{"id":12111,"date":"2023-07-07T10:37:03","date_gmt":"2023-07-07T08:37:03","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=12111"},"modified":"2024-02-05T16:38:43","modified_gmt":"2024-02-05T15:38:43","slug":"byung-suk-lee","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/byung-suk-lee\/","title":{"rendered":"Byung Suk Lee"},"excerpt":{"rendered":"

Visiting Professor<\/p>\n","protected":false},"featured_media":12112,"template":"","people_teams":[19,20],"class_list":["post-12111","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-research","people_teams-visiting-scientists"],"yoast_head":"\nByung Suk Lee - Centre for Computational Personalized 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:\/\/sano.science\/people\/byung-suk-lee\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Byung Suk Lee\" \/>\n<meta property=\"og:description\" content=\"Visiting Professor\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/byung-suk-lee\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for Computational Personalized Medicine\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/sano.science\/\" \/>\n<meta property=\"article:modified_time\" content=\"2024-02-05T15:38:43+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/byung_suk_lee.png\" \/>\n\t<meta property=\"og:image:width\" content=\"350\" \/>\n\t<meta property=\"og:image:height\" content=\"350\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sanoscience\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/byung-suk-lee\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/byung-suk-lee\\\/\",\"name\":\"Byung Suk Lee - 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He received the B.S. degree from Seoul National University, M.S. degree from KAIST, and Ph.D. degree from Stanford University. His research interests include data and database management, data mining, data science, data stream processing, information retrieval, information system architecture, and machine learning, with primary applications in environment, healthcare, transportation, smart facility, and citizen science. He has been a PI and Co-PI of nearly 20 funded research projects, an author of more thans 80 peer-reviewed publications, and has served as an organizer, chair, and member of program committees in about 50 international conferences.<\/p>\n","email":"","social_media":false,"tabs":false,"quote":"","position_with_team":{"text_before_link":"","link_text":"","text_after_link":"","link":""},"publications":[{"ID":15035,"post_author":"5","post_date":"2024-01-18 10:23:08","post_date_gmt":"2024-01-18 09:23:08","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-rQfA5d\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Ahmed Abdeen Hamed; Jakub Jonczyk; Mohammad Zaiyan Alam; Ewa Deelman; Byung Suk Lee<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-ySoCXT\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-d34jLw\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">This paper presents a computational approach designed to construct and query a literature-based knowledge graph for predicting novel drug therapeutics. The main objective is to offer a platform that discovers drug combinations from FDA-approved drugs and accelerates their investigations by domain scientists. Specifically, the paper introduced the following algorithms: (1) an algorithm for constructing the knowledge graph from drug, gene, and disease mentions in the biomedical literature; (2) an algorithm for vetting the knowledge graph from drug combinations that may pose a risk of drug interaction; (3) and two querying algorithms for searching the knowledge graph by a single drug or a combination of drugs. The resulting knowledge graph had 844 drugs, 306 gene\/protein features, and 19 disease mentions. The original number of drug combinations generated was 2,001. We queried the knowledge graph to eliminate noise generated from chemicals that are not drugs. This step resulted in 614 drug combinations. When vetting the knowledge graph to eliminate the potentially risky drug combinations, it resulted in predicting 200 combinations. Our domain expert manually eliminated extra 54 combinations which left only 146 combination candidates. Our three-layered knowledge graph, empowered by our algorithms, offered a tool that predicted drug combination therapeutics for scientists who can further investigate from the viewpoint of drug targets and side effects.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-ySoCXT\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_65a8ede86c296\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/ieeexplore.ieee.org\/document\/10029987\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Mining Literature-Based Knowledge Graph for Predicting Combination Therapeutics: A COVID-19 Use Case","post_excerpt":"In: IEEE Xplore, 2023.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"mining-literature-based-knowledge-graph-for-predicting-combination-therapeutics-a-covid-19-use-case","to_ping":"","pinged":"","post_modified":"2024-01-18 10:23:08","post_modified_gmt":"2024-01-18 09:23:08","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=15035","menu_order":35,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":12697,"post_author":"5","post_date":"2023-07-13 13:51:07","post_date_gmt":"2023-07-13 11:51:07","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-t8PrKt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\">Hamed, Ahmed Abdeen; Fandy, Tamer E.; Tkaczuk, Karolina L.; Lee, Byung Suk<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-QsVBmI\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-bvpyWp\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Background: With the Coronavirus becoming a new reality of our world, global efforts continue to seek answers to many questions regarding the spread, variants, vaccinations, and medications. Particularly, with the emergence of several strains (e.g., Delta, Omicron), vaccines will need further development to offer complete protection against the new variants. It is critical to identify antiviral treatments while the development of vaccines continues. In this regard, the repurposing of already FDA-approved drugs remains a major effort. In this paper, we investigate the hypothesis that a combination of FDA-approved drugs may be considered as a candidate for COVID-19 treatment if (1) there exists an evidence in the COVID-19 biomedical literature that suggests such a combination, and (2) there is match in the clinical trials space that validates this drug combination. Methods: We present a computational framework that is designed for detecting drug combinations, using the following components (a) a Text-mining module: to extract drug names from the abstract section of the biomedical publications and the intervention\/treatment sections of clinical trial records. (b) a network model constructed from the drug names and their associations, (c) a clique similarity algorithm to identify candidate drug treatments. Result and Conclusions: Our framework has identified treatments in the form of two, three, or four drug combinations (e.g., hydroxychloroquine, doxycycline, and azithromycin). The identifications of the various treatment candidates provided sufficient evidence that supports the trustworthiness of our hypothesis.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-3o8Ev6\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_64afe50b33d5a\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.mdpi.com\/1999-4923\/14\/3\/567\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"COVID-19 Drug Repurposing: a Network-based Framework for Exploring BioMedical Literature and Clinical Trials for Possible Treatments\u00a0","post_excerpt":"In: Pharmaceutics, 2022.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"covid-19-drug-repurposing-a-network-based-framework-for-exploring-biomedical-literature-and-clinical-trials-for-possible-treatments","to_ping":"","pinged":"","post_modified":"2024-01-05 14:55:40","post_modified_gmt":"2024-01-05 13:55:40","post_content_filtered":"","post_parent":0,"guid":"https:\/\/new.sano.science\/?post_type=research&p=12697","menu_order":72,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12111","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/people"}],"version-history":[{"count":2,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12111\/revisions"}],"predecessor-version":[{"id":15323,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12111\/revisions\/15323"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/12112"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=12111"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=12111"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}