{"id":42,"date":"2014-07-07T19:55:40","date_gmt":"2014-07-07T19:55:40","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/jgibbons\/?page_id=42"},"modified":"2014-09-14T15:35:38","modified_gmt":"2014-09-14T15:35:38","slug":"research","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/jgibbons\/research\/","title":{"rendered":"Research"},"content":{"rendered":"<p>We study how evolutionary forces\u00a0shape the genome and how these changes influence\u00a0phenotype. To address this topic we heavily utilize next-generation sequencing and \u00a0combine\u00a0comparative, functional, and population genomics.<\/p>\n<hr \/>\n<h2><strong>Fungal Domestication<\/strong><\/h2>\n<p style=\"padding-left: 60px\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone  wp-image-87 alignright\" src=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/297\/2014\/07\/Domestication_pic-300x153.jpg\" alt=\"Domestication_pic\" width=\"320\" height=\"163\" srcset=\"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Domestication_pic-300x153.jpg 300w, https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Domestication_pic-624x319.jpg 624w, https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Domestication_pic.jpg 954w\" sizes=\"auto, (max-width: 320px) 100vw, 320px\" \/>For thousands of years, humans have utilized various fungal species\u00a0for use as fermenting agents, flavor enhancers, and food sources (think\u00a0wine, cheese,\u00a0shiitake mushrooms etc.). During this process, humans propagated\u00a0isolates with specific desired characteristics, and in doing so, altered\u00a0these fungal genomes.\u00a0Domestication genomics offers an excellent model to understand the\u00a0influence of selection on the genome. We employ population genomics and functional genomics to\u00a0identify\u00a0regions of the genome shaped\u00a0by the domestication process.<\/p>\n<hr \/>\n<h2><strong>Fungal\u00a0Pathogenicity<\/strong><\/h2>\n<p style=\"padding-left: 60px\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone  wp-image-88 alignright\" src=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/297\/2014\/07\/Fungal_Pathogen_pic-300x181.jpg\" alt=\"Fungal_Pathogen_pic\" width=\"154\" height=\"93\" srcset=\"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Fungal_Pathogen_pic-300x181.jpg 300w, https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Fungal_Pathogen_pic-624x377.jpg 624w, https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/Fungal_Pathogen_pic.jpg 932w\" sizes=\"auto, (max-width: 154px) 100vw, 154px\" \/>Opportunistic fungal pathogens are an emerging threat to human health. Pinpointing\u00a0the\u00a0genetic toolkit and the functional\u00a0mechanisms which\u00a0allow fungi to invade\u00a0and colonize host tissue is essential for the their treatment and control. We interrogate genome sequencing data and gene expression data to identify genomic regions underlying pathogenicity.<\/p>\n<hr \/>\n<h2><strong>Copy Number Variation<\/strong><\/h2>\n<p style=\"padding-left: 60px\">Copy\u00a0Number Var<img loading=\"lazy\" decoding=\"async\" class=\"wp-image-86 alignright\" src=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/297\/2014\/07\/CNV_pic-290x300.jpg\" alt=\"CNV_pic\" width=\"113\" height=\"116\" srcset=\"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/CNV_pic-290x300.jpg 290w, https:\/\/wordpress.clarku.edu\/jgibbons\/wp-content\/uploads\/sites\/297\/2014\/07\/CNV_pic.jpg 432w\" sizes=\"auto, (max-width: 113px) 100vw, 113px\" \/>iation (CNV) is widespread across eukaryotic\u00a0genomes and is an important source of genetic diversity\u00a0and phenotypic variation.\u00a0In the past, due to technical limitations, CNV was\u00a0difficult to identify. However, advances in DNA sequencing technologies and computational methods have greatly improved CNV detection. We\u00a0use next-generation sequencing data\u00a0to characterize (a) population-level patterns and (b) functional significance of CNV.<\/p>\n<hr \/>\n<p style=\"padding-left: 60px\">\n","protected":false},"excerpt":{"rendered":"<p>We study how evolutionary forces\u00a0shape the genome and how these changes influence\u00a0phenotype. To address this topic we heavily utilize next-generation sequencing and \u00a0combine\u00a0comparative, functional, and population genomics. Fungal Domestication For [&hellip;]<\/p>\n","protected":false},"author":421,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-42","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages\/42","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/users\/421"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/comments?post=42"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/pages\/42\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/jgibbons\/wp-json\/wp\/v2\/media?parent=42"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}