Genomics to fluxomics and physiomics—pathway engineering

K Sanford, P Soucaille, G Whited, G Chotani - Current opinion in …, 2002 - Elsevier
Developments in microanalytical methods are enabling quantitative measurement of
multiple metabolic fluxes and, in conjunction with transcript and proteomic profiling, are …

FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data

Z Zhang, H Zhu, P Dang, J Wang, W Chang… - Nucleic Acids …, 2023 - academic.oup.com
Quantitative assessment of single cell fluxome is critical for understanding the metabolic
heterogeneity in diseases. Unfortunately, laboratory-based single cell fluxomics is currently …

[HTML][HTML] Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification

TH Yang, O Frick, E Heinzle - BMC Systems Biology, 2008 - Springer
Background The importance and power of isotope-based metabolic flux analysis and its
contribution to understanding the metabolic network is increasingly recognized. Its …

Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering

D Ando, H Garcia Martin - Synthetic Metabolic Pathways: Methods and …, 2018 - Springer
Abstract Accelerating the Design–Build–Test–Learn (DBTL) cycle in synthetic biology is
critical to achieving rapid and facile bioengineering of organisms for the production of, eg …

[HTML][HTML] ScalaFlux: a scalable approach to quantify fluxes in metabolic subnetworks

P Millard, U Schmitt, P Kiefer, JA Vorholt… - PLoS computational …, 2020 - journals.plos.org
13C-metabolic flux analysis (13C-MFA) allows metabolic fluxes to be quantified in living
organisms and is a major tool in biotechnology and systems biology. Current 13C-MFA …

Towards high resolution analysis of metabolic flux in cells and tissues

JK Sims, S Manteiga, K Lee - Current opinion in biotechnology, 2013 - Elsevier
Highlights•The metabolic state of a cell is an important determinant of cellular
phenotype.•Current methods for global metabolic flux quantification characterize bulk …

[HTML][HTML] An objective function exploiting suboptimal solutions in metabolic networks

EH Wintermute, TD Lieberman, PA Silver - BMC systems biology, 2013 - Springer
Abstract Background Flux Balance Analysis is a theoretically elegant, computationally
efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models …

Understanding metabolism with flux analysis: From theory to application

Z Dai, JW Locasale - Metabolic engineering, 2017 - Elsevier
Quantitative and qualitative knowledge of metabolic rates (ie fluxes) over a metabolic
network and in specific cellular compartments gives insights into the regulation of …

Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments

YJ Chang, PF Suthers… - Biotechnology and …, 2008 - Wiley Online Library
Metabolic flux analysis (MFA) methods use external flux and isotopic measurements to
quantify the magnitude of metabolic flows in metabolic networks. A key question in this …

High-throughput phenomics: experimental methods for mapping fluxomes

U Sauer - Current opinion in Biotechnology, 2004 - Elsevier
Many technologies have been developed to help explain the phenotypic consequences of
genetic and/or environmental modifications in areas like functional genomics …