{"id":10201,"date":"2024-10-24T17:54:01","date_gmt":"2024-10-24T08:54:01","guid":{"rendered":"https:\/\/www.ibs.re.kr\/bimag\/?post_type=tribe_events&p=10201"},"modified":"2024-10-29T12:41:02","modified_gmt":"2024-10-29T03:41:02","slug":"batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci","status":"publish","type":"tribe_events","link":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/","title":{"rendered":"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI"},"content":{"rendered":"

In this talk, we discuss the paper : “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment” by Leech et al<\/em>, nature biotechnology, https:\/\/doi.org\/10.1371\/journal.pcbi.1011879<\/a>.<\/p>\n

Zoom: https:\/\/us06web.zoom.us\/j\/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09<\/a><\/p>\n

Abstract<\/strong><\/p>\n

Collective alignment of cell populations is a commonly observed phenomena in biology. An important example are aligning fibroblasts in healthy or scar tissue. In this work we derive and simulate a mechanistic agent-based model of the collective behaviour of actively moving and interacting cells, with a focus on understanding collective alignment. The derivation strategy is based on energy minimisation. The model ingredients are motivated by data on the behaviour of different populations of aligning fibroblasts and include: Self-propulsion, overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces. We find that there is an optimal ratio of self-propulsion speed and overlap avoidance that maximises collective alignment. Further we find that deformability aids alignment, and that cell-cell junctions by themselves hinder alignment. However, if cytoskeletal forces are transmitted via cell-cell junctions we observe strong collective alignment over large spatial scales.<\/p>\n","protected":false},"excerpt":{"rendered":"

In this talk, we discuss the paper : “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment” … <\/p>\n

Continue reading “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI”<\/span><\/a><\/p>\n","protected":false},"author":9,"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-10201","tribe_events","type-tribe_events","status-publish","hentry","tribe_events_cat-journal-club","cat_journal-club"],"yoast_head":"\nDerivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group<\/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:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group\" \/>\n<meta property=\"og:description\" content=\"In this talk, we discuss the paper : “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment” … Continue reading "Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI"\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Mathematics Group\" \/>\n<meta property=\"article:modified_time\" content=\"2024-10-29T03:41:02+00:00\" \/>\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\\\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\\\/\",\"name\":\"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\"},\"datePublished\":\"2024-10-24T08:54:01+00:00\",\"dateModified\":\"2024-10-29T03:41:02+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Events\",\"item\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/events\\\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\",\"name\":\"Biomedical Mathematics Group\",\"description\":\"\uae30\ucd08\uacfc\ud559\uc5f0\uad6c\uc6d0 \uc758\uc0dd\uba85\uc218\ud559\uadf8\ub8f9\",\"publisher\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#organization\",\"name\":\"IBS Biomedical Mathematics Group\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#\\\/schema\\\/logo\\\/image\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/cms\\\/wp-content\\\/uploads\\\/2021\\\/02\\\/ibs-circle-1.png\",\"contentUrl\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/cms\\\/wp-content\\\/uploads\\\/2021\\\/02\\\/ibs-circle-1.png\",\"width\":250,\"height\":250,\"caption\":\"IBS Biomedical Mathematics Group\"},\"image\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#\\\/schema\\\/logo\\\/image\\\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/","og_locale":"en_US","og_type":"article","og_title":"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group","og_description":"In this talk, we discuss the paper : “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment” … Continue reading \"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI\"","og_url":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/","og_site_name":"Biomedical Mathematics Group","article_modified_time":"2024-10-29T03:41:02+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/","url":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/","name":"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment - Kevin SPINICCI - Biomedical Mathematics Group","isPartOf":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#website"},"datePublished":"2024-10-24T08:54:01+00:00","dateModified":"2024-10-29T03:41:02+00:00","breadcrumb":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/batch-effects-in-single-cell-rna-sequencing-data-are-corrected-by-matching-mutual-nearest-neighbors-kevin-spinicci\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ibs.re.kr\/bimag\/"},{"@type":"ListItem","position":2,"name":"Events","item":"https:\/\/www.ibs.re.kr\/bimag\/events\/"},{"@type":"ListItem","position":3,"name":"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment – Kevin SPINICCI"}]},{"@type":"WebSite","@id":"https:\/\/www.ibs.re.kr\/bimag\/#website","url":"https:\/\/www.ibs.re.kr\/bimag\/","name":"Biomedical Mathematics Group","description":"\uae30\ucd08\uacfc\ud559\uc5f0\uad6c\uc6d0 \uc758\uc0dd\uba85\uc218\ud559\uadf8\ub8f9","publisher":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ibs.re.kr\/bimag\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/www.ibs.re.kr\/bimag\/#organization","name":"IBS Biomedical Mathematics Group","url":"https:\/\/www.ibs.re.kr\/bimag\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.ibs.re.kr\/bimag\/#\/schema\/logo\/image\/","url":"https:\/\/www.ibs.re.kr\/bimag\/cms\/wp-content\/uploads\/2021\/02\/ibs-circle-1.png","contentUrl":"https:\/\/www.ibs.re.kr\/bimag\/cms\/wp-content\/uploads\/2021\/02\/ibs-circle-1.png","width":250,"height":250,"caption":"IBS Biomedical Mathematics Group"},"image":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#\/schema\/logo\/image\/"}}]}},"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"dimag-thumbnail":false,"twentyseventeen-featured-image":false,"twentyseventeen-thumbnail-avatar":false},"uagb_author_info":{"display_name":"spinicck","author_link":"https:\/\/www.ibs.re.kr\/bimag\/author\/spinicck\/"},"uagb_comment_info":0,"uagb_excerpt":"In this talk, we discuss the paper : “Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment” … Continue reading \"Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment…","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10201","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\/9"}],"version-history":[{"count":2,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10201\/revisions"}],"predecessor-version":[{"id":10212,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10201\/revisions\/10212"}],"wp:attachment":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/media?parent=10201"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tags?post=10201"},{"taxonomy":"tribe_events_cat","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events_cat?post=10201"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}