Published in Genome Res on August 18, 2005
The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res (2006) 8.26
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res (2005) 2.23
Uneven chromosome contraction and expansion in the maize genome. Genome Res (2006) 1.96
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell (2008) 1.55
Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics (2008) 1.30
Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell (2006) 1.27
Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol (2007) 1.19
Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics (2007) 1.17
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol (2008) 1.14
Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics (2007) 1.06
Synteny of Prunus and other model plant species. BMC Genomics (2009) 1.02
Identification of a major QTL controlling the content of B-type starch granules in Aegilops. J Exp Bot (2011) 0.95
Molecular and phylogenetic analysis of MADS-box genes of MIKC type and chromosome location of SEP-like genes in wheat (Triticum aestivum L.). Mol Genet Genomics (2007) 0.94
Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res (2007) 0.90
Overexpression of CuZnSOD from Arachis hypogaea alleviates salinity and drought stress in tobacco. Plant Cell Rep (2015) 0.85
Insular organization of gene space in grass genomes. PLoS One (2013) 0.85
Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genomics (2007) 0.85
Genome-wide analysis of conservation and divergence of microsatellites in rice. Mol Genet Genomics (2009) 0.84
Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram. Ann Bot (2011) 0.80
Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). J Biomed Biotechnol (2010) 0.80
Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics. Mol Biol Evol (2009) 0.77
Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals. Front Plant Sci (2014) 0.75
Rice yellow mottle virus stress responsive genes from susceptible and tolerant rice genotypes. BMC Plant Biol (2008) 0.75
Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture. Trop Life Sci Res (2016) 0.75
Two Trichome Birefringence-like proteins Mediate Xylan Acetylation, Which Is Essential for Leaf Blight Resistance in Rice. Plant Physiol (2016) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
Ab initio gene finding in Drosophila genomic DNA. Genome Res (2000) 19.23
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res (2001) 8.44
Cereal genome evolution. Grasses, line up and form a circle. Curr Biol (1995) 8.33
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics (1998) 6.82
Comparative genetics in the grasses. Proc Natl Acad Sci U S A (1998) 6.35
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet (2002) 5.98
Contigs built with fingerprints, markers, and FPC V4.7. Genome Res (2000) 5.56
Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35
The genome sequence and structure of rice chromosome 1. Nature (2002) 4.99
Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet (1993) 4.70
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res (2004) 4.43
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res (2004) 4.31
In-depth view of structure, activity, and evolution of rice chromosome 10. Science (2003) 3.80
Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol (2002) 3.80
Comparative DNA sequence analysis of wheat and rice genomes. Genome Res (2003) 3.63
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
Enrichment of gene-coding sequences in maize by genome filtration. Science (2003) 3.41
A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics (2004) 3.37
An integrated physical and genetic map of the rice genome. Plant Cell (2002) 3.07
Annotation of the Arabidopsis genome. Plant Physiol (2003) 3.06
High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics (2003) 3.02
Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci U S A (1992) 2.81
Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell (2002) 2.40
A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell (2002) 2.39
High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci U S A (1999) 2.26
Access to the maize genome: an integrated physical and genetic map. Plant Physiol (2002) 2.04
High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J (2004) 1.93
The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol (2005) 1.84
Toward a cytological characterization of the rice genome. Genome Res (2001) 1.83
Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J (2004) 1.31
Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics (2002) 1.28
Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis. Plant Mol Biol (2001) 1.10
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A (2004) 33.85
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Grading quality of evidence and strength of recommendations. BMJ (2004) 26.08
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24
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 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
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Prepublication data sharing. Nature (2009) 12.24
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Selling sickness: the pharmaceutical industry and disease mongering. BMJ (2002) 10.98
Big data: The future of biocuration. Nature (2008) 10.81
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
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
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res (2006) 8.89
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res (2006) 8.26
Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A (2009) 8.25
Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet (2005) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods (2009) 8.15
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol (2004) 7.95
Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
Minimus: a fast, lightweight genome assembler. BMC Bioinformatics (2007) 7.65