[HTML][HTML] Pathway thermodynamics highlights kinetic obstacles in central metabolism
In metabolism research, thermodynamics is usually used to determine the directionality of a
reaction or the feasibility of a pathway. However, the relationship between thermodynamic …
reaction or the feasibility of a pathway. However, the relationship between thermodynamic …
Bridging the gaps in systems biology
Abstract Systems biology aims at creating mathematical models, ie, computational
reconstructions of biological systems and processes that will result in a new level of …
reconstructions of biological systems and processes that will result in a new level of …
[HTML][HTML] Quantitative metabolomics and instationary 13C-metabolic flux analysis reveals impact of recombinant protein production on trehalose and energy …
Pichia pastoris has been recognized as an effective host for recombinant protein production.
In this work, we combine metabolomics and instationary 13 C metabolic flux analysis (INST …
In this work, we combine metabolomics and instationary 13 C metabolic flux analysis (INST …
Language-oriented rule-based reaction network generation and analysis: Algorithms of RING
S Rangarajan, T Kaminski, E Van Wyk, A Bhan… - Computers & Chemical …, 2014 - Elsevier
The underlying algorithms of the language interface and post-generation analysis modules
in RING, a network generation and analysis tool, are discussed. The front-end is a domain …
in RING, a network generation and analysis tool, are discussed. The front-end is a domain …
[HTML][HTML] Network thermodynamic curation of human and yeast genome-scale metabolic models
Genome-scale models are used for an ever-widening range of applications. Although there
has been much focus on specifying the stoichiometric matrix, the predictive power of …
has been much focus on specifying the stoichiometric matrix, the predictive power of …
A thermodynamic investigation of the glucose-6-phosphate isomerization
In this work, Δ R g+ values for the enzymatic G6P isomerization were determined as a
function of the G6P equilibrium molality between 25° C and 37° C. The reaction mixtures …
function of the G6P equilibrium molality between 25° C and 37° C. The reaction mixtures …
[HTML][HTML] A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen
M Ederer, S Steinsiek, S Stagge, MD Rolfe… - Frontiers in …, 2014 - frontiersin.org
The efficient redesign of bacteria for biotechnological purposes, such as biofuel production,
waste disposal or specific biocatalytic functions, requires a quantitative systems-level …
waste disposal or specific biocatalytic functions, requires a quantitative systems-level …
[HTML][HTML] Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
Background An important step in the reconstruction of a metabolic network is annotation of
metabolites. Metabolites are generally annotated with various database or structure based …
metabolites. Metabolites are generally annotated with various database or structure based …
Ion-pairing chromatography on a porous graphitic carbon column coupled with time-of-flight mass spectrometry for targeted and untargeted profiling of amino acid …
X Chen, H Wu, Y Cao, X Yao, L Zhao, T Wang… - Molecular …, 2014 - pubs.rsc.org
Background: Candida albicans, the most common fungal pathogen related to colonization
and biofilm formation on the surfaces of indwelling medical devices, shows high resistance …
and biofilm formation on the surfaces of indwelling medical devices, shows high resistance …
[HTML][HTML] Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses
Constraint-based approaches have been used for integrating data in large-scale metabolic
networks to obtain insights into metabolism of various organisms. Due to the underlying …
networks to obtain insights into metabolism of various organisms. Due to the underlying …