Published in Nucleic Acids Res on January 01, 2006
BioMart--biological queries made easy. BMC Genomics (2009) 11.06
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform (2009) 5.44
Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol (2009) 3.06
PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics (2007) 3.01
AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res (2006) 2.92
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol (2006) 2.27
A genome-wide characterization of microRNA genes in maize. PLoS Genet (2009) 2.23
The FLOWERING LOCUS T-like gene family in barley (Hordeum vulgare). Genetics (2007) 2.21
Multiple models for Rosaceae genomics. Plant Physiol (2008) 2.08
How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS One (2009) 1.73
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics (2008) 1.68
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics (2009) 1.58
Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol (2008) 1.57
MaizeGDB's new data types, resources and activities. Nucleic Acids Res (2007) 1.56
Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci. Genetics (2008) 1.49
TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol (2009) 1.48
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
GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol (2008) 1.38
Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol (2006) 1.31
The banana genome hub. Database (Oxford) (2013) 1.29
Genome halving with an outgroup. Evol Bioinform Online (2007) 1.27
Gramene QTL database: development, content and applications. Database (Oxford) (2009) 1.25
Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol (2009) 1.23
Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies. PLoS One (2014) 1.20
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One (2007) 1.16
Salt stress response in rice: genetics, molecular biology, and comparative genomics. Funct Integr Genomics (2006) 1.11
Genome sequencing and genome resources in model legumes. Plant Physiol (2007) 1.04
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res (2007) 1.00
Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. Plant Physiol (2007) 0.97
Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance. PLoS One (2015) 0.97
DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes. Plant Physiol (2011) 0.95
Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnol Biofuels (2012) 0.94
Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics (2010) 0.93
Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res (2013) 0.93
RiceNet v2: an improved network prioritization server for rice genes. Nucleic Acids Res (2015) 0.91
How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis. Front Plant Sci (2013) 0.90
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. Plant J (2013) 0.90
Genome mapping of white clover (Trifolium repens L.) and comparative analysis within the Trifolieae using cross-species SSR markers. Theor Appl Genet (2007) 0.88
Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass. G3 (Bethesda) (2015) 0.88
Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biol (2013) 0.88
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice (N Y) (2013) 0.86
Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics (2012) 0.85
Transcriptome profiling of leaf elongation zone under drought in contrasting rice cultivars. PLoS One (2013) 0.84
Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress. Funct Integr Genomics (2015) 0.83
OsiSAP1 overexpression improves water-deficit stress tolerance in transgenic rice by affecting expression of endogenous stress-related genes. Plant Cell Rep (2014) 0.83
Multi-source and ontology-based retrieval engine for maize mutant phenotypes. Database (Oxford) (2011) 0.80
A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database. Database (Oxford) (2011) 0.80
Analysis on genetic diversification and heterosis in autotetraploid rice. Springerplus (2013) 0.80
Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One (2012) 0.79
Computable visually observed phenotype ontological framework for plants. BMC Bioinformatics (2011) 0.78
A comparative map viewer integrating genetic maps for Brassica and Arabidopsis. BMC Plant Biol (2007) 0.78
Upregulation of jasmonate biosynthesis and jasmonate-responsive genes in rice leaves in response to a bacterial pathogen mimic. Funct Integr Genomics (2014) 0.78
Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling. Front Plant Sci (2016) 0.76
Advanced genomic data mining. PLoS Comput Biol (2008) 0.76
Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Sci Rep (2017) 0.75
Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes. Physiol Mol Biol Plants (2016) 0.75
Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PLoS One (2017) 0.75
Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance. PLoS One (2017) 0.75
The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Res (2017) 0.75
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
The map-based sequence of the rice genome. Nature (2005) 24.17
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
Ensembl 2005. Nucleic Acids Res (2005) 15.13
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics (2004) 5.06
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18
The institute for genomic research Osa1 rice genome annotation database. Plant Physiol (2005) 3.96
Querying and computing with BioCyc databases. Bioinformatics (2005) 3.55
