Formalizing Phenotypes of Regeneration

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dc.contributor.authorLobo, Daniel
dc.date.accessioned2022-04-11T13:23:59Z
dc.date.available2022-04-11T13:23:59Z
dc.date.issued2022-04-01
dc.description.abstractRegeneration experiments can produce complex phenotypes including morphological outcomes and gene expression patterns that are crucial for the understanding of the mechanisms of regeneration. However, due to their inherent complexity, variability between individuals, and heterogeneous data spreading across the literature, extracting mechanistic knowledge from them is a current challenge. Toward this goal, here we present protocols to unambiguously formalize the phenotypes of regeneration and their experimental procedures using precise mathematical morphological descriptions and standardized gene expression patterns. We illustrate the application of the methodology with step-by-step protocols for planaria and limb regeneration phenotypes. The curated datasets with these methods are not only helpful for human scientists, but they represent a key formalized resource that can be easily integrated into downstream reverse engineering methodologies for the automatic extraction of mechanistic knowledge. This approach can pave the way for discovering comprehensive systems-level models of regeneration.en_US
dc.description.sponsorshipI thank the members of the Lobo Lab for their dedicated work and discussions. This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R35GM137953. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.en_US
dc.description.urihttps://link.springer.com/protocol/10.1007/978-1-0716-2172-1_36en_US
dc.format.extent17 pagesen_US
dc.genrebook chaptersen_US
dc.identifierdoi:10.13016/m2jevh-jqqy
dc.identifier.citationLobo D. (2022) Formalizing Phenotypes of Regeneration. In: Blanchoud S., Galliot B. (eds) Whole-Body Regeneration. Methods in Molecular Biology, vol 2450. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2172-1_36en_US
dc.identifier.urihttps://doi.org/10.1007/978-1-0716-2172-1_36
dc.identifier.urihttp://hdl.handle.net/11603/24529
dc.language.isoen_USen_US
dc.publisherSpringeren_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleFormalizing Phenotypes of Regenerationen_US
dc.typeTexten_US
dcterms.creatorhttps://orcid.org/0000-0003-4666-6118en_US

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