Published in Plant Physiol on July 01, 2005
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol (2006) 4.33
Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell (2005) 4.13
PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics (2006) 3.34
Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol (2006) 2.55
Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol (2008) 2.43
A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet (2005) 2.32
Arabidopsis ABA INSENSITIVE4 regulates lipid mobilization in the embryo and reveals repression of seed germination by the endosperm. Plant Cell (2006) 2.27
Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol (2006) 2.25
Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells. Proc Natl Acad Sci U S A (2008) 2.17
Inhibition of SNF1-related protein kinase1 activity and regulation of metabolic pathways by trehalose-6-phosphate. Plant Physiol (2009) 2.13
Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol (2006) 2.10
Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri. Plant Physiol (2006) 2.09
Metabolite profiling of human colon carcinoma--deregulation of TCA cycle and amino acid turnover. Mol Cancer (2008) 2.02
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res (2009) 1.98
Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol (2007) 1.90
General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis. Plant Cell (2008) 1.87
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol (2010) 1.82
Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell (2009) 1.79
Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol (2008) 1.73
The absence of ALTERNATIVE OXIDASE1a in Arabidopsis results in acute sensitivity to combined light and drought stress. Plant Physiol (2008) 1.73
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J (2011) 1.66
PAMP (pathogen-associated molecular pattern)-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity. J Biol Chem (2010) 1.59
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics (2009) 1.58
Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol Biol (2008) 1.58
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol (2012) 1.58
Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc (2010) 1.51
Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol (2011) 1.51
Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol (2008) 1.45
Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol (2009) 1.44
The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol (2006) 1.43
Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Ann Bot (2008) 1.43
Dynamic plastid redox signals integrate gene expression and metabolism to induce distinct metabolic states in photosynthetic acclimation in Arabidopsis. Plant Cell (2009) 1.41
An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. Plant Cell (2006) 1.37
Upgrading root physiology for stress tolerance by ectomycorrhizas: insights from metabolite and transcriptional profiling into reprogramming for stress anticipation. Plant Physiol (2009) 1.37
Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol (2011) 1.32
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics (2010) 1.30
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27
The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula. Plant Physiol (2007) 1.27
Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. Plant Physiol (2011) 1.26
Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiol (2006) 1.26
Distinct signalling pathways and transcriptome response signatures differentiate ammonium- and nitrate-supplied plants. Plant Cell Environ (2010) 1.26
GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics (2007) 1.25
Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods (2007) 1.24
Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol (2009) 1.23
PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. Nucleic Acids Res (2012) 1.21
Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. Plant Physiol (2007) 1.21
Transcriptome analysis of Arabidopsis wild-type and gl3-sst sim trichomes identifies four additional genes required for trichome development. Mol Plant (2009) 1.19
Global expression profiling applied to the analysis of Arabidopsis stamen development. Plant Physiol (2007) 1.17
Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC Plant Biol (2009) 1.15
Deciphering transcriptional and metabolic networks associated with lysine metabolism during Arabidopsis seed development. Plant Physiol (2009) 1.15
The interaction of Arabidopsis with Piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts. BMC Plant Biol (2015) 1.14
Mild reductions in mitochondrial citrate synthase activity result in a compromised nitrate assimilation and reduced leaf pigmentation but have no effect on photosynthetic performance or growth. Plant Physiol (2008) 1.13
Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol (2008) 1.13
GabiPD: the GABI primary database--a plant integrative 'omics' database. Nucleic Acids Res (2008) 1.12
MADS-complexes regulate transcriptome dynamics during pollen maturation. Genome Biol (2007) 1.12
Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics (2011) 1.11
Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior. Plant Physiol (2012) 1.08
Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis. PLoS One (2011) 1.07
Mutations in the Arabidopsis homolog of LST8/GβL, a partner of the target of Rapamycin kinase, impair plant growth, flowering, and metabolic adaptation to long days. Plant Cell (2012) 1.05
