Next-Generation Genome-Scale Models Incorporating Multilevel ‘Omics Data: From Yeast to Human

  • Tunahan Çakır
  • Emel Kökrek
  • Gülben Avşar
  • Ecehan Abdik
  • Pınar PirEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2049)


Genome-scale modelling in eukaryotes has been pioneered by the yeast Saccharomyces cerevisiae. Early metabolic networks have been reconstructed based on genome sequence and information accumulated in the literature on biochemical reactions. Protein–protein interaction networks have been constructed based on experimental observations such as yeast-2-hybrid method. Gene regulatory networks were based on a variety of data types, including information on TF-promoter binding and gene coexpression. The aforementioned networks have been improved gradually, and methods for their integration were developed. Incorporation of omics data including genomics, metabolomics, transcriptomics, fluxome, and phosphoproteome led to next-generation genome-scale models. The methods tested on yeast have later been implemented in human, further, cellular components found to be important in yeast physiology under (ab)normal conditions, and (dis)regulation mechanisms in yeast shed light to the healthy and disease states in human. This chapter provides a historical perspective on next-generation genome-scale models incorporating multilevel ‘omics data, from yeast to human.

Key words

Data integration Transcriptional regulatory networks Metabolic networks Protein–protein interaction networks Transcriptomics Proteomics Metabolomics 



This work was financially supported by The Turkish Academy of Sciences—Outstanding Young Scientists Award Program (TUBA-GEBIP) and TÜBİTAK BİDEB 2232 Programme (116C062).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Tunahan Çakır
    • 1
  • Emel Kökrek
    • 1
  • Gülben Avşar
    • 1
  • Ecehan Abdik
    • 1
  • Pınar Pir
    • 1
    Email author
  1. 1.Computational Systems Biology Group, Department of BioengineeringGebze Technical UniversityKocaeliTurkey

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