{"id":1429,"date":"2012-09-11T08:19:25","date_gmt":"2012-09-10T23:19:25","guid":{"rendered":"http:\/\/www.genome.rcast.u-tokyo.ac.jp\/?p=1429"},"modified":"2018-03-23T14:02:36","modified_gmt":"2018-03-23T05:02:36","slug":"%e4%bb%b2%e6%9c%a8-%e7%ab%9c","status":"publish","type":"post","link":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/%e4%bb%b2%e6%9c%a8-%e7%ab%9c\/","title":{"rendered":"Ryo Nakaki"},"content":{"rendered":"<p><strong>Personal Profile<\/strong><\/p>\n<p>A computational biologist specializing in computational and statistical analysis of high-dimensional biological data, with many experiences in researches based on next generation sequencing data. Current focus is to elucidate the switching mechanisms of the combinational associations among transcriptional regulators in different contexts. Develops new algorithms based on the three following interests;<\/p>\n<ol>\n<li>Transcriptional co-factors: Co-localization analysis though comparing multiple epi-genome data (e.g., ChIP-seq data for transcriptional regulators and histone modifications, open chromatin regions)<\/li>\n<li>Recognition sequences and chromatin structures: Footprint analysis integrating recognition motifs and DNase I cleavages obtained by DNase-seq and ATAC-seq<\/li>\n<li>Genome-wide interactions: Mapping analysis integrating the binding sites of transcriptional regulators and genome-wide interactions obtained by ChIA-PET and HiC<\/li>\n<\/ol>\n<p>Email:\u00a0<a href=\"mailto:nakaki@genome.rcast.u-tokyo.ac.jp\">nakaki@genome.rcast.u-tokyo.ac.jp<\/a><\/p>\n<p><strong>Skills and competence<\/strong><\/p>\n<p>Data processing for next generation sequencing:<\/p>\n<ul>\n<li>Mapping (Bowtie, BWA, BatMis, TopHat)<\/li>\n<li>Peak calling (MACS, PeakSeq, SICER, PeakRanger)<\/li>\n<li><em>De novo<\/em> motif identification (MODIC, MDscan, Weeder, DME, Bioprospector, MEME)<\/li>\n<\/ul>\n<p>Programming language:<\/p>\n<ul>\n<li>Software development (Java, Python, Java, C)<\/li>\n<li>Web development (PHP, Javascript, HTML)<\/li>\n<li>Analysis (R, Python)<\/li>\n<li>Others (Perl)<\/li>\n<\/ul>\n<p>Expertise of cellular Biology:<\/p>\n<ul>\n<li>Hematopoietic differentiation<\/li>\n<li>Myocardial differentiation<\/li>\n<li>Endothelial differentiation<\/li>\n<li>Adipocyte differentiation<\/li>\n<\/ul>\n<p><strong>Work experience<\/strong><\/p>\n<ul>\n<li>2015-present <strong>Chief Executive Officer at Rhelixa Inc.<\/strong>, Tokyo, Japan (See: <a href=\"http:\/\/rhelixa.com\/\" target=\"_blank\" rel=\"noopener\">Rhelixa&#8217;s Homepage<\/a>)<\/li>\n<li>2015-present <strong>Special research Fellowship for Young Scientists<\/strong> (for Ph.D), Japan\u2019s Society for the Promoter of Science (JSPS), Tokyo, Japan<\/li>\n<li>2014-present<strong> Chief Analytics Officer at SYMAX Inc.<\/strong>, Tokyo, Japan<\/li>\n<\/ul>\n<p><strong>Achievements<\/strong><\/p>\n<ul>\n<li>2015 <strong>Best Poster Award<\/strong>, the 11th International Workshop on Advanced Genomics, Tokyo, Japan<\/li>\n<li>2015 <strong>Runner-up<\/strong>, Japan Business Model Competition 2015, Tokyo, Japan<\/li>\n<li>2014 <strong>Championship<\/strong>, Business Model competition, University of Tokyo, Tokyo, Japan<\/li>\n<li>2013 <strong>Most Valuable Presenter Award<\/strong>, Tokyo, the 87th Annual Meeting of the Japanese