04 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":""}}}