Special Issue "Metabolic Network Models Volume 2"
Deadline for manuscript submissions: closed (31 March 2018).
Interests: constraint-based modeling, large-scale data integration, robustness and plasticity of phenotypes, genotype-phenotype mapping, evolutionary metabolomics
Interests: computational biology, algorithm development, metabolic modeling, plant-microbe interactions, metabolic engineering, systems biology, retrosynthesis, synthetic biology, network analysis
The last two decades of systems biology research have propelled the construction of large-scale models of metabolism in diverse organisms across all kingdoms of life. These models formalize the description of the entirety of characterized biochemical reactions in a biological system across different organizational scales (e.g., pathways, organelles, cell types, and interconnected organs). The development of these medium- and large-scale metabolic model backbones have been coupled with development of computational approaches that allow for inferring genotype–phenotype relationships, characterizing the effect of particular environments and cellular contexts on the traits of interest. These methodological advances go hand-in-hand with headway in technologies for high-throughput profiling of cellular components. Altogether, integrative data-driven large-scale modeling has provide the possibility to posit hypotheses about metabolic functions and to test their validity in particular scenarios.
Yet, despite these advances, there is still the need to develop methods that can provide testable predictions by integrating large-scale models with measurable read-outs (e.g., protein abundance, metabolite content). These methods should allow for augmenting the structural backbone of the metabolic models with additional information about: (i) the type of kinetic law governing the reaction rates, (ii) constraints concerning feasible parameter values for the respective kinetic, and (iii) thermodynamic feasibility of reactions. They should also be coupled with appropriate approaches for model selection based on steady-state and time-resolved data from multiple experimental scenarios. Therefore, this Special Issue of Metabolites will be dedicated to publishing current advances on medium- and large-scale metabolic network modeling that address these pressing challenges by providing case studies of hypotheses that can be tested by integration of data from modern metabolomics technologies.
Dr. Zoran Nikoloski
Dr. Georg Basler
Manuscript Submission Information
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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
- metabolic network
- constraint-based modeling
- reaction kinetic
- thermodynamic constraints
- model selection
- multi-view data
- regulation of reaction rates
- metabolomics data
- network robustness and plasticity