Published in Nature on December 14, 2000
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
MicroRNAs in plants. Genes Dev (2002) 20.12
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol (2004) 19.29
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol (2003) 13.32
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Endogenous and silencing-associated small RNAs in plants. Plant Cell (2002) 10.07
The Atlas genome assembly system. Genome Res (2004) 9.78
The tomato genome sequence provides insights into fleshy fruit evolution. Nature (2012) 9.47
Abscisic acid signaling in seeds and seedlings. Plant Cell (2002) 9.02
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res (2003) 8.39
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell (2003) 7.66
AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol (2003) 7.59
A high-throughput Arabidopsis reverse genetics system. Plant Cell (2002) 7.58
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell (2004) 7.11
Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell (2006) 7.06
Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci U S A (2001) 7.01
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res (2005) 6.98
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell (2004) 6.81
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66
Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet (2011) 6.59
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell (2004) 6.52
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
A millennial myosin census. Mol Biol Cell (2001) 6.13
Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res (2003) 6.04
Na+ tolerance and Na+ transport in higher plants. Ann Bot (2003) 5.83
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res (2004) 5.82
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis. EMBO J (2003) 5.79
Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol (2006) 5.74
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res (2003) 5.73
Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics (2011) 5.35
Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res (2009) 5.24
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science (2010) 5.19
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res (2002) 5.15
Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature (2011) 5.13
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol (2002) 5.09
The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A (2002) 5.00
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol (2011) 4.98
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol (2004) 4.94
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Genome structure of the legume, Lotus japonicus. DNA Res (2008) 4.93
Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics (2008) 4.62
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell (2004) 4.59
Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev (2005) 4.50
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics (2002) 4.49
Human diallelic insertion/deletion polymorphisms. Am J Hum Genet (2002) 4.44
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res (2004) 4.43
Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell (2005) 4.41
Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell (2001) 4.38
Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell (2001) 4.35
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res (2004) 4.31
Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29
Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics (2005) 4.28
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet (2013) 4.20
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One (2012) 4.18
Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res (2001) 4.17
ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol (2003) 4.15
RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell (2007) 4.13
The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A (2009) 4.11
The 1001 genomes project for Arabidopsis thaliana. Genome Biol (2009) 4.10
Plant circadian rhythms. Plant Cell (2006) 4.06
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res (2002) 4.05
Sugar sensing and signaling in plants. Plant Cell (2002) 4.05
Assessing the gene space in draft genomes. Nucleic Acids Res (2008) 4.03
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02
Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell (2005) 4.01
Gibberellin biosynthesis and response during Arabidopsis seed germination. Plant Cell (2003) 3.96
The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol (2003) 3.96
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res (2002) 3.93
Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci U S A (2001) 3.91
Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell (2002) 3.91
Mechanisms of recent genome size variation in flowering plants. Ann Bot (2005) 3.86
The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A (2002) 3.82
Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell (2003) 3.80
When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol (2004) 3.80
Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics (2005) 3.78
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
Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics (2002) 3.67
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol (2015) 3.66