{"id":38,"date":"2026-07-24T08:35:47","date_gmt":"2026-07-24T08:35:47","guid":{"rendered":"https:\/\/grns.reresearch.org\/?page_id=38"},"modified":"2026-07-24T18:00:05","modified_gmt":"2026-07-24T18:00:05","slug":"rotor-analyzer","status":"publish","type":"page","link":"https:\/\/grns.reresearch.org\/","title":{"rendered":"ROTOR ANALYZER"},"content":{"rendered":"\n<div class=\"wp-block-group alignfull is-layout-flow wp-block-group-is-layout-flow\" style=\"margin-top:0;margin-bottom:0\">\n<div class=\"wp-block-columns alignfull is-not-stacked-on-mobile is-layout-flex wp-container-core-columns-is-layout-dfbe8ba9 wp-block-columns-is-layout-flex\" style=\"margin-top:0;margin-bottom:0;padding-top:var(--wp--preset--spacing--40);padding-right:var(--wp--preset--spacing--40);padding-bottom:var(--wp--preset--spacing--80);padding-left:var(--wp--preset--spacing--40)\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:66.66%\">\n<div class=\"wp-block-group is-vertical is-content-justification-stretch is-layout-flex wp-container-core-group-is-layout-fc21d69c wp-block-group-is-layout-flex\">\n<h2 class=\"wp-block-heading has-xx-large-font-size\">With the rotor's phase and old-young, track cell fate and drug targets at whole-genome scale.<\/h2>\n\n\n\n<p class=\"has-x-large-font-size wp-block-paragraph\"><\/p>\n\n\n\n<div style=\"height:0px\" aria-hidden=\"true\" class=\"wp-block-spacer wp-container-content-36c51660\"><\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:12vw\"><\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<div class=\"wp-block-group is-content-justification-right is-nowrap is-layout-flex wp-container-core-group-is-layout-7eb86478 wp-block-group-is-layout-flex\">\n<p class=\"has-text-align-left wp-block-paragraph\" style=\"line-height:0.6;text-transform:uppercase;writing-mode:vertical-rl\">ROTOR ANALYZER<\/p>\n<\/div>\n<\/div>\n<\/div>\n\n\n<script>var RotorGRN = {\"restUrl\":\"https:\\\/\\\/grns.reresearch.org\\\/index.php?rest_route=\\\/rotor-grn\\\/v1\",\"nonce\":\"3de5b3ea8d\",\"me\":{\"tier\":\"\\u8a2a\\u5ba2\",\"caps\":{\"rotor_fate\":false,\"rotor_targeting\":false,\"rotor_boolean\":false,\"rotor_phase\":false,\"rotor_algebra\":false,\"rotor_upload\":false},\"max_nodes\":200,\"logged_in\":false},\"networks\":[{\"id\":\"li2004\",\"kind\":\"threshold\",\"label\":\"Li 2004 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style=\"flex-basis:50%\">\n<div class=\"wp-block-group is-vertical is-content-justification-stretch is-layout-flex wp-container-core-group-is-layout-704e8966 wp-block-group-is-layout-flex\" style=\"min-height:33vh;padding-top:var(--wp--preset--spacing--50);padding-right:var(--wp--preset--spacing--50);padding-bottom:var(--wp--preset--spacing--50);padding-left:var(--wp--preset--spacing--50)\">\n<p class=\"wp-block-paragraph\"><strong>The Whole-Genome Rotor Analyzer<\/strong>&nbsp;is a toolset that brings the&nbsp;<strong>rotor computational architecture<\/strong>&nbsp;to bear on attractor analysis of gene regulatory networks. The \"rotor\" treats each gene's state as a twofold composite of&nbsp;<strong>phase (yin-yang \/ group \/ reversible) and old-young (strong-weak \/ semigroup \/ irreversible)<\/strong>&nbsp;\u2014 precisely the two primitives of all finite computation in the Krohn\u2013Rhodes sense. Building on this, it replaces the crude on\/off Boolean with a&nbsp;<strong>four-image encoding<\/strong>&nbsp;(silent \u00b7 weak \u00b7 strong \u00b7 saturated) that preserves the expression-strength dimension of real, graded data. More crucially, it&nbsp;<strong>evolves along a single trajectory and never enumerates the 2\u207f state space<\/strong>&nbsp;\u2014 so it can track, at&nbsp;<strong>whole-genome scale (twenty thousand to a hundred thousand nodes)<\/strong>, which stable fate a cell moves toward, and can perform an in-silico knockout of each gene to screen out the&nbsp;<strong>core control genes that actually change that fate (candidate drug targets)<\/strong>. Rather than fitting statistical co-expression, it evolves the network dynamics directly, tackling the one gap among the four facing AI gene foundation models that is genuinely computational in nature \u2014 the&nbsp;collapse at&nbsp;whole-genome&nbsp;scale.&nbsp;Its&nbsp;results&nbsp;have&nbsp;been&nbsp;cross-validated&nbsp;bit-for-bit&nbsp;against&nbsp;published&nbsp;benchmarks:&nbsp;it&nbsp;exactly&nbsp;reproduces&nbsp;the&nbsp;basin&nbsp;distribution&nbsp;of&nbsp;the&nbsp;budding-yeast&nbsp;cell&nbsp;cycle&nbsp;(Li&nbsp;2004)&nbsp;and&nbsp;the&nbsp;experimentally&nbsp;validated&nbsp;therapeutic&nbsp;targets&nbsp;of&nbsp;the&nbsp;T-LGL&nbsp;leukemia&nbsp;survival&nbsp;network.<\/p>\n\n\n\n<div style=\"height:0px\" aria-hidden=\"true\" class=\"wp-block-spacer wp-container-content-6388d5dc\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-xx-large-font-size\"><a href=\"#\">RSVP<\/a><\/h2>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:50%\">\n<div class=\"wp-block-cover is-light\"><img decoding=\"async\" class=\"wp-block-cover__image-background\" alt=\"Close up photo of white flowers on a grey background\" src=\"https:\/\/grns.reresearch.org\/wp-content\/themes\/twentytwentyfive\/assets\/images\/botany-flowers-closeup.webp\" data-object-fit=\"cover\"\/><span aria-hidden=\"true\" class=\"wp-block-cover__background has-background-dim-0 has-background-dim\"><\/span><div class=\"wp-block-cover__inner-container is-layout-flow wp-block-cover-is-layout-flow\">\n<div style=\"height:var(--wp--preset--spacing--20)\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>With the rotor&#8217;s phase and old-young, track cell  [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_members_access_role":[],"_members_access_error":""},"class_list":["post-38","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/pages\/38","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=38"}],"version-history":[{"count":4,"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/pages\/38\/revisions"}],"predecessor-version":[{"id":63,"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=\/wp\/v2\/pages\/38\/revisions\/63"}],"wp:attachment":[{"href":"https:\/\/grns.reresearch.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=38"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}