{"id":1652,"date":"2019-01-18T20:09:09","date_gmt":"2019-01-18T20:09:09","guid":{"rendered":"http:\/\/ladam.info\/?p=1652"},"modified":"2019-01-18T20:09:09","modified_gmt":"2019-01-18T20:09:09","slug":"research-on-language-and-biology","status":"publish","type":"post","link":"https:\/\/ladam.info\/index.php\/2019\/01\/18\/research-on-language-and-biology\/","title":{"rendered":"Research on Language and Biology"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"> The theory: Formal language and Genetic <\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">This is related to the work I have done at<a href=\"http:\/\/peccoud.vbi.vt.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\"> Peccoud&#8217;s synthetic biology lab<\/a> from 2008 to 2013:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/ladam.info\/formal-languages-and-dna-molecules\/\">Formal languages and DNA molecules<\/a><\/li><li><a href=\"https:\/\/ladam.info\/design-of-languages-for-systems-and-synthetic-biology\/\">Design of Languages for Systems and Synthetic Biology<\/a><\/li><li><a href=\"https:\/\/ladam.info\/adam-l-formal-languages-to-map-genotype-to-phenotype-in-natural-genomes-gbcb-seminar-2012\/\">Biological Languages to Design Nat<\/a><a href=\"https:\/\/ladam.info\/biological-languages-to-design-natural-genomes\/\">ural Genomes<\/a><\/li><li><a href=\"https:\/\/ladam.info\/adam-l-formal-languages-to-map-genotype-to-phenotype-in-natural-genomes-gbcb-seminar-2012\/\">[Slides] Formal languages to map Genotype to Phenotype in Natural Genomes.<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Application: BioCAD tools<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">This is related to the work I have done at <a href=\"http:\/\/peccoud.vbi.vt.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Peccoud&#8217;s synthetic biology lab<\/a> from 2008 to 2013:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/ladam.info\/biocad-tools-mapping-genotype-to-phenotype-using-attribute-grammar\/\">My work on GenoCAD v2: design to simulation based on domain specific genetic langauges (GenoCAD.org)<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Overview:<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">My phd defense, GBCB program at VT from 2009-2013:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/ladam.info\/slides-defense-mapping-genotype-to-phenotype-using-attribute-grammar\/\">&nbsp;[Slides DEFENSE] Mapping Genotype to Phenotype using Attribute Grammar<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">My Related Publications:<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><u><strong>Peer-\u00ad\u2010Reviewed Journal Articles<\/strong><br><\/u> Michal Galdzicki, Mandy L Wilson, Cesar A Rodriguez, Ernst Oberortner, Matthew Pocock, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Gr\u00fcnberg, Jennifer Hallinan, Nathan J Hillson, Haiyao Huang, Jeffrey D Johnson, Allan Kuchinsky, Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Herbert M Sauro. (2014).\u00a0<strong>SBOL: A community standard for communicating designs in synthetic biology.\u00a0<\/strong>Nature Biotechnology, vol. 32, no. 6, pp. 545\u2013550.<br>M. L. Wilson, S. Okumoto, L. Adam, and J. Peccoud (2013).\u00a0<strong>Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors<\/strong>.\u00a0Bioinformatics, pp. 1\u20137.<br> Cai, Y., Lux, M. W., Adam, L., &amp; Peccoud, J. (2009).\u00a0Modeling structure-\u00ad\u2010function relationships in synthetic DNA sequences using attribute grammars.\u00a0PLoS computational biology, 5(10).<br><u><strong>Book Chapter\/Others<\/strong><br><\/u> Mandy L. Wilson, Russell Hertzberg, Laura Adam, and Jean Peccoud (2011).\u00a0<strong>A Step-\u00ad\u2010by-\u00ad\u2010Step Introduction to Rule-\u00ad\u2010Based Design of Synthetic Genetic Constructs Using GenoCAD.<\/strong>\u00a0Methods in Enzymology\/ Volume 498 -\u00ad\u2010 Synthetic Biology, Part B-\u00ad\u2010 Chapter 8<br> Wipat, Anil; Villalobos, Alan; Stan, Guy-\u00ad\u2010Bart; Smith, Trevor; Sauro, Herbert; Roehner, Nicholas; Pocock, Matthew; Plahar, Hector; Peccoud, Jean; Myers, Chris; Misirli, Goksel; Madsen, Curtis; Lux, Matthew; Kuchinsky, Allan; Ham, Timothy; Gr\u00fcnberg, Raik; Gennari, John; Endy, Drew; Drory, Omri; Densmore, Douglas; Chandran, Deepak; Beal, Jacob; Anderson, J. Christopher; Adler, Aaron; Adam, Laura; Rodriguez, Cesar; Wilson, Mandy; Galdzicki, Michal (2011).\u00a0<strong>Synthetic Biology Open Language (SBOL)Version1.0.0.\u00a0<\/strong>BBFRFC#84(http:\/\/hdl.handle.net\/1721.1\/66172)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The theory: Formal language and Genetic This is related to the work I have done at Peccoud&#8217;s synthetic biology lab from 2008 to 2013: Formal languages and DNA molecules Design of Languages for Systems and Synthetic Biology Biological Languages to Design Natural Genomes [Slides] Formal languages to map Genotype to Phenotype in Natural Genomes. Application:&nbsp;&hellip;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[260,272,254],"tags":[],"class_list":["post-1652","post","type-post","status-publish","format-standard","hentry","category-computational-biology","category-genocad","category-synthetic-biology"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1652","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/comments?post=1652"}],"version-history":[{"count":1,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1652\/revisions"}],"predecessor-version":[{"id":1653,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1652\/revisions\/1653"}],"wp:attachment":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media?parent=1652"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/categories?post=1652"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/tags?post=1652"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}