Kinetic modelling of plant metabolic pathways

Systems approaches to modelling pathways and networks

(2011) T. Pfau et al.   Briefings in Functional Genomics

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

Functional Incorporation of Sorghum Small Subunit Increases the Catalytic Turnover Rate of Rubisco in Transgenic Rice

(2011) C. Ishikawa et al.   PLANT PHYSIOLOGY

A Topological Map of the Compartmentalized Arabidopsis thaliana Leaf Metabolome

(2011) Stephan Krueger et al.   PLoS One

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

(2011) Rajib Saha et al.   PLoS One

A quantitative comparison of Calvin–Benson cycle models

(2011) Anne Arnold et al.   TRENDS IN PLANT SCIENCE

Flux-Balance Modeling of Plant Metabolism

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

Building and analysing genome-scale metabolic models

(2010) David A. Fell et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

(2010) Karin Radrich et al.   BMC Systems Biology

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

(2010) Karen van Eunen et al.   FEBS Journal

Reduced neutral invertase activity in the culm tissues of transgenic sugarcane plants results in a decrease in respiration and sucrose cycling and an increase in the sucrose to hexose ratio

(2010) Debra Rossouw et al.   FUNCTIONAL PLANT BIOLOGY

Kinetic and Thermodynamic Aspects of Enzyme Control and Regulation†

(2010) Johann M. Rohwer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A large-scale protein-function database

(2010) Rolf Apweiler et al.   Nature Chemical Biology

Network Analysis of Enzyme Activities and Metabolite Levels and Their Relationship to Biomass in a Large Panel of Arabidopsis Accessions

(2010) R. Sulpice et al.   PLANT CELL

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

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

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

Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

(2010) R. Rios-Estepa 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

Simulating Plant Metabolic Pathways with Enzyme-Kinetic Models

(2010) K. Schallau et al.   PLANT PHYSIOLOGY

Not just a circle: flux modes in the plant TCA cycle

(2010) Lee J. Sweetlove et al.   TRENDS IN PLANT SCIENCE

Insights into plant metabolic networks from steady-state metabolic flux analysis

(2009) Nicholas J. Kruger et al.   BIOCHIMIE

A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana

(2009) Junli Liu et al.   BIOPHYSICAL CHEMISTRY

FiPy: Partial Differential Equations with Python

(2009) Jonathan E. Guyer et al.   COMPUTING IN SCIENCE & ENGINEERING

Systems biology: model based evaluation and comparison of potential explanations for given biological data

(2009) Gunnar Cedersund et al.   FEBS Journal

Systems biology: from possible to plausible to actual models

(2009) Frank J. Bruggeman   FEBS Journal

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Linking phloem function to structure: Analysis with a coupled xylem–phloem transport model

(2009) T. Hölttä et al.   JOURNAL OF THEORETICAL BIOLOGY

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

(2009) Gilles Curien et al.   Molecular Systems Biology

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

(2009) Maria Piques et al.   Molecular Systems Biology

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

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

Metabolic Flux Analysis in Plants: From Intelligent Design to Rational Engineering

(2008) Igor G.L. Libourel et al.   Annual Review of Plant Biology

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

A kinetic model structure for delayed fluorescence from plants

(2008) Ya Guo et al.   BIOSYSTEMS

Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production withChlamydomonas reinhardtii: Part I. Model development and parameter identification

(2008) Swanny Fouchard et al.   BIOTECHNOLOGY AND BIOENGINEERING

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

(2008) Sebastian Wahl et al.   BMC BIOINFORMATICS

Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways

(2008) Rajat K De et al.   BMC Systems Biology

Modelling phloem and xylem transport within a complex architecture

(2008) André Lacointe et al.   FUNCTIONAL PLANT BIOLOGY

On the approaches applied in formulation of a kinetic model of photosystem II: Different approaches lead to different simulations of the chlorophyll a fluorescence transients

(2008) Dušan Lazár et al.   JOURNAL OF THEORETICAL BIOLOGY

Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves

(2008) Beate Knoke et al.   PHYTOCHEMISTRY REVIEWS

Temperature and nitrogen effects on regulators and products of the flavonoid pathway: experimental and kinetic model studies

(2008) KRISTINE M. OLSEN et al.   PLANT CELL AND ENVIRONMENT

A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint

(2008) R. Rios-Estepa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA