Promises and pitfalls of untargeted metabolomics
I Gertsman, BA Barshop - Journal of inherited metabolic disease, 2018 - Springer
Metabolomics is one of the newer omics fields, and has enabled researchers to complement
genomic and protein level analysis of disease with both semi-quantitative and quantitative …
genomic and protein level analysis of disease with both semi-quantitative and quantitative …
DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals
Chemical synthesis is a well established route for producing many chemicals on a large
scale, but some drawbacks still exist in this process, such as unstable intermediates …
scale, but some drawbacks still exist in this process, such as unstable intermediates …
Leveraging knowledge engineering and machine learning for microbial bio-manufacturing
Genome scale modeling (GSM) predicts the performance of microbial workhorses and helps
identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and …
identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and …
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation …
O Hädicke, A von Kamp, T Aydogan… - PLoS computational …, 2018 - journals.plos.org
Constraint-based modeling techniques have become a standard tool for the in silico
analysis of metabolic networks. To further improve their accuracy, recent methodological …
analysis of metabolic networks. To further improve their accuracy, recent methodological …
Statistical mechanics for metabolic networks during steady state growth
D De Martino, A Mc Andersson, T Bergmiller… - Nature …, 2018 - nature.com
Which properties of metabolic networks can be derived solely from stoichiometry? Predictive
results have been obtained by flux balance analysis (FBA), by postulating that cells set …
results have been obtained by flux balance analysis (FBA), by postulating that cells set …
[HTML][HTML] Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential
J Asplund-Samuelsson, M Janasch, EP Hudson - Metabolic engineering, 2018 - Elsevier
Introducing biosynthetic pathways into an organism is both reliant on and challenged by
endogenous biochemistry. Here we compared the expansion potential of the metabolic …
endogenous biochemistry. Here we compared the expansion potential of the metabolic …
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling
Metabolic modelling has entered a mature phase with dozens of methods and software
implementations available to the practitioner and the theoretician. It is not easy for a …
implementations available to the practitioner and the theoretician. It is not easy for a …
Temperature-dependent estimation of Gibbs energies using an updated group-contribution method
Reaction-equilibrium constants determine the metabolite concentrations necessary to drive
flux through metabolic pathways. Group-contribution methods offer a way to estimate …
flux through metabolic pathways. Group-contribution methods offer a way to estimate …
Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks
Adipic acid, a nylon-6, 6 precursor, has recently gained popularity in synthetic biology. Here,
16 different production routes to adipic acid were evaluated using a novel tool for network …
16 different production routes to adipic acid were evaluated using a novel tool for network …
[图书][B] Cybernetic modeling for bioreaction engineering
D Ramkrishna, HS Song - 2018 - books.google.com
Uniquely focusing on dynamic modeling, this volume incorporates metabolic regulation as a
survival mechanism for cells, by driving metabolism through optimal investment of its …
survival mechanism for cells, by driving metabolism through optimal investment of its …