{"id":93,"date":"2015-06-17T00:00:53","date_gmt":"2015-06-17T00:00:53","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=93"},"modified":"2025-10-20T20:06:58","modified_gmt":"2025-10-20T20:06:58","slug":"designing-synthetic-enhancers-for-thermodynamic-based-modeling","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=93","title":{"rendered":"Designing Synthetic Enhancers for thermodynamic-based modeling"},"content":{"rendered":"<p>When implementing a mathematical modeling approach, working with endogenous enhancers can often be difficult due to the complexity of the enhancer region. In early\u00a0<em>Drosophila<\/em>\u00a0development, enhancers often have 10 \u2013 20 TF binding sites for different transcription factors and different binding affinities, making accurate parameter estimation virtually impossible due to the large number of model parameters and potential parameter compensation.<\/p>\n<p>To combat this issue, we have begun designing synthetic enhancers to allow us to mathematically model and fit parameter values on simple enhancers. This will allow us to decipher the basic underlying rules behind the interactions between TFs before testing the model on more complex endogenous enhancers involved in embryonic development.<\/p>\n<p><a href=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone  wp-image-143\" src=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2.jpg\" alt=\"2LayerModel\" width=\"503\" height=\"220\" srcset=\"https:\/\/wordpress.clarku.edu\/jdresch\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2.jpg 3618w, https:\/\/wordpress.clarku.edu\/jdresch\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2-1000x436.jpg 1000w, https:\/\/wordpress.clarku.edu\/jdresch\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2-300x131.jpg 300w, https:\/\/wordpress.clarku.edu\/jdresch\/wp-content\/uploads\/sites\/383\/2015\/06\/Synthetics2-1024x447.jpg 1024w\" sizes=\"auto, (max-width: 503px) 100vw, 503px\" \/><\/a><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>When implementing a mathematical modeling approach, working with endogenous enhancers can often be difficult due to the complexity of the enhancer region. In early\u00a0Drosophila\u00a0development, enhancers often have 10 \u2013 20 TF binding sites for different transcription factors and different binding &hellip; <a href=\"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=93\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":571,"featured_media":0,"parent":29,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-93","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/93","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/users\/571"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=93"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/93\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/29"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=93"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}