Published in Plant J on February 07, 2008
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics (2009) 2.21
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
SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics (2008) 1.68
Recommendations for reporting metabolite data. Plant Cell (2011) 1.61
MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J (2009) 1.55
Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc (2010) 1.51
AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol (2009) 1.46
Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. BMC Bioinformatics (2009) 1.44
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics (2010) 1.41
MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data. Metabolomics (2011) 1.37
SNP discovery and linkage map construction in cultivated tomato. DNA Res (2010) 1.36
Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Physiol (2009) 1.34
Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol (2010) 1.33
Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28
Metabolic networks: how to identify key components in the regulation of metabolism and growth. Plant Physiol (2009) 1.27
Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet (2009) 1.24
On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence. Plant Physiol (2012) 1.23
Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Physiol (2011) 1.19
TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Plant Cell Physiol (2011) 1.16
Extending biochemical databases by metabolomic surveys. J Biol Chem (2011) 1.09
Differential tomato transcriptomic responses induced by pepino mosaic virus isolates with differential aggressiveness. Plant Physiol (2011) 1.06
PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant Cell Physiol (2013) 1.02
Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry. Rapid Commun Mass Spectrom (2011) 1.00
Toward the storage metabolome: profiling the barley vacuole. Plant Physiol (2011) 1.00
Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. Plant Cell (2014) 1.00
Transcriptional regulation of fruit ripening by tomato FRUITFULL homologs and associated MADS box proteins. Plant Cell (2014) 0.99
GLYCOALKALOID METABOLISM1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato. Plant Cell (2011) 0.99
Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology. Comput Struct Biotechnol J (2013) 0.98
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res (2010) 0.98
Identification of genes in the phenylalanine metabolic pathway by ectopic expression of a MYB transcription factor in tomato fruit. Plant Cell (2011) 0.95
Recent progress in the development of metabolome databases for plant systems biology. Front Plant Sci (2013) 0.94
Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity. Front Plant Sci (2011) 0.94
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol (2012) 0.94
Recent advances of metabolomics in plant biotechnology. Plant Biotechnol Rep (2011) 0.93
Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway. BMC Plant Biol (2014) 0.93
Cranberries and their bioactive constituents in human health. Adv Nutr (2013) 0.93
Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. Plant Cell (2015) 0.92
Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. Curr Genomics (2008) 0.92
From models to crop species: caveats and solutions for translational metabolomics. Front Plant Sci (2011) 0.91
Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. PLoS One (2009) 0.89
Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics. Metabolomics (2014) 0.87
Diel changes in nitrogen and carbon resource status and use for growth in young plants of tomato (Solanum lycopersicum). Ann Bot (2009) 0.85
AMDORAP: non-targeted metabolic profiling based on high-resolution LC-MS. BMC Bioinformatics (2011) 0.83
Light Remodels Lipid Biosynthesis in Nannochloropsis gaditana by Modulating Carbon Partitioning between Organelles. Plant Physiol (2016) 0.82
LC-MS-based Metabolomics of Xenobiotic-induced Toxicities. Comput Struct Biotechnol J (2013) 0.82
Reduction of inositol (1,4,5)-trisphosphate affects the overall phosphoinositol pathway and leads to modifications in light signalling and secondary metabolism in tomato plants. J Exp Bot (2011) 0.82
System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato. Plant Physiol (2013) 0.82
Small and remarkable: The Micro-Tom model system as a tool to discover novel hormonal functions and interactions. Plant Signal Behav (2010) 0.82
Updating the Micro-Tom TILLING platform. Breed Sci (2013) 0.81
Accumulation of Flavonols over Hydroxycinnamic Acids Favors Oxidative Damage Protection under Abiotic Stress. Front Plant Sci (2016) 0.81
Spatially Resolved Plant Metabolomics: Some Potentials and Limitations of Laser-Ablation Electrospray Ionization Mass Spectrometry Metabolite Imaging. Plant Physiol (2015) 0.80
Temporally resolved GC-MS-based metabolic profiling of herbicide treated plants treated reveals that changes in polar primary metabolites alone can distinguish herbicides of differing mode of action. Metabolomics (2008) 0.80
Emerging applications of metabolomics in studying chemopreventive phytochemicals. AAPS J (2013) 0.79
Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit. BMC Plant Biol (2017) 0.78
Integrated LC-MS/MS system for plant metabolomics. Comput Struct Biotechnol J (2013) 0.76
Metabolomics reveal 1-palmitoyl lysophosphatidylcholine production by peroxisome proliferator-activated receptor α. J Lipid Res (2014) 0.76
Biomarkers for nutrient intake with focus on alternative sampling techniques. Genes Nutr (2016) 0.76
Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor. Plant Physiol (2016) 0.75
Identification of Loci Affecting Accumulation of Secondary Metabolites in Tomato Fruit of a Solanum lycopersicum × Solanum chmielewskii Introgression Line Population. Front Plant Sci (2016) 0.75
Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL. Front Plant Sci (2016) 0.75
Technical Challenges in Mass Spectrometry-Based Metabolomics. Mass Spectrom (Tokyo) (2016) 0.75
The WEIZMASS spectral library for high-confidence metabolite identification. Nat Commun (2016) 0.75
Gene-Metabolite Networks of Volatile Metabolism in Airen and Tempranillo Grape Cultivars Revealed a Distinct Mechanism of Aroma Bouquet Production. Front Plant Sci (2016) 0.75
Plastid Proteomic Analysis in Tomato Fruit Development. PLoS One (2015) 0.75
Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape. Front Plant Sci (2017) 0.75
Transcriptome Profiling of Tomato Uncovers an Involvement of Cytochrome P450s and Peroxidases in Stigma Color Formation. Front Plant Sci (2017) 0.75
Changes in Polyphenols Contents and Antioxidant Capacities of Organically and Conventionally Cultivated Tomato (Solanum lycopersicum L.) Fruits during Ripening. Int J Anal Chem (2017) 0.75
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics. Gigascience (2017) 0.75
Seed Metabolome Analysis of a Transgenic Rice Line Expressing Cholera Toxin B-subunit. Sci Rep (2017) 0.75
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J (2004) 15.51
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
METLIN: a metabolite mass spectral database. Ther Drug Monit (2005) 10.15
Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell (2000) 6.12
Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol (2006) 4.47
Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell (2001) 4.42
The genetics of plant metabolism. Nat Genet (2006) 4.28
Genetic regulation of fruit development and ripening. Plant Cell (2004) 4.20
Genome annotation: from sequence to biology. Nat Rev Genet (2001) 3.83
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J (2005) 3.73
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics (2007) 3.70
The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol (2005) 3.65
Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc (2007) 3.41
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 3.41
Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics (2006) 3.02
MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol (2005) 3.00
A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol (2005) 2.95
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
Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS (2002) 2.32
SetupX--a public study design database for metabolomic projects. Pac Symp Biocomput (2007) 2.20
A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol (2006) 2.08
Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry (2003) 1.99
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol (2005) 1.90
UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana. J Biol Chem (2003) 1.78
Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep (2003) 1.76
Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol (2006) 1.72
Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J Exp Bot (2004) 1.66
The light-hyperresponsive high pigment-2dg mutation of tomato: alterations in the fruit metabolome. New Phytol (2005) 1.63
A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics. Plant Cell Physiol (2005) 1.60
A biologist's view of the Drosophila genome annotation assessment project. Genome Res (2000) 1.60
Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem (2007) 1.52
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics (2003) 1.45
Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J Exp Bot (2005) 1.31
Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J (2006) 1.18
Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol (2006) 1.11
Characterization and content of flavonoid glycosides in genetically modified tomato (Lycopersicon esculentum) fruits. J Agric Food Chem (2003) 1.10
Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. Phytochemistry (2007) 1.02
A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes: discovery of novel compounds. Plant Cell Rep (2004) 0.99
Cysteinyl-flavan-3-ol conjugates from grape procyanidins. Antioxidant and antiproliferative properties. Bioorg Med Chem (2002) 0.85
Determination of brassinosteroids in the sub-femtomolar range using dansyl-3-aminophenylboronate derivatization and electrospray mass spectrometry. Rapid Commun Mass Spectrom (2004) 0.84
Steroidal alkaloid glycosides, esculeosides C and D, from the ripe fruit of cherry tomato. Chem Pharm Bull (Tokyo) (2006) 0.79
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom (2010) 6.16
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci U S A (2007) 4.13
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J (2005) 3.73
Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol Microbiol (2002) 3.68
Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol (2002) 3.47
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 3.41
Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol (2007) 3.13
Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem (2005) 2.98
Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics (2006) 2.92
12-oxo-phytodienoic acid triggers expression of a distinct set of genes and plays a role in wound-induced gene expression in Arabidopsis. Plant Physiol (2005) 2.72
Informatics for unveiling hidden genome signatures. Genome Res (2003) 2.60
Loss of anthocyanins in red-wine grape under high temperature. J Exp Bot (2007) 2.21
