Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

Anthocyanin biosynthetic genes in Brassica rapa

(2014) Ning Guo et al.   BMC GENOMICS

Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production

(2014) A. Arnold et al.   PLANT PHYSIOLOGY

Plastidial NAD-Dependent Malate Dehydrogenase Is Critical for Embryo Development and Heterotrophic Metabolism in Arabidopsis

(2014) S. Beeler et al.   PLANT PHYSIOLOGY

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves

(2014) C. Y. M. Cheung et al.   PLANT PHYSIOLOGY

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

(2014) Samuel M. D. Seaver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting microbial growth

(2014) J. Monk et al.   SCIENCE

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Transcript abundance on its own cannot be used to infer fluxes in central metabolism

(2014) Jörg Schwender et al.   Frontiers in Plant Science

Phosphorylation ofArabidopsistransketolase at Ser428provides a potential paradigm for the metabolic control of chloroplast carbon metabolism

(2013) Agostinho G. Rocha et al.   BIOCHEMICAL JOURNAL

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

The Plastid-Localized NAD-Dependent Malate Dehydrogenase Is Crucial for Energy Homeostasis in Developing Arabidopsis thaliana Seeds

(2013) Jennifer Selinski et al.   Molecular Plant

Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis

(2013) N. Topfer et al.   PLANT CELL

Seed Architecture Shapes Embryo Metabolism in Oilseed Rape

(2013) Ljudmilla Borisjuk et al.   PLANT CELL

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

Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis

(2013) M. Lakshmanan et al.   PLANT PHYSIOLOGY

Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale

(2013) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

(2013) M. G. Poolman et al.   PLANT PHYSIOLOGY

Systems analysis of metabolic phenotypes: what have we learnt?

(2013) Lee J. Sweetlove et al.   TRENDS IN PLANT SCIENCE

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

(2012) Michael Weitzel et al.   BIOINFORMATICS

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

(2012) Nanette R Boyle et al.   BMC Systems Biology

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

(2012) Michael J McAnulty et al.   BMC Systems Biology

A proof for loop-law constraints in stoichiometric metabolic networks

(2012) Elad Noor et al.   BMC Systems Biology

Plant genome-scale metabolic reconstruction and modelling

(2012) Cristiana Gomes de Oliveira Dal’Molin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Frontiers in metabolic reconstruction and modeling of plant genomes

(2012) S. M. D. Seaver et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

(2012) Sandra K. Tanz et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

Predictive Modeling of Biomass Component Tradeoffs in Brassica napus Developing Oilseeds Based on in Silico Manipulation of Storage Metabolism

(2012) J. Schwender et al.   PLANT PHYSIOLOGY

Are we ready for genome-scale modeling in plants?

(2012) Eva Collakova et al.   PLANT SCIENCE

Tissue-Specific Distribution of Secondary Metabolites in Rapeseed (Brassica napus L.)

(2012) Jingjing Fang et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Syntenic gene analysis between Brassica rapa and other Brassicaceae species

(2012) Feng Cheng et al.   Frontiers in Plant Science

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

(2011) Eleftherios Pilalis et al.   BIOTECHNOLOGY AND BIOENGINEERING

AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome

(2011) Cristiana Gomes de Oliveira Dal’Molin et al.   BMC GENOMICS

Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance

(2011) Anna M. J. Kliphuis et al.   JOURNAL OF APPLIED PHYCOLOGY

Proteomic Comparison of Plastids from Developing Embryos and Leaves ofBrassica napus

(2011) Diogo Ribeiro Demartini et al.   JOURNAL OF PROTEOME RESEARCH

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

Combined Noninvasive Imaging and Modeling Approaches Reveal Metabolic Compartmentation in the Barley Endosperm

(2011) Hardy Rolletschek et al.   PLANT CELL

Comparative deep transcriptional profiling of four developing oilseeds

(2011) Manuel A. Troncoso-Ponce et al.   PLANT JOURNAL

Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to 13C metabolic flux analysis

(2011) Jordan Hay et al.   PLANT JOURNAL

Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos

(2011) Jordan Hay et al.   PLANT JOURNAL

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental flux measurements on a network scale

(2011) Jörg Schwender   Frontiers in Plant Science

Flux-Balance Modeling of Plant Metabolism

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

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Expansion and subfunctionalisation of flavonoid 3',5'-hydroxylases in the grapevine lineage

(2010) Luigi Falginella et al.   BMC GENOMICS

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

(2010) Ines Thiele et al.   Nature Protocols

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

A Genome-Scale Metabolic Model Accurately Predicts Fluxes in Central Carbon Metabolism under Stress Conditions

(2010) Thomas C.R. Williams et al.   PLANT PHYSIOLOGY

Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses

(2010) J. M. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Metabolic network analysis integrated with transcript verification for sequenced genomes

(2009) Ani Manichaikul et al.   NATURE METHODS

Analysis of Metabolic Flux Phenotypes for Two Arabidopsis Mutants with Severe Impairment in Seed Storage Lipid Synthesis

(2009) J. Lonien et al.   PLANT PHYSIOLOGY

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

(2009) M. G. Poolman et al.   PLANT PHYSIOLOGY

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

Metabolic flux analysis as a tool in metabolic engineering of plants

(2008) Jörg Schwender   CURRENT OPINION IN BIOTECHNOLOGY

Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism

(2008) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY