In this talk, we discuss the paper “Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function” by Kelly Maggs et al., bioRxiv, 2025.<\/p>\n
\n
Standard single-cell RNA-seq analysis frameworks aggregate over-lapping biological processes and impose a single parametrization, conflating distinct programs. Here, we introduce a topological framework that detects and disentangles multiple cyclic processes directly from single-cell transcriptomic data. We validate this approach on synthetic datasets and scRNA-seq profiles of human dermal fibroblasts under control conditions and following androgen receptor (AR) silencing, as well as in vivo mouse prostate regeneration under androgen receptor add-back. We show robust cell cycle structure across conditions, identify an unbiased AR-linked stress signature related to the senescence and proliferation across organisms, and uncover cholesterol homeostasis as an AR-linked program in tissue regeneration. This framework enables identification and separation of concurrent cyclic processes from snapshot single-cell data, revealing complex multi-dimensional regulatory dynamics inaccessible to standard clustering analysis.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
In this talk, we discuss the paper “Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function” by Kelly Maggs et al., bioRxiv, 2025. Abstract: Standard single-cell RNA-seq … <\/p>\n
Continue reading “Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function – Seongjin Choi”<\/span><\/a><\/p>\n","protected":false},"author":13,"featured_media":0,"template":"","meta":{"_editorskit_title_hidden":false,"_editorskit_reading_time":0,"_editorskit_is_block_options_detached":false,"_editorskit_block_options_position":"{}","_uag_custom_page_level_css":"","_tribe_events_status":"","_tribe_events_status_reason":"","footnotes":""},"tags":[],"tribe_events_cat":[219],"class_list":["post-12700","tribe_events","type-tribe_events","status-publish","hentry","tribe_events_cat-journal-club","cat_journal-club"],"yoast_head":"\nTopology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function - Seongjin Choi - Biomedical Mathematics Group<\/title>\n<meta name=\"description\" content=\"Standard single-cell RNA-seq analysis frameworks aggregate over-lapping biological processes and impose a single parametrization, conflating distinct programs. Here, we introduce a topological framework that detects and disentangles multiple cyclic processes directly from single-cell transcriptomic data. We validate this approach on synthetic datasets and scRNA-seq profiles of human dermal fibroblasts under control conditions and following androgen receptor (AR) silencing, as well as in vivo mouse prostate regeneration under androgen receptor add-back. We show robust cell cycle structure across conditions, identify an unbiased AR-linked stress signature related to the senescence and proliferation across organisms, and uncover cholesterol homeostasis as an AR-linked program in tissue regeneration. This framework enables identification and separation of concurrent cyclic processes from snapshot single-cell data, revealing complex multi-dimensional regulatory dynamics inaccessible to standard clustering analysis.\" \/>\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.ibs.re.kr\/bimag\/event\/topology-identifies-concurrent-cyclic-processes-in-single-cell-transcriptomics-and-androgen-receptor-function-seongjin-choi\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function - Seongjin Choi - Biomedical Mathematics Group\" \/>\n<meta property=\"og:description\" content=\"Standard single-cell RNA-seq analysis frameworks aggregate over-lapping biological processes and impose a single parametrization, conflating distinct programs. Here, we introduce a topological framework that detects and disentangles multiple cyclic processes directly from single-cell transcriptomic data. We validate this approach on synthetic datasets and scRNA-seq profiles of human dermal fibroblasts under control conditions and following androgen receptor (AR) silencing, as well as in vivo mouse prostate regeneration under androgen receptor add-back. We show robust cell cycle structure across conditions, identify an unbiased AR-linked stress signature related to the senescence and proliferation across organisms, and uncover cholesterol homeostasis as an AR-linked program in tissue regeneration. This framework enables identification and separation of concurrent cyclic processes from snapshot single-cell data, revealing complex multi-dimensional regulatory dynamics inaccessible to standard clustering analysis.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ibs.re.kr\/bimag\/event\/topology-identifies-concurrent-cyclic-processes-in-single-cell-transcriptomics-and-androgen-receptor-function-seongjin-choi\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Mathematics Group\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\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:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/topology-identifies-concurrent-cyclic-processes-in-single-cell-transcriptomics-and-androgen-receptor-function-seongjin-choi\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/topology-identifies-concurrent-cyclic-processes-in-single-cell-transcriptomics-and-androgen-receptor-function-seongjin-choi\\\/\",\"name\":\"Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function - Seongjin Choi - Biomedical Mathematics Group\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\"},\"datePublished\":\"2026-07-13T06:21:27+00:00\",\"description\":\"Standard single-cell RNA-seq analysis frameworks aggregate over-lapping biological processes and impose a single parametrization, conflating distinct programs. 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Abstract: Standard single-cell RNA-seq … Continue reading \"Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function – Seongjin Choi\"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/12700","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events"}],"about":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/types\/tribe_events"}],"author":[{"embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/users\/13"}],"version-history":[{"count":1,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/12700\/revisions"}],"predecessor-version":[{"id":12702,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/12700\/revisions\/12702"}],"wp:attachment":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/media?parent=12700"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tags?post=12700"},{"taxonomy":"tribe_events_cat","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events_cat?post=12700"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}