Published in Plant Physiol on June 01, 2005
Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol (2006) 2.36
Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol (2008) 2.28
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol (2009) 1.81
Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One (2011) 1.31
Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol (2008) 1.21
A genetic screen for nitrate regulatory mutants captures the nitrate transporter gene NRT1.1. Plant Physiol (2009) 1.17
Network news: prime time for systems biology of the plant circadian clock. Curr Opin Genet Dev (2010) 1.07
A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol (2009) 0.96
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. Nucleic Acids Res (2010) 0.95
Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. Wiley Interdiscip Rev Syst Biol Med (2010) 0.93
From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat. Front Plant Sci (2015) 0.91
Arabidopsis thaliana as a model organism in systems biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.90
Systematic comparison of C3 and C4 plants based on metabolic network analysis. BMC Syst Biol (2012) 0.85
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. Plant Cell (2014) 0.80
Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis. Plant Cell (2013) 0.79
Members of BTB Gene Family of Scaffold Proteins Suppress Nitrate Uptake and Nitrogen Use Efficiency. Plant Physiol (2016) 0.79
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11
A gene expression map of the Arabidopsis root. Science (2003) 9.95
A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet (2001) 7.79
A classification of tasks in bioinformatics. Bioinformatics (2001) 1.73
A strategy for database interoperation. J Comput Biol (1995) 1.45
Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol (2003) 0.97
In silico biotechnology. Era of reconstruction and interrogation. Curr Opin Biotechnol (2004) 0.96
Adaptive combinatorial design to explore large experimental spaces: approach and validation. Syst Biol (Stevenage) (2004) 0.95
A gene expression map of the Arabidopsis root. Science (2003) 9.95
Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A (2008) 3.17
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A (2008) 2.17
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.03
OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics (2006) 1.90
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol (2010) 1.57
Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol (2004) 1.53
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S A (2011) 1.46
Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol (2004) 1.44
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol (2010) 1.34
Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Mol Biol Evol (2002) 1.33
Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol (2003) 1.29
Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis. Plant Physiol (2003) 1.28
ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol (2006) 1.24
Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration. Plant Physiol (2002) 1.19
A framework integrating plant growth with hormones and nutrients. Trends Plant Sci (2011) 1.19
Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot (2007) 1.16
Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol (2003) 1.08
Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis. Plant Physiol (2003) 1.06
The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One (2009) 1.06
Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J (2002) 1.04
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst Biol (2008) 1.02
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". BMC Syst Biol (2009) 1.01
A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol (2009) 1.00
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A (2013) 0.99
EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics (2005) 0.98
Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol (2003) 0.97
A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol (2009) 0.96
Molecular and physiological analysis of Arabidopsis mutants defective in cytosolic or chloroplastic aspartate aminotransferase. Plant Physiol (2002) 0.95
Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol (2010) 0.93
Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (2006) 0.92
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. BMC Syst Biol (2010) 0.92
TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant (2013) 0.89
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics (2013) 0.88
Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genet (2013) 0.87
RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiol (2013) 0.85
A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA. Plant Mol Biol (2009) 0.83
High nitrogen insensitive 9 (HNI9)-mediated systemic repression of root NO3- uptake is associated with changes in histone methylation. Proc Natl Acad Sci U S A (2011) 0.81
Predicting genome-wide redundancy using machine learning. BMC Evol Biol (2010) 0.79
In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. BMC Bioinformatics (2009) 0.78
Rational design of temperature-sensitive alleles using computational structure prediction. PLoS One (2011) 0.78
Plant systems biology: lessons from a fruitful collaboration. Plant Physiol (2003) 0.77