A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

Cruz, Fernando; Faria, José P.; Rocha, Miguel; Rocha, Isabel; Dias, Oscar

doi:10.1042/bst20190840

Title: A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

Journal Article · 16 September 2020 · Biochemical Society Transactions

DOI: https://doi.org/10.1042/bst20190840 · OSTI ID:1756918

^[1]; Faria, José P. ^[2]; Rocha, Miguel ^[1]; Rocha, Isabel ^[3];

^[1]

Univ. of Minho (Portugal)
Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. Nova de Lisboa (Portugal)

The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: European Regional Development Fund (ERDF)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1756918

Journal Information:: Biochemical Society Transactions, Journal Name: Biochemical Society Transactions Journal Issue: 5 Vol. 48; ISSN 0300-5127

Publisher:: Portland PressCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Bioinformatics
Biotechnology
Computational Biology
Gene Expression & Regulation
Metabolism
Systems Biology & Networks
flux balance analysis
gene expression and regulation
genome-scale metabolic models
genome-scale regulatory networks
metabolism
transcriptional regulatory networks

Title: A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

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