PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models

PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models

Summary: Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different...

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Main Authors: Anush Chiappino-Pepe, Vassily Hatzimanikatis
Format: Article
Language:English
Published: Elsevier 2021-03-01
Series:STAR Protocols
Subjects:
Bioinformatics
Metabolism
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166720302677
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spelling doaj-d3a8fd6f1e8b486094b1206fcbaa360f2021-03-22T12:52:59ZengElsevierSTAR Protocols2666-16672021-03-0121100280PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic modelsAnush Chiappino-Pepe0Vassily Hatzimanikatis1Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland; Corresponding authorLaboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, SwitzerlandSummary: Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different conditions. Here, we present PhenoMapping, a protocol that uses GEMs, omics, and phenotypic data to map cellular processes and observed phenotypes. PhenoMapping also classifies genes as conditionally and unconditionally essential and guides a comprehensive curation of GEMs.For complete details on the use and execution of this protocol, please refer to Stanway et al. (2019) and Krishnan et al. (2020).http://www.sciencedirect.com/science/article/pii/S2666166720302677BioinformaticsMetabolism
collection DOAJ
language English
format Article
sources DOAJ
author Anush Chiappino-Pepe
Vassily Hatzimanikatis
spellingShingle Anush Chiappino-Pepe
Vassily Hatzimanikatis
PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
STAR Protocols
Bioinformatics
Metabolism
author_facet Anush Chiappino-Pepe
Vassily Hatzimanikatis
author_sort Anush Chiappino-Pepe
title PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
title_short PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
title_full PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
title_fullStr PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
title_full_unstemmed PhenoMapping: A protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
title_sort phenomapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
publisher Elsevier
series STAR Protocols
issn 2666-1667
publishDate 2021-03-01
description Summary: Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different conditions. Here, we present PhenoMapping, a protocol that uses GEMs, omics, and phenotypic data to map cellular processes and observed phenotypes. PhenoMapping also classifies genes as conditionally and unconditionally essential and guides a comprehensive curation of GEMs.For complete details on the use and execution of this protocol, please refer to Stanway et al. (2019) and Krishnan et al. (2020).
topic Bioinformatics
Metabolism
url http://www.sciencedirect.com/science/article/pii/S2666166720302677
work_keys_str_mv AT anushchiappinopepe phenomappingaprotocoltomapcellularphenotypestometabolicbottlenecksidentifyconditionalessentialityandcuratemetabolicmodels
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