Bioinformatics computation of metabolic models from sequenced genomes

@inproceedings{Karp2015BioinformaticsCO,
  title={Bioinformatics computation of metabolic models from sequenced genomes},
  author={Peter D. Karp and Christos A. Ouzounis},
  year={2015}
}
In the early days of the human genome project (HGP), during the late 1980s and early 1990s, there was skepticism that the genome project would produce biologically meaningful information. The reality is that bioinformatics has allowed us to extract far more biology from sequenced genomes than any published predictions in the early 1990s. Thanks to the efforts of many researchers in several subfields of bioinformatics, we can now process a sequenced genome through a series of computations to… 

Figures from this paper

Population FBA predicts metabolic phenotypes in yeast
TLDR
The partitioning of flux between fermentation and respiration predicted by the Population FBA model agrees with recent 13C fluxomics experiments, and the Crabtree effect is largely recovered, while FBA without proteomics constraints predicts respirative metabolism almost exclusively.
Developing computational biology at meridian 23° E, and a little eastwards
  • C. Ouzounis
  • Education
    Journal of Biological Research-Thessaloniki
  • 2018
TLDR
The paper reports on the recent research activities, the development of training initiatives in the wider region during the past years, and the lessons learned regarding the efforts away from major epicenters, within the general context of open science.

References

SHOWING 1-10 OF 34 REFERENCES
From bioinformatics to computational biology.
TLDR
It is argued that the uncertainty about the number of human genes appears to increase as the determination of the human genome sequence is nearing completion, and that “bioinformatics”—a term coined in 1990 to define the use of computers in sequence analysis—is no longer developing in directions relevant to biology.
Automated genome sequence analysis and annotation
TLDR
An automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts is presented.
Genome-scale models of bacterial metabolism: reconstruction and applications
TLDR
An introduction to the key ideas of metabolic modeling is provided, the methods, and resources that enable model reconstruction and refinement are surveyed, and applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities are charted.
KEGG for integration and interpretation of large-scale molecular data sets
TLDR
KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets and recent enhancements to the K EGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
TLDR
Taken together, the studies performed over the past decade have established a genome‐scale mechanistic understanding of genotype–phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species.
A beginner's guide to eukaryotic genome annotation
TLDR
An overview of the genome annotation process and the available tools is provided and some best-practice approaches are described.
The Human Genome
TLDR
Even in this unpolished state, these two books provide the most comprehensive look at the human genome ever possible; they offer a tantalizing glimpse at the wealth of information contained in the sequence.
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
TLDR
The results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized and strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannation.
Reconciliation of metabolites and biochemical reactions for metabolic networks
TLDR
Three recent initiatives that aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models are reviewed, namely BKM-react, MetRxn and MNXref, which provides a pre-compiled reconciliation of many of the most commonly used metabolic resources.
Optimization based automated curation of metabolic reconstructions
TLDR
This work proposes systematic methods to identify and fill gaps in genome-scale metabolic reconstructions and demonstrates this procedure for the genome- scale reconstruction of Escherichia coli and also Saccharomyces cerevisiae wherein compartmentalization of intra-cellular reactions results in a more complex topology of the metabolic network.
...
...