Published in Genome Res on January 08, 2007
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PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol (2007) 1.74
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell (2008) 1.55
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Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 1.46
Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC Plant Biol (2011) 1.44
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A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A (2007) 1.23
The Rice Oligonucleotide Array Database: an atlas of rice gene expression. Rice (N Y) (2012) 1.20
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PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. BMC Genomics (2007) 1.10
Ectopic overexpression of the transcription factor OsGLK1 induces chloroplast development in non-green rice cells. Plant Cell Physiol (2009) 1.07
Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis. BMC Genomics (2010) 1.05
Tolerance to various environmental stresses conferred by the salt-responsive rice gene ONAC063 in transgenic Arabidopsis. Planta (2009) 1.03
RiceFREND: a platform for retrieving coexpressed gene networks in rice. Nucleic Acids Res (2012) 1.03
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Transcriptional profiling of the PDR gene family in rice roots in response to plant growth regulators, redox perturbations and weak organic acid stresses. Planta (2008) 0.96
Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interaction. BMC Plant Biol (2012) 0.95
DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes. Plant Physiol (2011) 0.95
Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. Plant J (2014) 0.95
Outlook on Thailand's genomics and computational biology research and development. PLoS Comput Biol (2008) 0.94
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol (2011) 0.93
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics (2010) 0.93
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Comparative molecular biological analysis of membrane transport genes in organisms. Plant Mol Biol (2008) 0.92
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Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol Plant (2013) 0.91
The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis. PLoS One (2012) 0.91
Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res (2013) 0.89
Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. Plant J (2011) 0.89
Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics (2014) 0.89
OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol (2011) 0.88
The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell (2017) 0.86
Community gene annotation in practice. Database (Oxford) (2012) 0.86
Genes controlling root development in rice. Rice (N Y) (2014) 0.84
Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice. Mol Genet Genomics (2010) 0.84
Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants. PLoS Genet (2010) 0.84
UniVIO: a multiple omics database with hormonome and transcriptome data from rice. Plant Cell Physiol (2013) 0.83
Natural and artificial mutants as valuable resources for functional genomics and molecular breeding. Int J Biol Sci (2010) 0.83
Manually curated database of rice proteins. Nucleic Acids Res (2013) 0.82
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. BMC Genomics (2007) 0.82
Identification and characterization of a gibberellin-regulated protein, which is ASR5, in the basal region of rice leaf sheaths. Mol Genet Genomics (2008) 0.81
Efficient plant gene identification based on interspecies mapping of full-length cDNAs. DNA Res (2010) 0.81
OryzaGenome: Genome Diversity Database of Wild Oryza Species. Plant Cell Physiol (2015) 0.81
Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice. Mol Genet Genomics (2009) 0.80
Characterization of chromosome ends on the basis of the structure of TrsA subtelomeric repeats in rice (Oryza sativa L.). Mol Genet Genomics (2008) 0.79
Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Mol Breed (2013) 0.79
Cell wall proteomics of crops. Front Plant Sci (2013) 0.79
Orymold: ontology based gene expression data integration and analysis tool applied to rice. BMC Bioinformatics (2009) 0.79
Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi. Cell Rep (2016) 0.78
Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome. PLoS One (2013) 0.78
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. Plant Cell Physiol (2014) 0.77
Development in rice genome research based on accurate genome sequence. Int J Plant Genomics (2008) 0.75
Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. Rice (N Y) (2016) 0.75
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InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22
The map-based sequence of the rice genome. Nature (2005) 24.17
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
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Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
The genome sequence and structure of rice chromosome 1. Nature (2002) 4.99
Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol (2004) 4.08
MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell (2005) 3.88
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Cloning and characterization of microRNAs from rice. Plant Cell (2005) 3.72
Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell (2003) 3.45
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res (2006) 2.90
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Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell (2002) 2.39
Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol (2004) 2.24
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
Rice mutant resources for gene discovery. Plant Mol Biol (2004) 1.99
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res (2004) 1.97
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Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol (2001) 1.76
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Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol (2003) 1.57
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Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res (2004) 1.39
Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiol (2005) 1.27
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The new genes of rice: a closer look. Trends Plant Sci (2004) 1.17
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Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. Nucleic Acids Res (2004) 1.14
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Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol (2005) 1.09
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Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2005) 37.39
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res (2008) 26.04
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2005) 22.62
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2006) 20.92
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol (2002) 15.13
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (2009) 15.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res (2011) 14.04
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
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A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
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The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res (2008) 10.64
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
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The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res (2008) 10.21
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De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res (2009) 9.42
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Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet (2010) 8.75
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol (2006) 8.44
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Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet (2005) 8.23
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
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Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Mapping human genetic diversity in Asia. Science (2009) 7.40
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2005) 7.18
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17