Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes

(2014) S. Lori Tausta et al.   JOURNAL OF EXPERIMENTAL BOTANY

Increasing water use efficiency along the C3 to C4 evolutionary pathway: a stomatal optimization perspective

(2014) Danielle A. Way et al.   JOURNAL OF EXPERIMENTAL BOTANY

Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis

(2014) Yu Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Correlation of mRNA and protein abundance in the developing maize leaf

(2014) Lalit Ponnala et al.   PLANT JOURNAL

Elements Required for an Efficient NADP-Malic Enzyme Type C4 Photosynthesis

(2014) Y. Wang et al.   PLANT PHYSIOLOGY

A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize

(2014) A. J. Studer 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

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

(2014) M. Simons et al.   PLANT PHYSIOLOGY

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

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

(2014) Daniel Machado et al.   PLoS Computational Biology

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu 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

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

(2014) Sushma Naithani et al.   Frontiers in Plant Science

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

(2013) Cameron Cotten et al.   BMC BIOINFORMATICS

Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

(2013) David Heckmann et al.   CELL

The Genome Database for Rosaceae (GDR): year 10 update

(2013) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Acclimation to low light by C4 maize: implications for bundle sheath leakiness

(2013) CHANDRA BELLASIO et al.   PLANT CELL AND ENVIRONMENT

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

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

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

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

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Integrating C4 photosynthesis into C3 crops to increase yield potential

(2012) Sarah Covshoff et al.   CURRENT OPINION IN BIOTECHNOLOGY

You're so vein: bundle sheath physiology, phylogeny and evolution in C3 and C4 plants

(2012) HOWARD GRIFFITHS et al.   PLANT CELL AND ENVIRONMENT

The Development of C4 Rice: Current Progress and Future Challenges

(2012) S. von Caemmerer et al.   SCIENCE

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1

(2012) Xueyang Feng et al.   PLoS Computational Biology

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

The grass leaf developmental gradient as a platform for a systems understanding of the anatomical specialization of C4 leaves

(2011) T. Nelson   JOURNAL OF EXPERIMENTAL BOTANY

Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types?

(2011) R. T. Furbank   JOURNAL OF EXPERIMENTAL BOTANY

The C4 plant lineages of planet Earth

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

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

(2011) Rajib Saha et al.   PLoS One

The Regulation of Gene Expression Required for C4Photosynthesis

(2010) Julian M. Hibberd et al.   Annual Review of Plant Biology

Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

(2010) Neema Jamshidi et al.   BIOPHYSICAL JOURNAL

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

(2010) Fahimeh Salimi et al.   Biotechnology Journal

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux

(2010) Yikun Tan et al.   METABOLIC ENGINEERING

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

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

(2010) Ines Thiele et al.   Nature Protocols

Structural and Metabolic Transitions of C4 Leaf Development and Differentiation Defined by Microscopy and Quantitative Proteomics in Maize

(2010) W. Majeran et al.   PLANT CELL

Can the progressive increase of C4 bundle sheath leakiness at low PFD be explained by incomplete suppression of photorespiration?

(2010) JOHANNES KROMDIJK et al.   PLANT CELL AND ENVIRONMENT

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

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics

(2009) Pascal-Antoine Christin et al.   Genome Biology and Evolution

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

LibSBML: an API Library for SBML

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

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH