{"id":319096,"date":"2021-08-09T12:01:14","date_gmt":"2021-08-09T09:01:14","guid":{"rendered":"https:\/\/en.buradabiliyorum.com\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/"},"modified":"2021-08-09T12:01:14","modified_gmt":"2021-08-09T09:01:14","slug":"how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases","status":"publish","type":"post","link":"https:\/\/buradabiliyorum.com\/en\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/","title":{"rendered":"#How machine learning could help develop cures for COVID-19 and other diseases"},"content":{"rendered":"<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_84 counter-hierarchy ez-toc-counter ez-toc-custom ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-6a2e25357173f\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #dd3333;color:#dd3333\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #dd3333;color:#dd3333\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-6a2e25357173f\" checked aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/buradabiliyorum.com\/en\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/#The_big_idea\" >The big idea<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/buradabiliyorum.com\/en\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/#Why_it_matters\" >Why it matters<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/buradabiliyorum.com\/en\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/#What_other_research_is_being_done\" >What other research is being done<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/buradabiliyorum.com\/en\/how-machine-learning-could-help-develop-cures-for-covid-19-and-other-diseases\/#Whats_next\" >What\u2019s next<\/a><\/li><\/ul><\/nav><\/div>\n<p>&#8220;<strong>#How machine learning could help develop cures for COVID-19 and other diseases<\/strong>&#8221;<\/p>\n<div>\n<h2><span class=\"ez-toc-section\" id=\"The_big_idea\"><\/span>The big idea<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>We combined a machine learning algorithm with knowledge gleaned from hundreds of biological experiments to develop <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1101\/gr.265595.120\">a technique<\/a> that allows biomedical researchers to figure out the functions of the proteins that turn genes on and off in cells, called tran<a href=\"https:\/\/buradabiliyorum.com\/en\/category\/download-scripts-themes-apps\/\" data-internallinksmanager029f6b8e52c=\"9\" title=\"Download Scripts &amp; Themes &amp; Apps\" target=\"_blank\" rel=\"noopener\">script<\/a>ion factors. This knowledge could make it easier to develop drugs for a wide range of diseases.<\/p>\n<p>Early on during the COVID-19 pandemic, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1016\/j.cell.2020.04.035\">scientists who worked out the genetic code of the RNA molecules of cells in the lungs and intestines<\/a> found that only a small group of cells in these organs were most vulnerable to being infected by the SARS-CoV-2 virus. That allowed researchers to focus on blocking the virus\u2019s ability to enter these cells. Our technique could make it easier for researchers to find this kind of information.<\/p>\n<p>The biological knowledge we work with comes from this kind of RNA sequencing, which gives researchers a snapshot of the hundreds of thousands of RNA molecules in a cell as they are being translated into proteins. A widely praised machine learning tool, the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1016\/j.cell.2021.04.048\">Seurat analysis platform<\/a>, has helped researchers all across the world discover new cell populations in healthy and diseased organs. This machine learning tool processes data from single-cell RNA sequencing without any information ahead of time about how these genes function and relate to each other.<\/p>\n<p>Our technique takes a different approach by adding knowledge about certain genes and cell types to find clues about the distinct roles of cells. There has been more than a decade of research identifying all the potential targets of transcription factors.<\/p>\n<p>Armed with this knowledge, we used a mathematical approach called <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/towardsdatascience.com\/what-is-bayesian-inference-4eda9f9e20a6\">Bayesian inference<\/a>. In this technique, prior knowledge is converted into probabilities that can be calculated on a computer. In our case, it\u2019s the probability of a gene being regulated by a given transcription factor. We then used a machine learning algorithm to figure out the function of the transcription factors in each one of the thousands of cells we analyzed.<\/p>\n<p>We <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1101\/gr.265595.120\">published our technique<\/a>, called Bayesian Inference Transcription Factor Activity Model, in the journal Genome Research and also made the software <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/github.com\/jaleesr\/BITFAM\">freely available<\/a> so that other researchers can test and use it.<\/p>\n<h2><span class=\"ez-toc-section\" id=\"Why_it_matters\"><\/span>Why it matters<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>Our approach works across a broad range of cell types and organs and could be used to develop treatments for diseases like COVID-19 or Alzheimer\u2019s. Drugs for these difficult-to-treat diseases work best if they target cells that cause the disease and avoid collateral damage to other cells. Our technique makes it easier for researchers to hone in on these targets.