{"id":5582,"date":"2025-07-31T15:02:17","date_gmt":"2025-07-31T19:02:17","guid":{"rendered":"https:\/\/www.med.unc.edu\/compmed\/?page_id=5582"},"modified":"2025-12-08T13:24:58","modified_gmt":"2025-12-08T18:24:58","slug":"2018-2","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/","title":{"rendered":"2018 Publications"},"content":{"rendered":"<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2814 size-medium\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-300x201.jpg\" alt=\"a group of scientists analyze data on a large computer screen\" width=\"300\" height=\"201\" srcset=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-300x201.jpg 300w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-1024x687.jpg 1024w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-768x512.jpg 768w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-1536x1031.jpg 1536w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-2048x1375.jpg 2048w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-600x403.jpg 600w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>The recent publication using genomic and computational approaches to identify and annotate non-coding RNAs transcribed at enhancer regions known as enhancer RNAs in breast cancer cells: <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29273624\/\">Enhancer transcription revealed subtype-specific gene expression programs controlling breast cancer pathogenesis<\/a>.<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2840 size-full\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/MJ-Zylka-Publication.jpg\" alt=\"a microscopic picture of brain molecules\" width=\"275\" height=\"243\" \/><\/p>\n<p>Zylka lab, studies genetic and environmental risks for autism.\u00a0 In addition, Zylka lab study molecular and brain mechanisms that underlie pain sensation.\u00a0 Their long-term goal is to uncover new treatments for chronic pain and neurodevelopmental disorders, like autism, Rett syndrome and Angelman syndrome. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/myncbi\/browse\/collection\/40337945\/?sort=date&amp;direction=descending\">A collection of the publications can be found on the NIH website.<\/a><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2838 size-medium\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/PLOS-Computaitonal-Biology-300x191.jpg\" alt=\"an image and graph shows a rendering of cell morphogenesis\" width=\"300\" height=\"191\" srcset=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/PLOS-Computaitonal-Biology-300x191.jpg 300w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/PLOS-Computaitonal-Biology.jpg 311w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>Many studies employ shape descriptors globally to probe mechanisms of cell morphogenesis. Here, we examined cell behavior very locally along the cell edge. The Hilbert-Huang transform (HHT) was used to extract spectra of instantaneous edge motion frequency and magnitude along the entire cell edge, and these were then used to classify subcellular edge sectors with distinct dynamics. When optogenetics was used to acutely inhibit specific signaling pathways, we found changes in the frequency spectra, but not in the magnitude spectra. After clustering cell edge sectors with distinct morphodynamics we observed that sectors with different frequency spectra are associated with specific signaling dynamics and motility behavior. Together these observations let us conclude that the frequency spectrum encodes the wiring of the molecular circuitry that regulates edge movements, whereas the magnitude captures the activation level of circuitry. Full results can be found in the publication: <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1006321\">Profiling cellular morphodynamics by spatiotemporal spectrum decomposition.<\/a><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2839 size-medium\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01-300x289.jpg\" alt=\"A data visualization program rendering of IncRNA sequencing\" width=\"300\" height=\"289\" srcset=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01-300x289.jpg 300w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01-1024x988.jpg 1024w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01-768x741.jpg 768w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01-600x579.jpg 600w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/human_lncRNA_communities-01.jpg 1284w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>Calabrese Lab developed a new method to quantify sequence similarity between evolutionarily unrelated lncRNAs. The method allows us to take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. Full results can be found in the publication: <a href=\"https:\/\/www.nature.com\/articles\/s41588-018-0207-8\">Functional classification of long non-coding RNAs by k-mer content.<\/a><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2841 size-medium\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/MicroRNA-Profiling-300x146.jpg\" alt=\"a graph shows data points related to a Crohn's Disease study\" width=\"300\" height=\"146\" srcset=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/MicroRNA-Profiling-300x146.jpg 300w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/MicroRNA-Profiling-600x291.jpg 600w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/MicroRNA-Profiling.jpg 608w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>MicroRNA profiling in the colon from Crohn\u2019s disease (CD) patients revealed two distinct molecular subtypes, with miR-31 the most significantly differentially expressed between the two. Low colonic miR-31 expression levels at the time of surgery were associated with worse disease outcome\u00a0in adults and with future development of fibrostenotic ileal CD requiring surgery in children. Full results can be found in the publication: <a href=\"https:\/\/insight.jci.org\/articles\/view\/122788\">Colonic epithelial miR-31 associates with the development of Crohn\u2019s phenotypes.