Gramene, a tool for grass genomics. Plant Physiol (2002) 3.14
RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics (1994) 2.60
The Plant Ontology Consortium and plant ontologies. Comp Funct Genomics (2002) 2.50
BarleyBase--an expression profiling database for plant genomics. Nucleic Acids Res (2005) 2.34
Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiol (2004) 2.19
Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genomics (2002) 2.16
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol (2005) 2.06
GrainGenes, the genome database for small-grain crops. Nucleic Acids Res (2003) 1.68
The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiol (2005) 1.52
Entrez: making use of its power. Brief Bioinform (2003) 1.41
It's all GO for plant scientists. Plant Physiol (2005) 1.30
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet (2005) 20.97
The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19
TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics (2007) 14.95
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science (2005) 12.02
Unlocking the secrets of the genome. Nature (2009) 11.80
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
The genetic architecture of maize flowering time. Science (2009) 9.27
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
Mixed linear model approach adapted for genome-wide association studies. Nat Genet (2010) 8.47
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
Genetic properties of the maize nested association mapping population. Science (2009) 7.78
A first-generation haplotype map of maize. Science (2009) 6.82
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res (2002) 6.65
Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science (2010) 6.04
Structure of linkage disequilibrium in plants. Annu Rev Plant Biol (2003) 5.87
Genetic structure and diversity in Oryza sativa L. Genetics (2005) 5.74
Clinical findings in 111 cases of influenza A (H7N9) virus infection. N Engl J Med (2013) 5.38
A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet (2003) 5.34
Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet (2011) 5.16
Complications of colonoscopy in an integrated health care delivery system. Ann Intern Med (2006) 5.10
Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease. J Clin Oncol (2010) 4.94
Genetic design and statistical power of nested association mapping in maize. Genetics (2008) 4.92
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nat Genet (2012) 4.73
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science (2013) 4.71
Proton pump inhibitor and histamine 2 receptor antagonist use and vitamin B12 deficiency. JAMA (2013) 4.67
Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell (2009) 4.59
Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59
Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J (2005) 4.59
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom (2003) 4.56
Impact of endoscopic surveillance on mortality from Barrett's esophagus-associated esophageal adenocarcinomas. Gastroenterology (2013) 4.43
Probable limited person-to-person transmission of highly pathogenic avian influenza A (H5N1) virus in China. Lancet (2008) 4.17
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16
The Ensembl Web site: mechanics of a genome browser. Genome Res (2004) 4.10
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
Abdominal obesity and body mass index as risk factors for Barrett's esophagus. Gastroenterology (2007) 3.94
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
Comparative population genomics of maize domestication and improvement. Nat Genet (2012) 3.78
Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74
Gramene: a resource for comparative grass genomics. Nucleic Acids Res (2002) 3.72
WormBase 2007. Nucleic Acids Res (2007) 3.69
GAPIT: genome association and prediction integrated tool. Bioinformatics (2012) 3.66
A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics (2008) 3.57
Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet (2011) 3.51
Neuronal SIRT1 activation as a novel mechanism underlying the prevention of Alzheimer disease amyloid neuropathology by calorie restriction. J Biol Chem (2006) 3.40
Genetic association mapping and genome organization of maize. Curr Opin Biotechnol (2006) 3.34
Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol (2004) 3.30
A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One (2011) 3.30
A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25
Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci U S A (2002) 3.20
Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature (2011) 3.19
Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One (2009) 3.17
Gramene, a tool for grass genomics. Plant Physiol (2002) 3.14
Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res (2013) 3.08
Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science (2008) 3.06
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A (2008) 2.92
Phosphatase SHP-1 promotes TLR- and RIG-I-activated production of type I interferon by inhibiting the kinase IRAK1. Nat Immunol (2008) 2.89
Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A (2011) 2.89
Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A (2013) 2.88
Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet (2013) 2.83
Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell (2006) 2.82