<\/p>\n<figure class=\"align-center zoomable\">\n<p><figure class=\"post-image post-mediaBleed aligncenter\"><a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/images.theconversation.com\/files\/414689\/original\/file-20210804-5434-1c9381h.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=1000&amp;fit=clip\"><img loading=\"lazy\" decoding=\"async\" alt=\"A blob is covered with tiny spheres\" width=\"600\" height=\"516\" class=\"js-lazy\" src=\"https:\/\/images.theconversation.com\/files\/414689\/original\/file-20210804-5434-1c9381h.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;fit=clip\"\/><noscript><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/images.theconversation.com\/files\/414689\/original\/file-20210804-5434-1c9381h.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;fit=clip\" alt=\"A blob is covered with tiny spheres\" width=\"600\" height=\"516\" class=\"\" srcset=\"\"\/><\/noscript><\/a><figcaption><a rel=\"nofollow noopener\" target=\"_blank\" href=\"#\" data-url=\"https:\/\/twitter.com\/intent\/tweet?url=https%3A%2F%2Feditorial.thenextweb.com%2Fneural%2F2021%2F08%2F09%2Fmachine-learning-develop-cures-covid-19-other-diseases-syndication%2F&amp;via=thenextweb&amp;related=thenextweb&amp;text=Check out this picture on: A human cell (greenish blob) is heavily infected with SARS-CoV-2 (orange dots), the virus that causes COVID-19, in this colorized microscope image. National Institute of Allergy and Infectious Diseases\" data-title=\"Share A human cell (greenish blob) is heavily infected with SARS-CoV-2 (orange dots), the virus that causes COVID-19, in this colorized microscope image. National Institute of Allergy and Infectious Diseases on Twitter\" data-width=\"685\" data-height=\"500\" class=\"post-image-share popitup\" title=\"Share A human cell (greenish blob) is heavily infected with SARS-CoV-2 (orange dots), the virus that causes COVID-19, in this colorized microscope image. National Institute of Allergy and Infectious Diseases on Twitter\"><i class=\"icon icon--inline icon--twitter--dark\"\/><\/a>A human cell (greenish blob) is heavily infected with SARS-CoV-2 (orange dots), the virus that causes COVID-19, in this colorized microscope image. National Institute of Allergy and Infectious Diseases<\/figcaption><\/figure><figcaption\/><\/p>\n<\/figure>\n<h2><span class=\"ez-toc-section\" id=\"What_other_research_is_being_done\"><\/span>What other research is being done<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>Single-cell RNA-sequencing has revealed how each organ can have 10, 20, or even more subtypes of specialized cells, each with distinct functions. A very exciting new development is the emergence of spatial transcriptomics, in which RNA sequencing is performed in a spatial grid that allows researchers to study the RNA of cells at specific locations in an organ.<\/p>\n<p>A <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1038\/s41587-021-00935-2\">recent paper<\/a> used a Bayesian statistics approach similar to ours to figure out distinct roles of cells while taking into account their proximity to one another. Another research group <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1038\/s41587-021-00830-w\">combined spatial data with single-cell RNA-sequencing data<\/a> and studied the distinct functions of neighboring cells.<\/p>\n<h2><span class=\"ez-toc-section\" id=\"Whats_next\"><\/span>What\u2019s next<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>We plan to work with colleagues to use our new technique to study complex diseases such as Alzheimer\u2019s disease and COVID-19, work that could lead to new drugs for these diseases. We also want to work with colleagues to better understand the complexity of interactions among cells.<\/p>\n<p><em>Article by <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/profiles\/shang-gao-1253208\">Shang Gao<\/a>, Doctoral student in Bioinformatics, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/institutions\/university-of-illinois-at-chicago-776\">University of Illinois at Chicago<\/a> and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/profiles\/jalees-rehman-98663\">Jalees Rehman<\/a>, Professor of Medicine, Pharmacology and Biomedical Engineering, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/institutions\/university-of-illinois-at-chicago-776\">University of Illinois at Chicago<\/a><\/em><\/p>\n<p><em>This article is republished from <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\">The Conversation<\/a> under a Creative Commons license. Read the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/machine-learning-plus-insights-from-genetic-research-shows-the-workings-of-cells-and-may-help-develop-new-drugs-for-covid-19-and-other-diseases-164992\">original article<\/a>.<\/em><\/p>\n<\/div>\n<p><script async src=\"\/\/platform.twitter.com\/widgets.js\" charset=\"utf-8\"><\/script><\/p>\n<blockquote><p><strong><span style=\"color: #ff6600;\">If you liked the article, do not forget to share it with your friends. 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