{"id":648398,"date":"2025-01-08T22:05:24","date_gmt":"2025-01-08T19:05:24","guid":{"rendered":"https:\/\/en.buradabiliyorum.com\/scientists-create-scalable-solution-for-analyzing-single-cell-data\/"},"modified":"2025-01-08T22:05:24","modified_gmt":"2025-01-08T19:05:24","slug":"scientists-create-scalable-solution-for-analyzing-single-cell-data","status":"publish","type":"post","link":"https:\/\/buradabiliyorum.com\/en\/scientists-create-scalable-solution-for-analyzing-single-cell-data\/","title":{"rendered":"#Scientists create scalable solution for analyzing single-cell data"},"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-6a2f38d5ca2d9\" 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-6a2f38d5ca2d9\" 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\/scientists-create-scalable-solution-for-analyzing-single-cell-data\/#Unsupervised_machine_learning_for_single-cell_analysis\" >Unsupervised machine learning for single-cell analysis<\/a><\/li><\/ul><\/nav><\/div>\n<div>\n<div class=\"article-gallery lightGallery\">\n<div data-thumb=\"https:\/\/scx1.b-cdn.net\/csz\/news\/tmb\/2025\/scientists-create-scal.jpg\" data-src=\"https:\/\/scx2.b-cdn.net\/gfx\/news\/2025\/scientists-create-scal.jpg\" data-sub-html=\"Graphical abstract. Credit: &lt;i&gt;Cell Genomics&lt;\/i&gt; (2025). DOI: 10.1016\/j.xgen.2024.100739\">\n<figure class=\"article-img\">\n            <img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/scx1.b-cdn.net\/csz\/news\/800a\/2025\/scientists-create-scal.jpg\" alt=\"Scientists create scalable solution for analyzing single-cell data\" title=\"Graphical abstract. Credit: Cell Genomics (2025). DOI: 10.1016\/j.xgen.2024.100739\" width=\"800\" height=\"530\"\/><figcaption class=\"text-darken text-low-up text-truncate-js text-truncate mt-3\">\n                Graphical abstract. Credit: <i>Cell Genomics<\/i> (2025). DOI: 10.1016\/j.xgen.2024.100739<br \/>\n            <\/figcaption><\/figure>\n<\/p><\/div>\n<\/div>\n<p>Researchers have amassed vast single-cell gene expression databases to understand how the smallest details impact human biology. However, current analysis methods struggle with the large volume of data and, as a result, produce biased and contradictory findings.<\/p>\n<p>Scientists at St. Jude Children&#8217;s Research Hospital created a machine-learning algorithm capable of scaling with these single-cell data repositories to deliver more accurate results. The new method was <a rel=\"nofollow\" target=\"_blank\" href=\"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666979X24003689\" target=\"_blank\">published<\/a> today (Jan. 8) in <i>Cell Genomics<\/i>.<\/p>\n<p>Before single-cell analysis, bulk gene expression data gave high-level but unrefined results for many diseases. Single-cell analysis enables researchers to look at individual cells of interest, a difference akin to looking at an individual corn kernel instead of a field. These detailed insights have already made breakthroughs in understanding some diseases and treatments, but difficulty replicating and scaling analyses for data that keeps increasing in size has stymied progress.<\/p>\n<p>&#8220;We&#8217;ve implemented a new toolset that can be scaled as these single-cell RNA sequencing datasets continue to grow,&#8221; said corresponding author Paul Geeleher, Ph.D., St. Jude Department of Computational Biology. &#8220;There has been an exponential explosion in the compute time for single-cell analysis, and our method brings accurate analysis back into a tractable timeframe.&#8221;<\/p>\n<p>All techniques for studying single-cell gene expression create large amounts of data. When scientists test millions of cells simultaneously, the amount of computer memory and processing power needed to handle the data is enormous. Geeleher&#8217;s team turned to a different kind of hardware to help solve the problem.<\/p>\n<p>&#8220;We created a method that uses graphics processing units or GPUs,&#8221; said first author Xueying Liu, Ph.D., St. Jude Department of Computational Biology. &#8220;The GPU integration gave us the processing power to perform the computational load in a scalable way.&#8221;<\/p>\n<h2><span class=\"ez-toc-section\" id=\"Unsupervised_machine_learning_for_single-cell_analysis\"><\/span>Unsupervised machine learning for single-cell analysis<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>The volume of data often forces researchers to make concessions and assumptions that introduce biases when conducting analyses with standard methods. The St. Jude scientists used an artificial intelligence <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\">app<\/a>roach that removes such bias from these selections.<\/p>\n<p>&#8220;Our method uses unsupervised machine learning, which automatically determines more robust and less arbitrary parameters for the analysis,&#8221; Liu said. &#8220;It learns how to group cells based on their different active biological processes or cell type identities.&#8221;<\/p>\n<p>Since the algorithm learns and derives its analysis from the data presented, researchers could use it on any sizeable single-cell RNA sequencing dataset. As it investigates each new large dataset individually and only uses those expression program clues to make conclusions, the researchers called the approach the Consensus and Scalable Inference of Gene Expression Programs (CSI-GEP).