Biochemical Society, Japan<\/li>\n<li>2012 <strong>National Certificate of Radiation Protection Supervision (Category 1)<\/strong>, Tokyo, Japan, 2012<\/li>\n<\/ul>\n<p><strong>Publications<\/strong><\/p>\n<ul>\n<li>2015 Y. Abe, R. Rozqie, Y. Matsumura, T. Kawamura, <strong>Nakaki<\/strong>, Y. Tsurutani, K. Tanimura-Inagaki, A. Shiono, K. Magoori, K. Nakamura, S. Kajimura, H. Kimura, T. Tanaka, K. Fukami, TF. Osborne, T. Kodama, H. Aburatani, T. Inagaki, J. Sakai \u201cPKA phospho-switch on JMJD1A Regulates Long-range Chromatin Association with SWI\/SNF and PPAR\u03b3 for BAT Function.\u201d <em>Nature communications<\/em><\/li>\n<li>2015 T. Inagaki, S. Iwasaki, Y. Matsumura, T. Kawamura, T. Tanaka, Y. Abe, A. Yamasaki, Y. Tsurutani, A. Yoshida, Y. Chikaoka, K. Nakamura, K. Magoori, <strong>Nakaki<\/strong>, TF. Osborne, K. Fukami, H. Aburatani, T. Kodama, J. Sakai. \u201cThe FBXL10\/KDM2B scaffolding protein associates with novel polycomb repressive complex-1 to regulate adipogenesis.\u201d <em>J Biol Chem.<\/em> Feb 13;290(7):4163-77<\/li>\n<li>2012 <strong>Nakaki<\/strong>, J. Kang, M. Tateno, \u201cA novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal\/noise distributions.\u201d <em>Nucleic Acids Res.<\/em> Oct;40(18):8835-48<\/li>\n<\/ul>\n<p><strong>Scholarships<\/strong><\/p>\n<ul>\n<li>2014-2015 <strong>Special research Fellowship for Young Scientists<\/strong>, JSPS, Tokyo, Japan<\/li>\n<li>2013-2014 <strong>Special Research Fellowship for Engineering<\/strong>, University of Tokyo, Tokyo, Japan<\/li>\n<li>2012-2013 <strong>Special Research Fellowship for Engineering<\/strong>, Global CEO Program of Japan, Tokyo, Japan<\/li>\n<\/ul>\n<p><strong>Interests:<\/strong><\/p>\n<ul>\n<li>Designing and creating Lego robots<\/li>\n<li>Stained glass art<\/li>\n<li>Modern Japanese history<\/li>\n<li>Changing the notion on hair loss<\/li>\n<li>Creating new Japanese dishes (4-year experience cooking at a traditional Japanese restaurant)<\/li>\n<\/ul>\n<p><\/p>","protected":false},"excerpt":{"rendered":"<p>Personal Profile A computational biologist specializing in computational and statistical analysis of high-dime &hellip; <a href=\"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/%e4%bb%b2%e6%9c%a8-%e7%ab%9c\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":54,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[14],"tags":[],"class_list":["post-1429","post","type-post","status-publish","format-standard","hentry","category-profile"],"_links":{"self":[{"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/posts\/1429","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/users\/54"}],"replies":[{"embeddable":true,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/comments?post=1429"}],"version-history":[{"count":39,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/posts\/1429\/revisions"}],"predecessor-version":[{"id":3812,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/posts\/1429\/revisions\/3812"}],"wp:attachment":[{"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/media?parent=1429"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/categories?post=1429"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.genome.rcast.u-tokyo.ac.jp\/en\/wp-json\/wp\/v2\/tags?post=1429"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}