Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.

Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic development and wound healing, and contributes to many diseases including cancer and rheumatoid arthritis. The structure of the resulting vessel ne...

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Autores principales:	John T Nardini, Bernadette J Stolz, Kevin B Flores, Heather A Harrington, Helen M Byrne
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/24875cb0b6f143c9b9e5b1a630a64832
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spelling	oai:doaj.org-article:24875cb0b6f143c9b9e5b1a630a648322021-11-25T05:40:34ZTopological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.1553-734X1553-735810.1371/journal.pcbi.1009094https://doaj.org/article/24875cb0b6f143c9b9e5b1a630a648322021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009094https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic development and wound healing, and contributes to many diseases including cancer and rheumatoid arthritis. The structure of the resulting vessel networks determines their ability to deliver nutrients and remove waste products from biological tissues. Here we simulate the Anderson-Chaplain model of angiogenesis at different parameter values and quantify the vessel architectures of the resulting synthetic data. Specifically, we propose a topological data analysis (TDA) pipeline for systematic analysis of the model. TDA is a vibrant and relatively new field of computational mathematics for studying the shape of data. We compute topological and standard descriptors of model simulations generated by different parameter values. We show that TDA of model simulation data stratifies parameter space into regions with similar vessel morphology. The methodologies proposed here are widely applicable to other synthetic and experimental data including wound healing, development, and plant biology.John T NardiniBernadette J StolzKevin B FloresHeather A HarringtonHelen M ByrnePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 6, p e1009094 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 John T Nardini Bernadette J Stolz Kevin B Flores Heather A Harrington Helen M Byrne Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
description	Angiogenesis is the process by which blood vessels form from pre-existing vessels. It plays a key role in many biological processes, including embryonic development and wound healing, and contributes to many diseases including cancer and rheumatoid arthritis. The structure of the resulting vessel networks determines their ability to deliver nutrients and remove waste products from biological tissues. Here we simulate the Anderson-Chaplain model of angiogenesis at different parameter values and quantify the vessel architectures of the resulting synthetic data. Specifically, we propose a topological data analysis (TDA) pipeline for systematic analysis of the model. TDA is a vibrant and relatively new field of computational mathematics for studying the shape of data. We compute topological and standard descriptors of model simulations generated by different parameter values. We show that TDA of model simulation data stratifies parameter space into regions with similar vessel morphology. The methodologies proposed here are widely applicable to other synthetic and experimental data including wound healing, development, and plant biology.
format	article
author	John T Nardini Bernadette J Stolz Kevin B Flores Heather A Harrington Helen M Byrne
author_facet	John T Nardini Bernadette J Stolz Kevin B Flores Heather A Harrington Helen M Byrne
author_sort	John T Nardini
title	Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
title_short	Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
title_full	Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
title_fullStr	Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
title_full_unstemmed	Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
title_sort	topological data analysis distinguishes parameter regimes in the anderson-chaplain model of angiogenesis.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/24875cb0b6f143c9b9e5b1a630a64832
work_keys_str_mv	AT johntnardini topologicaldataanalysisdistinguishesparameterregimesintheandersonchaplainmodelofangiogenesis AT bernadettejstolz topologicaldataanalysisdistinguishesparameterregimesintheandersonchaplainmodelofangiogenesis AT kevinbflores topologicaldataanalysisdistinguishesparameterregimesintheandersonchaplainmodelofangiogenesis AT heatheraharrington topologicaldataanalysisdistinguishesparameterregimesintheandersonchaplainmodelofangiogenesis AT helenmbyrne topologicaldataanalysisdistinguishesparameterregimesintheandersonchaplainmodelofangiogenesis
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Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.

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