Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression

  • Fernando CruzEmail author
  • Diogo Lima
  • José P. Faria
  • Miguel Rocha
  • Oscar DiasEmail author
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 1005)


The reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and weaknesses concerning the reconstruction of integrated models for multiple prokaryotic organisms. Additionally, the main resources of regulatory information were also surveyed, as the existence of novel sources of regulatory information and gene expression data may contribute for the improvement of methodologies referred herein.


Genome-Scale Metabolic Models Genome-scale models of metabolism and gene expression Regulation of gene expression Databases of regulatory information 



This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020-Programa Operacional Regional do Norte. Fernando Cruz holds a doctoral fellowship (SFRH/BD/139198/2018) funded by the FCT. The authors thank project SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway (814408) funded by the European Commission.


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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Centre of Biological EngineeringUniversity of MinhoBragaPortugal
  2. 2.Mathematics and Computer Science DivisionArgonne National LaboratoryArgonneUSA

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