<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-2856 size-medium\" src=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/11\/TNBCvsLuminal-300x274.png\" alt=\"a plot chart shows the relation between characterized and uncharacterized kinases as part of a breast cancer research project\" width=\"300\" height=\"274\" srcset=\"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/11\/TNBCvsLuminal-300x274.png 300w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/11\/TNBCvsLuminal-768x700.png 768w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/11\/TNBCvsLuminal-600x547.png 600w, https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/11\/TNBCvsLuminal.png 887w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>Recent work by the Gomez and Johnson labs has led to the discovery of multiple protein kinases and related kinome subnetworks that have distinctive behaviors across breast cancer subtypes as well as in response to drug treatment. Of note was the identification of a number of poorly understood or \u201cdark\u201d kinases that had highly dynamic behavior and thus may represent valuable targets for future drug development. Full results can be found in the publication: <a href=\"https:\/\/www.oncotarget.com\/article\/24337\/\">Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp; The recent publication using genomic and computational approaches to identify and annotate non-coding RNAs transcribed at enhancer regions known as enhancer RNAs in breast cancer cells: Enhancer transcription revealed subtype-specific gene expression programs controlling breast cancer pathogenesis. &nbsp; &nbsp; &nbsp; Zylka lab, studies genetic and environmental risks for autism.\u00a0 In addition, Zylka lab study &hellip; <a href=\"https:\/\/www.med.unc.edu\/compmed\/2018-2\/\" aria-label=\"Read more about 2018 Publications\">Read more<\/a><\/p>\n","protected":false},"author":89430,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-5582","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>2018 Publications | Computational Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/compmed\/2018-2\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"2018 Publications | Computational Medicine\" \/>\n<meta property=\"og:description\" content=\"&nbsp; 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The recent publication using genomic and computational approaches to identify and annotate non-coding RNAs transcribed at enhancer regions known as enhancer RNAs in breast cancer cells: Enhancer transcription revealed subtype-specific gene expression programs controlling breast cancer pathogenesis. &nbsp; &nbsp; &nbsp; Zylka lab, studies genetic and environmental risks for autism.\u00a0 In addition, Zylka lab study &hellip; Read more","og_url":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/","og_site_name":"Computational Medicine","article_modified_time":"2025-12-08T18:24:58+00:00","og_image":[{"width":2560,"height":1718,"url":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-scaled.jpg","type":"image\/jpeg"}],"twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/","url":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/","name":"2018 Publications | Computational Medicine","isPartOf":{"@id":"https:\/\/www.med.unc.edu\/compmed\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/#primaryimage"},"image":{"@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/#primaryimage"},"thumbnailUrl":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-300x201.jpg","datePublished":"2025-07-31T19:02:17+00:00","dateModified":"2025-12-08T18:24:58+00:00","breadcrumb":{"@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.med.unc.edu\/compmed\/2018-2\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/#primaryimage","url":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-300x201.jpg","contentUrl":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/10\/9B7A8703-300x201.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.med.unc.edu\/compmed\/2018-2\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.med.unc.edu\/compmed\/"},{"@type":"ListItem","position":2,"name":"2018 Publications"}]},{"@type":"WebSite","@id":"https:\/\/www.med.unc.edu\/compmed\/#website","url":"https:\/\/www.med.unc.edu\/compmed\/","name":"Computational Medicine","description":"","publisher":{"@id":"https:\/\/www.med.unc.edu\/compmed\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.med.unc.edu\/compmed\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/www.med.unc.edu\/compmed\/#organization","name":"UNC Computational Medicine Program","url":"https:\/\/www.med.unc.edu\/compmed\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.med.unc.edu\/compmed\/#\/schema\/logo\/image\/","url":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/02\/COMPMEDlogoSMALLSWITCH.png","contentUrl":"https:\/\/www.med.unc.edu\/compmed\/wp-content\/uploads\/sites\/852\/2018\/02\/COMPMEDlogoSMALLSWITCH.png","width":300,"height":165,"caption":"UNC Computational Medicine Program"},"image":{"@id":"https:\/\/www.med.unc.edu\/compmed\/#\/schema\/logo\/image\/"}}]}},"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/pages\/5582","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/users\/89430"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/comments?post=5582"}],"version-history":[{"count":3,"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/pages\/5582\/revisions"}],"predecessor-version":[{"id":5882,"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/pages\/5582\/revisions\/5882"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/compmed\/wp-json\/wp\/v2\/media?parent=5582"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}