Transcription reprogramming during root nodule development in Medicago truncatula. PLoS One (2011) 1.05
Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination. Plant Physiol (2012) 1.05
Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol (2010) 1.04
Improper excess light energy dissipation in Arabidopsis results in a metabolic reprogramming. BMC Plant Biol (2009) 1.03
Expression profile in rice panicle: insights into heat response mechanism at reproductive stage. PLoS One (2012) 1.03
Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua. BMC Plant Biol (2013) 1.03
Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses. BMC Plant Biol (2012) 1.03
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana. BMC Bioinformatics (2007) 1.02
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. Proc Natl Acad Sci U S A (2011) 0.98
Upregulation of biosynthetic processes associated with growth by trehalose 6-phosphate. Plant Signal Behav (2010) 0.98
Mild reductions in mitochondrial NAD-dependent isocitrate dehydrogenase activity result in altered nitrate assimilation and pigmentation but do not impact growth. Mol Plant (2009) 0.97
Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. Plant Physiol (2012) 0.97
Graft union formation in grapevine induces transcriptional changes related to cell wall modification, wounding, hormone signalling, and secondary metabolism. J Exp Bot (2013) 0.97
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res (2010) 0.96
Targeted enhancement of glutamate-to-γ-aminobutyrate conversion in Arabidopsis seeds affects carbon-nitrogen balance and storage reserves in a development-dependent manner. Plant Physiol (2011) 0.96
A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus. Plant Mol Biol (2009) 0.95
Non-recognition-of-BTH4, an Arabidopsis mediator subunit homolog, is necessary for development and response to salicylic acid. Plant Cell (2012) 0.94
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. Plant Cell (2013) 0.94
The basic leucine zipper transcription factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 is an important transcriptional regulator of abscisic acid-dependent grape berry ripening processes. Plant Physiol (2013) 0.94
Heterografting with nonself rootstocks induces genes involved in stress responses at the graft interface when compared with autografted controls. J Exp Bot (2014) 0.93
Data integration through proximity-based networks provides biological principles of organization across scales. Plant Cell (2013) 0.93
Interactions between polyamines and abiotic stress pathway responses unraveled by transcriptome analysis of polyamine overproducers. OMICS (2011) 0.92
Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. Plant Cell (2014) 0.92
Genetic variation suggests interaction between cold acclimation and metabolic regulation of leaf senescence. Plant Physiol (2006) 0.91
Metabolism and growth in Arabidopsis depend on the daytime temperature but are temperature-compensated against cool nights. Plant Cell (2012) 0.91
Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine. BMC Plant Biol (2013) 0.91
Integrated network analysis and effective tools in plant systems biology. Front Plant Sci (2014) 0.90
Gene expression profiles in rice gametes and zygotes: identification of gamete-enriched genes and up- or down-regulated genes in zygotes after fertilization. J Exp Bot (2013) 0.90
Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development. J Exp Bot (2011) 0.90
Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress. Front Plant Sci (2013) 0.90
Transcriptional regulatory programs underlying barley germination and regulatory functions of Gibberellin and abscisic acid. BMC Plant Biol (2011) 0.89
A naturally associated rhizobacterium of Arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth. PLoS One (2011) 0.88
Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. BMC Genomics (2013) 0.87
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis. BMC Res Notes (2014) 0.87
Metabolic recovery of Arabidopsis thaliana roots following cessation of oxidative stress. Metabolomics (2011) 0.87
Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination. Plant Physiol (2014) 0.87
Functions of chloroplastic adenylate kinases in Arabidopsis. Plant Physiol (2007) 0.86
Temperature desynchronizes sugar and organic acid metabolism in ripening grapevine fruits and remodels their transcriptome. BMC Plant Biol (2016) 0.86
Bacteria-triggered systemic immunity in barley is associated with WRKY and ETHYLENE RESPONSIVE FACTORs but not with salicylic acid. Plant Physiol (2014) 0.86
Arabidopsis DPB3-1, a DREB2A interactor, specifically enhances heat stress-induced gene expression by forming a heat stress-specific transcriptional complex with NF-Y subunits. Plant Cell (2014) 0.86
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GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol (2004) 19.29
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res (2003) 18.69
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J (2004) 15.51
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
Metabolite profiling for plant functional genomics. Nat Biotechnol (2000) 8.74
A probabilistic functional network of yeast genes. Science (2004) 8.35
AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol (2003) 7.59
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res (2004) 5.82
Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol (2004) 4.99
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics (2004) 4.70
