{"id":259,"date":"2015-07-02T12:29:38","date_gmt":"2015-07-02T16:29:38","guid":{"rendered":"https:\/\/www.eg.bucknell.edu\/~brk009\/?p=259"},"modified":"2019-07-02T12:35:20","modified_gmt":"2019-07-02T16:35:20","slug":"chuqiao-ren-15","status":"publish","type":"post","link":"https:\/\/www.eg.bucknell.edu\/~brk009\/chuqiao-ren-15\/","title":{"rendered":"Chuqiao Ren, &#8217;15"},"content":{"rendered":"\n<p><strong>Project<\/strong>: A novel ensemble classifier for protein contact map prediction<br><strong>Duration<\/strong>: Summer 2013 &#8211; Spring 2015 <br><strong>Funding<\/strong>: Bucknell University Program for Undergraduate Research, BRK Startup Fund, Geisinger BGRI Grant, CS Dept. Fund<br><\/p>\n\n\n\n<p><u>ABSTRACT<\/u><\/p>\n\n\n\n<p>One of the greatest challenges in bioinformatics is how to predict the 3-D structure of a protein by understanding the relationship between a sequence and its amino acid structure.\u00a0 A <em>protein contact map<\/em> is a useful way of representing protein 3-D conformations. It is based on a distance matrix, which is a symmetric matrix that contains the Euclidean distance between each pair of C-alpha atoms in each residue in the folded protein. \u00a0<\/p>\n\n\n\n<p>Our goal is to improve existing machine learning algorithms for predicting a protein contact map from protein sequence, and develop a novel algorithm that improves the performance of existing contact map predictors. <\/p>\n\n\n\n<p><u>ACHIEVEMENTS<\/u><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><strong>Honors Thesis<\/strong> &#8211; Successfully defended, April 2015<\/li><li><strong>Short paper and poster<\/strong> &#8211; ACB BCB &#8217;14 &#8211; ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, Sept 20-23, Newport Beach, CA [<a href=\"https:\/\/dl.acm.org\/citation.cfm?id=2660818\">link<\/a>]<\/li><li><strong>Poster Presentation<\/strong> &#8211; Fourth Annual Susquehanna Valley Undergraduate Research Symposium, SVURS 2014, August 5, Geisinger Research, Danville, PA<\/li><li><strong>Poster<\/strong> &#8211; Kalman Research Symposium 2014, March 29, Bucknell University, Lewisburg, PA. <\/li><\/ul>\n\n\n\n<p><u>POST GRADUATION UPDATES<\/u><\/p>\n\n\n\n<p>Chuqiao successfully defended her honors thesis in April, 2015. She is staying for a bit longer this summer to help finish a journal publication and submit before she departs us. She is currently planning on pursuing her graduate degree in computer science at Columbia University, starting Fall 2015. Congratulations, Chuqiao!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Project: A novel ensemble classifier for protein contact map predictionDuration: Summer 2013 &#8211; Spring 2015 Funding: Bucknell University Program for Undergraduate Research, BRK Startup Fund, Geisinger BGRI Grant, CS Dept. Fund ABSTRACT One of the greatest challenges in bioinformatics is how to predict the 3-D structure of a protein by understanding the relationship between a &hellip; <a href=\"https:\/\/www.eg.bucknell.edu\/~brk009\/chuqiao-ren-15\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Chuqiao Ren, &#8217;15&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[19],"tags":[21,24,7,8],"post_folder":[],"class_list":["post-259","post","type-post","status-publish","format-standard","hentry","category-research-students","tag-bioinformatics","tag-honors-thesis","tag-research","tag-students"],"_links":{"self":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/posts\/259","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/comments?post=259"}],"version-history":[{"count":1,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/posts\/259\/revisions"}],"predecessor-version":[{"id":260,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/posts\/259\/revisions\/260"}],"wp:attachment":[{"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/media?parent=259"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/categories?post=259"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/tags?post=259"},{"taxonomy":"post_folder","embeddable":true,"href":"https:\/\/www.eg.bucknell.edu\/~brk009\/wp-json\/wp\/v2\/post_folder?post=259"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}