<\/p>\n<p>When applied to the largest single-cell RNA databases, CSI-GEP produced better results than every other method. Most impressively, the algorithm could identify cell types and the activity of biological processes missed by other methods.<\/p>\n<p>&#8220;We&#8217;ve created a tool broadly applicable to studying any disease through single-cell RNA analysis,&#8221; Geeleher said. &#8220;The method performed substantially better than all existing approaches we tested, so I hope other scientists consider using it to get better value out of their single-cell data.&#8221;<\/p>\n<p>CSI-GEP is freely <a rel=\"nofollow\" target=\"_blank\" href=\"https:\/\/github.com\/geeleherlab\/CSI-GEP\" target=\"_blank\">available<\/a> on GitHub.<\/p>\n<div class=\"article-main__more p-4\">\n<p><strong>More information:<\/strong><br \/>\n\t\t\t\t\t\t\t\t\t\t\t\tXueying Liu et al, CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data, <i>Cell Genomics<\/i> (2025). <a rel=\"nofollow\" target=\"_blank\" data-doi=\"1\" href=\"https:\/\/dx.doi.org\/10.1016\/j.xgen.2024.100739\" target=\"_blank\">DOI: 10.1016\/j.xgen.2024.100739<\/a><\/p>\n<\/p><\/div>\n<div class=\"d-inline-block text-medium mt-4\">\n<p>\n\t\t\t\t\t\t\t\t\t\t\t\t\tProvided by<br \/>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tSt. Jude Children&#8217;s Research Hospital<br \/>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<a rel=\"nofollow\" target=\"_blank\" class=\"icon_open\" href=\"http:\/\/www.stjude.org\" target=\"_blank\" rel=\"nofollow\"><br \/>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<svg>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<use href=\"https:\/\/phys.b-cdn.net\/tmpl\/v6\/img\/svg\/sprite.svg#icon_open\" x=\"0\" y=\"0\"\/>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/svg><br \/>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/p>\n<\/p><\/div>\n<p>\t\t\t\t\t\t\t\t\t\t<!-- print only --><\/p>\n<div class=\"d-none d-print-block\">\n<p>\n\t\t\t\t\t\t\t\t\t\t\t\t<strong>Citation<\/strong>:<br \/>\n\t\t\t\t\t\t\t\t\t\t\t\tScientists create scalable solution for analyzing single-cell data (2025, January 8)<br \/>\n\t\t\t\t\t\t\t\t\t\t\t\tretrieved 8 January 2025<br \/>\n\t\t\t\t\t\t\t\t\t\t\t\tfrom https:\/\/phys.org\/<a href=\"https:\/\/buradabiliyorum.com\/en\/category\/news\/\" data-internallinksmanager029f6b8e52c=\"2\" title=\"News\" target=\"_blank\" rel=\"noopener\">news<\/a>\/2025-01-scientists-scalable-solution-cell.html\n\t\t\t\t\t\t\t\t\t\t\t <\/p>\n<p>\n\t\t\t\t\t\t\t\t\t\t\t This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no<br \/>\n\t\t\t\t\t\t\t\t\t\t\t part may be reproduced without the written permission. The content is provided for information purposes only.\n\t\t\t\t\t\t\t\t\t\t\t <\/p>\n<\/p><\/div>\n<\/p><\/div>\n<p><script id=\"facebook-jssdk\" async=\"\" src=\"https:\/\/connect.facebook.net\/en_US\/sdk.js\"><\/script><\/p>\n<blockquote><p><strong><span style=\"color: #ff6600;\">If you liked the article, do not forget to share it with your friends. Follow us on\u00a0<span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/news.google.com\/publications\/CAAqBwgKMN63nwsw68G3Aw\" target=\"_blank\" rel=\"nofollow noopener noreferrer\">Google News<\/a><\/span>\u00a0too, click on the star and choose us from your favorites.<\/span><\/strong><\/p><\/blockquote>\n<blockquote>\n<p style=\"text-align: center;\"><strong>If you want to read more Like this articles, you can visit our <span style=\"color: #ff9900;\"><a style=\"color: #ff9900;\" href=\"https:\/\/en.buradabiliyorum.com\/category\/sciencee\/\" target=\"_blank\" >Science category.<\/a><\/span><\/strong><\/p>\n<\/blockquote>\n<p><span style=\"color: black;\"><a style=\"color: #ff9900;\" href=\"https:\/\/phys.org\/news\/2025-01-scientists-scalable-solution-cell.html\" target=\"_blank\" >Source<\/a><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Graphical abstract. Credit: Cell Genomics (2025). DOI: 10.1016\/j.xgen.2024.100739 Researchers have amassed vast single-cell gene expression databases to understand how the smallest details impact human biology. However, current analysis methods struggle with the large volume of data and, as a result, produce biased and contradictory findings. Scientists at St. Jude Children&#8217;s Research Hospital created a machine-learning&#8230;<\/p>\n","protected":false},"author":1,"featured_media":648399,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"fifu_image_url":"https:\/\/scx2.b-cdn.net\/gfx\/news\/2025\/scientists-create-scal.jpg","fifu_image_alt":"","footnotes":""},"categories":[16],"tags":[],"class_list":["post-648398","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-sciencee"],"_links":{"self":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/648398","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/comments?post=648398"}],"version-history":[{"count":0,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/648398\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media\/648399"}],"wp:attachment":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media?parent=648398"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/categories?post=648398"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/tags?post=648398"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}