Mutant of Arabidopsis deficient in xylem loading of phosphate. Plant Physiol (1991) 4.40
Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol (2003) 4.14
Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res (2002) 4.14
CSB.DB: a comprehensive systems-biology database. Bioinformatics (2004) 2.98
Molecular and functional regulation of two NO3- uptake systems by N- and C-status of Arabidopsis plants. Plant J (1999) 2.97
Identification and characterization of the Arabidopsis PHO1 gene involved in phosphate loading to the xylem. Plant Cell (2002) 2.79
Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol (2004) 2.57
Responses of primary and secondary metabolism to sugar accumulation revealed by microarray expression analysis of the Arabidopsis mutant, pho3. J Exp Bot (2004) 1.74
From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions. Curr Opin Biotechnol (2003) 1.56
pho3: a phosphorus-deficient mutant of Arabidopsis thaliana (L.) Heynh. Planta (2001) 1.50
Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett (2000) 1.42
Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. Physiol Genomics (2003) 1.39
Analysis of the eye developmental pathway in Drosophila using DNA microarrays. Proc Natl Acad Sci U S A (2003) 1.31
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. Bioinformatics (2003) 1.06
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J (2004) 15.51
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol (2005) 15.10
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res (2012) 7.48
GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics (2004) 7.33
Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J (2004) 6.58
Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol (2004) 4.99
PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol (2006) 4.33
Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell (2005) 4.13
pcaMethods--a bioconductor package providing PCA methods for incomplete data. Bioinformatics (2007) 3.84
Eleven golden rules of quantitative RT-PCR. Plant Cell (2008) 3.77
Coordination of carbon supply and plant growth. Plant Cell Environ (2007) 3.63
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46
Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana. Biochem J (2006) 3.36
PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics (2006) 3.34
GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett (2005) 3.29
Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression. Plant Physiol (2005) 2.99
CSB.DB: a comprehensive systems-biology database. Bioinformatics (2004) 2.98
Steps towards an integrated view of nitrogen metabolism. J Exp Bot (2002) 2.84
Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data. BMC Bioinformatics (2004) 2.83
A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ (2009) 2.77
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ (2009) 2.76
Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environ (2007) 2.71
Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet (2012) 2.70
The interdependence of mechanisms underlying climate-driven vegetation mortality. Trends Ecol Evol (2011) 2.67
Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science (2013) 2.66
MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J (2007) 2.65
ADP-glucose pyrophosphorylase is activated by posttranslational redox-modification in response to light and to sugars in leaves of Arabidopsis and other plant species. Plant Physiol (2003) 2.55
Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc Natl Acad Sci U S A (2010) 2.52
Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol (2006) 2.48
Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci U S A (2009) 2.47
The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2007) 2.44
Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol (2008) 2.43
Starch synthesis in potato tubers is regulated by post-translational redox modification of ADP-glucose pyrophosphorylase: a novel regulatory mechanism linking starch synthesis to the sucrose supply. Plant Cell (2002) 2.40
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res (2007) 2.40
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol (2009) 2.33
Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol (2006) 2.25
Adjustment of growth, starch turnover, protein content and central metabolism to a decrease of the carbon supply when Arabidopsis is grown in very short photoperiods. Plant Cell Environ (2009) 2.14
Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J (2007) 2.09
A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods (2007) 2.08
Sensitive and high throughput metabolite assays for inorganic pyrophosphate, ADPGlc, nucleotide phosphates, and glycolytic intermediates based on a novel enzymic cycling system. Plant J (2002) 2.08
Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol (2010) 2.04
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res (2009) 1.98
Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant J (2008) 1.94
Structural kinetic modeling of metabolic networks. Proc Natl Acad Sci U S A (2006) 1.88
Water deficits uncouple growth from photosynthesis, increase C content, and modify the relationships between C and growth in sink organs. J Exp Bot (2011) 1.87
Metabolomics of temperature stress. Physiol Plant (2008) 1.87
Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol (2009) 1.86
Deficiency of mitochondrial fumarase activity in tomato plants impairs photosynthesis via an effect on stomatal function. Plant J (2007) 1.84
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol (2010) 1.82