Mathematical optimization applications in metabolic networks
AR Zomorrodi, PF Suthers, S Ranganathan… - Metabolic …, 2012 - Elsevier
Genome-scale metabolic models are increasingly becoming available for a variety of
microorganisms. This has spurred the development of a wide array of computational tools …
microorganisms. This has spurred the development of a wide array of computational tools …
Network reduction methods for genome-scale metabolic models
D Singh, MJ Lercher - Cellular and Molecular Life Sciences, 2020 - Springer
Genome-scale metabolic models (GSMs) provide a comprehensive representation of
cellular metabolism. GSMs provide a mechanistic link between cellular genotypes and …
cellular metabolism. GSMs provide a mechanistic link between cellular genotypes and …
Designing metabolic division of labor in microbial communities
Microbes face a trade-off between being metabolically independent and relying on
neighboring organisms for the supply of some essential metabolites. This balance of …
neighboring organisms for the supply of some essential metabolites. This balance of …
A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth
Metabolic modeling and machine learning are key components in the emerging next
generation of systems and synthetic biology tools, targeting the genotype–phenotype …
generation of systems and synthetic biology tools, targeting the genotype–phenotype …
Sybil–efficient constraint-based modelling in R
G Gelius-Dietrich, AA Desouki, CJ Fritzemeier… - BMC systems …, 2013 - Springer
Background Constraint-based analyses of metabolic networks are widely used to simulate
the properties of genome-scale metabolic networks. Publicly available implementations tend …
the properties of genome-scale metabolic networks. Publicly available implementations tend …
DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae
Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses,
particularly when they imply intracellular molecules of interest. Unfortunately, the use of …
particularly when they imply intracellular molecules of interest. Unfortunately, the use of …
Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks
The temperature dependence of biological processes has been studied at the levels of
individual biochemical reactions and organism physiology (eg basal metabolic rates) but …
individual biochemical reactions and organism physiology (eg basal metabolic rates) but …
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
Abstract Background Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga
which has become a biotechnological target because of its high capacity to produce …
which has become a biotechnological target because of its high capacity to produce …
Control of fluxes in metabolic networks
Understanding the control of large-scale metabolic networks is central to biology and
medicine. However, existing approaches either require specifying a cellular objective or can …
medicine. However, existing approaches either require specifying a cellular objective or can …
Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization
The oomycete pathogen Phytophthora infestans causes potato and tomato late blight, a
disease that is a serious threat to agriculture. P. infestans is a hemibiotrophic pathogen, and …
disease that is a serious threat to agriculture. P. infestans is a hemibiotrophic pathogen, and …