Advances in metabolic flux analysis toward genome-scale profiling of higher organisms

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks

(2017) Leo d’Espaux et al.   METABOLIC ENGINEERING

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Multifaceted plant responses to circumvent Phe hyperaccumulation by downregulation of flux through the shikimate pathway and by vacuolar Phe sequestration

(2017) Joseph H. Lynch et al.   PLANT JOURNAL

On the effects of alternative optima in context-specific metabolic model predictions

(2017) Semidán Robaina-Estévez et al.   PLoS Computational Biology

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

(2016) Douglas McCloskey et al.   ANALYTICAL CHEMISTRY

iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models

(2016) Max Sajitz-Hermstein et al.   BIOINFORMATICS

WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism

(2016) Lian He et al.   BMC BIOINFORMATICS

Metabolite pools and carbon flow during C4photosynthesis in maize:13CO2labeling kinetics and cell type fractionation

(2016) Stéphanie Arrivault et al.   JOURNAL OF EXPERIMENTAL BOTANY

Optimal tracers for parallel labeling experiments and 13 C metabolic flux analysis: A new precision and synergy scoring system

(2016) Scott B. Crown et al.   METABOLIC ENGINEERING

Interactions of C 4 Subtype Metabolic Activities and Transport in Maize Are Revealed through the Characterization of DCT2 Mutants

(2016) Sarit Weissmann et al.   PLANT CELL

Can stable isotope mass spectrometry replace ‎radiolabelled approaches in metabolic studies?

(2016) Willian Batista Silva et al.   PLANT SCIENCE

Systems-level analysis of mechanisms regulating yeast metabolic flux

(2016) S. R. Hackett et al.   SCIENCE

Fluxes through plant metabolic networks: measurements, predictions, insights and challenges

(2015) Nicholas J. Kruger et al.   BIOCHEMICAL JOURNAL

Methods and advances in metabolic flux analysis: a mini-review

(2015) Maciek R. Antoniewicz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

(2015) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment

(2015) Sabrina Kleessen et al.   PLANT JOURNAL

Inference and prediction of metabolic network fluxes

(2015) Zoran Nikoloski et al.   PLANT PHYSIOLOGY

Quantifying Protein Synthesis and Degradation in Arabidopsis by Dynamic13CO2Labeling and Analysis of Enrichment in Individual Amino Acids in Their Free Pools and in Protein

(2015) Hirofumi Ishihara et al.   PLANT PHYSIOLOGY

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

(2015) Semidán Robaina Estévez et al.   PLoS One

Analyzing Arabidopsis thaliana root proteome provides insights into the molecular bases of enantioselective imazethapyr toxicity

(2015) Haifeng Qian et al.   Scientific Reports

A Method to Constrain Genome-Scale Models with 13C Labeling Data

(2015) Héctor García Martín et al.   PLoS Computational Biology

Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana

(2015) Robert Heise et al.   Frontiers in Plant Science

Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii

(2015) Stephen P. Chapman et al.   Frontiers in Plant Science

Integration of metabolomics data into metabolic networks

(2015) Nadine Töpfer et al.   Frontiers in Plant Science

INCA: a computational platform for isotopically non-stationary metabolic flux analysis

(2014) J. D. Young   BIOINFORMATICS

Dissecting the Subcellular Compartmentation of Proteins and Metabolites in Arabidopsis Leaves Using Non-aqueous Fractionation

(2014) Stéphanie Arrivault et al.   MOLECULAR & CELLULAR PROTEOMICS

Flux profiling of photosynthetic carbon metabolism in intact plants

(2014) Robert Heise et al.   Nature Protocols

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Isotopically nonstationary13C flux analysis of changes inArabidopsis thalianaleaf metabolism due to high light acclimation

(2014) Fangfang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OpenMebius: An Open Source Software for Isotopically Nonstationary13C-Based Metabolic Flux Analysis

(2014) Shuichi Kajihata et al.   Biomed Research International

Non-stationary13C-metabolic flux ratio analysis

(2013) Manuel Hörl et al.   BIOTECHNOLOGY AND BIOENGINEERING

Isotopically non-stationary metabolic flux analysis: complex yet highly informative

(2013) Wolfgang Wiechert et al.   CURRENT OPINION IN BIOTECHNOLOGY

Publishing 13C metabolic flux analysis studies: A review and future perspectives

(2013) Scott B. Crown et al.   METABOLIC ENGINEERING

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Metabolic Fluxes in an Illuminated Arabidopsis Rosette

(2013) M. Szecowka et al.   PLANT CELL

Analysis of metabolic flux using dynamic labelling and metabolic modelling

(2013) A. R. FERNIE et al.   PLANT CELL AND ENVIRONMENT

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

(2013) C. Y. Maurice Cheung et al.   PLANT JOURNAL

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Epigenetic and epigenomic variation in Arabidopsis thaliana

(2012) Robert J. Schmitz et al.   TRENDS IN PLANT SCIENCE

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

(2012) Ana Rita Brochado et al.   PLoS Computational Biology

Flux-Balance Modeling of Plant Metabolism

(2011) Lee J. Sweetlove et al.   Frontiers in Plant Science

A Decade of Systems Biology

(2010) Han-Yu Chuang et al.   Annual Review of Cell and Developmental Biology

Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli

(2010) Xuewen Chen et al.   METABOLIC ENGINEERING

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network ofPetunia hybrida

(2010) Amy Marshall Colón et al.   PLANT JOURNAL

Metabolic turnover analysis by a combination of in vivo13C-labelling from 13CO2 and metabolic profiling with CE-MS/MS reveals rate-limiting steps of the C3 photosynthetic pathway in Nicotiana tabacum leaves

(2009) Tomohisa Hasunuma et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic flux analysis in plants: coping with complexity

(2009) DOUG K. ALLEN et al.   PLANT CELL AND ENVIRONMENT

Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth

(2009) M. Stitt et al.   PLANT PHYSIOLOGY

Kinetic flux profiling for quantitation of cellular metabolic fluxes

(2008) Jie Yuan et al.   Nature Protocols