Trans-omics: how to reconstruct biochemical networks across multiple 'omic'layers
We propose 'trans-omic'analysis for reconstructing global biochemical networks across
multiple omic layers by use of both multi-omic measurements and computational data …
multiple omic layers by use of both multi-omic measurements and computational data …
[HTML][HTML] Advances in flux balance analysis by integrating machine learning and mechanism-based models
The availability of multi-omics data sets and genome-scale metabolic models for various
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements
Turnover numbers, also known as k cat values, are fundamental properties of enzymes.
However, k cat data are scarce and measured in vitro, thus may not faithfully represent the in …
However, k cat data are scarce and measured in vitro, thus may not faithfully represent the in …
EGRINs (Environmental Gene Regulatory Influence Networks) in rice that function in the response to water deficit, high temperature, and agricultural environments
Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate
of gene expression in response to environmental signals. EGRINs encompass many layers …
of gene expression in response to environmental signals. EGRINs encompass many layers …
Perspective: Dimensions of the scientific method
EO Voit - PLOS Computational Biology, 2019 - journals.plos.org
The scientific method has been guiding biological research for a long time. It not only
prescribes the order and types of activities that give a scientific study validity and a stamp of …
prescribes the order and types of activities that give a scientific study validity and a stamp of …
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
Genome-scale metabolic reconstructions have proven to be valuable resources in
enhancing our understanding of metabolic networks as they encapsulate all known …
enhancing our understanding of metabolic networks as they encapsulate all known …
Enhancing microbiome research through genome-scale metabolic modeling
Construction and analysis of genome-scale metabolic models (GEMs) is a well-established
systems biology approach that can be used to predict metabolic and growth phenotypes …
systems biology approach that can be used to predict metabolic and growth phenotypes …
Production of l-valine from metabolically engineered Corynebacterium glutamicum
X Wang, H Zhang, PJ Quinn - Applied microbiology and biotechnology, 2018 - Springer
Abstract l-Valine is one of the three branched-chain amino acids (valine, leucine, and
isoleucine) essential for animal health and important in metabolism; therefore, it is widely …
isoleucine) essential for animal health and important in metabolism; therefore, it is widely …
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
F Shen, R Sun, J Yao, J Li, Q Liu, ND Price… - PLoS computational …, 2019 - journals.plos.org
The ultimate goal of metabolic engineering is to produce desired compounds on an
industrial scale in a cost effective manner. To address challenges in metabolic engineering …
industrial scale in a cost effective manner. To address challenges in metabolic engineering …
Modeling plant metabolism: from network reconstruction to mechanistic models
Mathematical modeling of plant metabolism enables the plant science community to
understand the organization of plant metabolism, obtain quantitative insights into metabolic …
understand the organization of plant metabolism, obtain quantitative insights into metabolic …