Detectability of colorectal neoplasia with fluorine-18-2-fluoro-2-deoxy-D-glucose positron emission tomography and computed tomography (FDG-PET/CT). J Gastroenterol (2011) 2.07
Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis. Plant J (2005) 1.97
Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant J (2008) 1.91
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol (2005) 1.90
Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res (2006) 1.84
KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol (2011) 1.82
Pulmonary pleomorphic carcinoma: a clinicopathological study including EGFR mutation analysis. J Thorac Oncol (2010) 1.68
AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis. Plant Cell Physiol (2004) 1.64
The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics (2005) 1.63
Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol (2009) 1.60
An extracellular aspartic protease functions in Arabidopsis disease resistance signaling. EMBO J (2004) 1.58
Large-scale analysis of gene expression profiles during early stages of root nodule formation in a model legume, Lotus japonicus. DNA Res (2004) 1.52
Spermidine synthase genes are essential for survival of Arabidopsis. Plant Physiol (2004) 1.49
In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol (2012) 1.45
A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J Biol Chem (2004) 1.42
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics (2010) 1.41
A shift from colon- to ileum-predominant bacteria in ileal-pouch feces following total proctocolectomy. Dig Dis Sci (2012) 1.40
Clinicopathological characteristics of follicular lymphoma with peripheral blood involvement. Leuk Lymphoma (2014) 1.39
Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Plant J (2007) 1.39
Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation. Plant Cell (2007) 1.38
STOP1 regulates multiple genes that protect arabidopsis from proton and aluminum toxicities. Plant Physiol (2009) 1.38
Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res (2008) 1.32
The 14-kDa dynein light chain-family protein Dlc1 is required for regular oscillatory nuclear movement and efficient recombination during meiotic prophase in fission yeast. Mol Biol Cell (2002) 1.32
CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics (2010) 1.32
Efficacy of gefitinib for non-adenocarcinoma non-small-cell lung cancer patients harboring epidermal growth factor receptor mutations: a pooled analysis of published reports. Cancer Sci (2011) 1.30
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. Nucleic Acids Res (2010) 1.30
Prognostic impact of circulating tumor cells in patients with small cell lung cancer. J Thorac Oncol (2012) 1.29
A phylogenomic study of the OCTase genes in Pseudomonas syringae pathovars: the horizontal transfer of the argK-tox cluster and the evolutionary history of OCTase genes on their genomes. J Mol Evol (2002) 1.29
Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol (2008) 1.29
Biologic correlation of 2-[18F]-fluoro-2-deoxy-D-glucose uptake on positron emission tomography in thymic epithelial tumors. J Clin Oncol (2010) 1.27
Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor. Plant Physiol (2005) 1.25
Utility of 18FDG-PET for differentiating the grade of malignancy in thymic epithelial tumors. Lung Cancer (2008) 1.23
Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc Natl Acad Sci U S A (2006) 1.22
A randomized cross-over study of a traditional Japanese medicine (kampo), yokukansan, in the treatment of the behavioural and psychological symptoms of dementia. Int J Neuropsychopharmacol (2008) 1.22
gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12. J Biol Chem (2008) 1.20
Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J (2008) 1.20
Efficacy of chemotherapy with carboplatin and paclitaxel for unresectable thymic carcinoma. Lung Cancer (2009) 1.19
Novel plant immune-priming compounds identified via high-throughput chemical screening target salicylic acid glucosyltransferases in Arabidopsis. Plant Cell (2012) 1.18
TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Plant Cell Physiol (2011) 1.16
tRNADB-CE: tRNA gene database curated manually by experts. Nucleic Acids Res (2008) 1.16
Effective production of 3,4-dihydroxyphenyl-L-alanine (L-DOPA) with Erwinia herbicola cells carrying a mutant transcriptional regulator TyrR. J Biotechnol (2005) 1.15
Molecular characterization of His-Asp phosphorelay signaling factors in maize leaves: implications of the signal divergence by cytokinin-inducible response regulators in the cytosol and the nuclei. Plant Mol Biol (2003) 1.14
Autoprocessing of Helicobacter pylori gamma-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad. J Biol Chem (2006) 1.12
Arabidopsis response regulator, ARR22, ectopic expression of which results in phenotypes similar to the wol cytokinin-receptor mutant. Plant Cell Physiol (2004) 1.12
Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase. Plant Cell (2007) 1.11
Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol (2006) 1.11
Phase I and pharmacokinetic study of dacomitinib (PF-00299804), an oral irreversible, small molecule inhibitor of human epidermal growth factor receptor-1, -2, and -4 tyrosine kinases, in Japanese patients with advanced solid tumors. Invest New Drugs (2012) 1.11
Theory of hybrid dynamical systems and its applications to biological and medical systems. Philos Trans A Math Phys Eng Sci (2010) 1.11
NMDA-dependent proteolysis of presynaptic adhesion molecule L1 in the hippocampus by neuropsin. J Neurosci (2003) 1.10