Published in Proc Natl Acad Sci U S A on December 19, 2011
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res (2012) 1.71
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci U S A (2014) 1.20
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol (2013) 1.04
Responses to light intensity in a genome-scale model of rice metabolism. Plant Physiol (2013) 1.02
Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. Plant Cell (2013) 0.97
The carotenoid biosynthetic pathway: thinking in all dimensions. Plant Sci (2013) 0.97
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol (2013) 0.95
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Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. Plant Physiol (2014) 0.92
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Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis. Plant Physiol (2013) 0.88
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Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach. BMC Syst Biol (2012) 0.87
Integration of metabolomics data into metabolic networks. Front Plant Sci (2015) 0.86
Generalized framework for context-specific metabolic model extraction methods. Front Plant Sci (2014) 0.85
Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism. Plant Physiol (2012) 0.85
Metabolic fingerprinting of Arabidopsis thaliana accessions. Front Plant Sci (2015) 0.85
Mathematical modeling of plant metabolism-from reconstruction to prediction. Metabolites (2012) 0.85
Solving the differential biochemical Jacobian from metabolomics covariance data. PLoS One (2014) 0.84
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. Plant Physiol (2015) 0.83
Systems biology of host-microbe metabolomics. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. PLoS Comput Biol (2014) 0.82
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Front Plant Sci (2015) 0.82
Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. Plant Physiol (2015) 0.81
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Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. Front Plant Sci (2014) 0.81
Transcriptional evidence for inferred pattern of pollen tube-stigma metabolic coupling during pollination. PLoS One (2014) 0.81
Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wild-type and mutant roots. New Phytol (2015) 0.80
A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Front Plant Sci (2013) 0.80
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. Plant Cell (2014) 0.80
Linking metabolomics data to underlying metabolic regulation. Front Mol Biosci (2014) 0.80
Cell metabolomics. OMICS (2013) 0.80
Grand Challenges in Plant Systems Biology: Closing the Circle(s). Front Plant Sci (2012) 0.80
The Classification and Evolution of Enzyme Function. Biophys J (2015) 0.79
Using the SUBcellular database for Arabidopsis proteins to localize the Deg protease family. Front Plant Sci (2014) 0.79
Understanding genetic variation - the value of systems biology. Br J Clin Pharmacol (2014) 0.79
A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. BMC Syst Biol (2014) 0.79
Predictive sulfur metabolism - a field in flux. Front Plant Sci (2014) 0.78
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief Bioinform (2015) 0.78
Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions. Front Plant Sci (2016) 0.78
Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome-scale metabolic model of rice. Front Plant Sci (2014) 0.78
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. Plant Physiol (2015) 0.78
Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data. Front Mol Biosci (2016) 0.77
Phenotypic Characterization Analysis of Human Hepatocarcinoma by Urine Metabolomics Approach. Sci Rep (2016) 0.77
Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions. Plant Signal Behav (2013) 0.77
Metabolic Architecture of the Cereal Grain and Its Relevance to Maximize Carbon Use Efficiency. Plant Physiol (2015) 0.76
Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. Sci Rep (2015) 0.76
Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions. Front Plant Sci (2012) 0.76
Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls. Sci Rep (2016) 0.75
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol (2017) 0.75
Flux Control in a Defense Pathway in Arabidopsis thaliana Is Robust to Environmental Perturbations and Controls Variation in Adaptive Traits. G3 (Bethesda) (2015) 0.75
In silico metabolic network analysis of Arabidopsis leaves. BMC Syst Biol (2016) 0.75
Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses. Front Plant Sci (2016) 0.75
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Front Microbiol (2015) 0.75
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. Database (Oxford) (2014) 0.75
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation. PLoS One (2012) 0.75
Identification and Expression Analysis of Candidate Genes Involved in Carotenoid Biosynthesis in Chickpea Seeds. Front Plant Sci (2016) 0.75
Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response, and protein locations to aid in identifying transport functions. Front Plant Sci (2014) 0.75
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. BMC Plant Biol (2016) 0.75
Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing. FEBS Open Bio (2016) 0.75
Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? Front Bioeng Biotechnol (2016) 0.75
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. Front Plant Sci (2016) 0.75
A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. Front Plant Sci (2016) 0.75
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. Nucleic Acids Res (2016) 0.75
ChloroKB:a web-application for the integration of knowledge related to chloroplast metabolic network. Plant Physiol (2017) 0.75
Modelling compartmentalization towards elucidation and engineering of spatial organization in biochemical pathways. Sci Rep (2017) 0.75
Bioenergetics of Monoterpenoid Essential Oil Biosynthesis in Non-Photosynthetic Glandular Trichomes. Plant Physiol (2017) 0.75
Resolving the central metabolism of Arabidopsis guard cells. Sci Rep (2017) 0.75
Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ (2017) 0.75
Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets. Front Genet (2017) 0.75
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A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A (2007) 11.46
Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol (2005) 10.66
Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41
AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol (2003) 7.59
A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64
High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol (2010) 6.08
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng (2003) 5.53
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics (2003) 4.49
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science (2008) 4.38
SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res (2006) 3.63
Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A (2005) 2.99
Sites and regulation of auxin biosynthesis in Arabidopsis roots. Plant Cell (2005) 2.94
Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J (2008) 2.89
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
The biomass objective function. Curr Opin Microbiol (2010) 2.32
AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol (2004) 2.11
Organ-specific expression of brassinosteroid-biosynthetic genes and distribution of endogenous brassinosteroids in Arabidopsis. Plant Physiol (2003) 1.95
A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol (2009) 1.95
Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant J (2005) 1.85
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol (2009) 1.81
Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J (2011) 1.64
Volatile science? Metabolic engineering of terpenoids in plants. Trends Plant Sci (2005) 1.40
Compartmentation in plant metabolism. J Exp Bot (2006) 1.38
The plastidial MEP pathway: unified nomenclature and resources. Trends Plant Sci (2008) 1.33
Phytoene synthase activity controls the biosynthesis of carotenoids and the supply of their metabolic precursors in dark-grown Arabidopsis seedlings. Plant J (2009) 1.33
Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet (2009) 1.24
beta-Cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis. Plant Physiol (2000) 1.23
Metabolic flux analysis in plants: from intelligent design to rational engineering. Annu Rev Plant Biol (2008) 1.18
Network-based prediction of metabolic enzymes' subcellular localization. Bioinformatics (2009) 1.10
Discovery of ubiquinone (coenzyme Q) and an overview of function. Mitochondrion (2007) 1.08
Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol (2009) 1.04
A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome. PLoS One (2011) 0.99
Lysine catabolism, an effective versatile regulator of lysine level in plants. Amino Acids (2006) 0.96
The plant ER-Golgi interface: a highly structured and dynamic membrane complex. J Exp Bot (2006) 0.94
The plant biotin synthase reaction. Identification and characterization of essential mitochondrial accessory protein components. J Biol Chem (2003) 0.93
Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. In Silico Biol (2001) 0.92
Ureidoglycolate amidohydrolase from developing French bean fruits (Phaseolus vulgaris [L.].). Arch Biochem Biophys (1991) 0.91
Colors in the dark: a model for the regulation of carotenoid biosynthesis in etioplasts. Plant Signal Behav (2009) 0.90
Mutation analysis of violaxanthin de-epoxidase identifies substrate-binding sites and residues involved in catalysis. J Biol Chem (2010) 0.89
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature (2011) 4.32
Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol (2010) 3.65
Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol (2011) 3.65
A key role for mitochondrial gatekeeper pyruvate dehydrogenase in oncogene-induced senescence. Nature (2013) 3.46
Genetic engineering of terpenoid metabolism attracts bodyguards to Arabidopsis. Science (2005) 3.46
Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A (2010) 3.40
Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet (2006) 3.25
PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol (2011) 3.22
Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A (2005) 2.99
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23
A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol (2007) 2.15
Actor-critic models of the basal ganglia: new anatomical and computational perspectives. Neural Netw (2002) 2.12
The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci U S A (2008) 1.96
Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell (2011) 1.88
The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol (2007) 1.80
TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. Plant J (2009) 1.77
The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res (2010) 1.75
Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun (2011) 1.75
Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol (2008) 1.70
Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput Biol (2011) 1.66
Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proc Natl Acad Sci U S A (2007) 1.65
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics (2010) 1.65
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Recommendations for reporting metabolite data. Plant Cell (2011) 1.61
Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60
Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci U S A (2006) 1.59
Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol (2009) 1.59
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics (2006) 1.56
Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol Syst Biol (2013) 1.56
Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development. Plant Physiol (2008) 1.53
Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput Biol (2012) 1.51
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics (2009) 1.51
Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev (2007) 1.47
QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics (2006) 1.46
The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators. Plant Physiol (2008) 1.46
Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44
Unsupervised learning of natural languages. Proc Natl Acad Sci U S A (2005) 1.44
Functional characterization of enzymes forming volatile esters from strawberry and banana. Plant Physiol (2004) 1.43
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res (2010) 1.42
SHINE transcription factors act redundantly to pattern the archetypal surface of Arabidopsis flower organs. PLoS Genet (2011) 1.42
The Arabidopsis DCR encoding a soluble BAHD acyltransferase is required for cutin polyester formation and seed hydration properties. Plant Physiol (2009) 1.41
INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol (2012) 1.40
Toward accurate reconstruction of functional protein networks. Mol Syst Biol (2009) 1.40
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
iMAT: an integrative metabolic analysis tool. Bioinformatics (2010) 1.32
QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27
Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res (2011) 1.24
Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet (2009) 1.24
Combining drug and gene similarity measures for drug-target elucidation. J Comput Biol (2011) 1.23
Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity. PLoS Comput Biol (2006) 1.21
A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20
Increased microRNA activity in human cancers. PLoS One (2009) 1.18
Systematic identification of gene annotation errors in the widely used yeast mutation collections. Nat Methods (2012) 1.17
The Arabidopsis ABCG13 transporter is required for flower cuticle secretion and patterning of the petal epidermis. New Phytol (2011) 1.17
Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16
Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. PLoS Genet (2012) 1.14
Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive isocitrate dehydrogenase (IDH) flux. J Biol Chem (2013) 1.13
High-resolution metabolic mapping of cell types in plant roots. Proc Natl Acad Sci U S A (2013) 1.13
Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res (2012) 1.13
Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol (2007) 1.11
Redirection of flavonoid biosynthesis through the down-regulation of an anthocyanidin glucosyltransferase in ripening strawberry fruit. Plant Physiol (2008) 1.11
Reverse genetics of floral scent: application of tobacco rattle virus-based gene silencing in Petunia. Plant Physiol (2007) 1.11
Feature selection via coalitional game theory. Neural Comput (2007) 1.11
ANAT: a tool for constructing and analyzing functional protein networks. Sci Signal (2011) 1.11
Network-based prediction of metabolic enzymes' subcellular localization. Bioinformatics (2009) 1.10
Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment. Proc Natl Acad Sci U S A (2014) 1.09
Meta-analysis of gene expression data: a predictor-based approach. Bioinformatics (2007) 1.07
The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol Plant (2009) 1.07
Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters. PLoS Comput Biol (2012) 1.07
The tomato SlSHINE3 transcription factor regulates fruit cuticle formation and epidermal patterning. New Phytol (2012) 1.05