Published in PLoS One on March 14, 2007
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell (2008) 1.85
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol (2008) 1.62
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell (2009) 1.27
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol (2011) 1.26
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol (2009) 1.19
Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol (2009) 1.18
Green transcription factors: a chlamydomonas overview. Genetics (2008) 1.13
Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. Plant Physiol (2008) 0.98
Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress. PLoS One (2010) 0.96
A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol (2007) 0.96
Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiol (2012) 0.88
Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell (2011) 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
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping. BMC Res Notes (2009) 0.84
Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum. BMC Genomics (2016) 0.82
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol (2008) 0.82
RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening. J Exp Bot (2015) 0.80
Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. BMC Plant Biol (2015) 0.80
Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray. PLoS One (2011) 0.80
A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data. Bioinformatics (2010) 0.80
A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly. Plant Methods (2016) 0.75
Upregulation of LINC-AP2 is negatively correlated with AP2 gene expression with Turnip crinkle virus infection in Arabidopsis thaliana. Plant Cell Rep (2016) 0.75
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
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol (2001) 14.57
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Experimental annotation of the human genome using microarray technology. Nature (2001) 10.39
Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol (1999) 9.35
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol (2003) 8.54
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet (1999) 6.77
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36
A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (2004) 5.38
Pack-MULE transposable elements mediate gene evolution in plants. Nature (2004) 5.13
The genome sequence and structure of rice chromosome 1. Nature (2002) 4.99
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res (2003) 4.64
The role of RNA interference in heterochromatic silencing. Nature (2004) 4.56
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet (2005) 4.56
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
The institute for genomic research Osa1 rice genome annotation database. Plant Physiol (2005) 3.96
Applications of DNA tiling arrays for whole-genome analysis. Genomics (2005) 3.94
In-depth view of structure, activity, and evolution of rice chromosome 10. Science (2003) 3.80
Antisense transcripts in the human genome. Trends Genet (2002) 3.33
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res (2006) 2.95
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol (2005) 2.80
Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem (1991) 1.98
Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res (2005) 1.77
Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69
MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell (2006) 1.54
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res (2005) 1.54
Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol (2006) 1.50
Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE) Plant J (1999) 1.49
Transposable element annotation of the rice genome. Bioinformatics (2004) 1.41
NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics (2006) 1.30
The new genes of rice: a closer look. Trends Plant Sci (2004) 1.17
Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene. J Biol Chem (1995) 1.12
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol (2005) 1.09
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics (2005) 0.95
SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods (2006) 0.91
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Mechanisms and functional implications of adult neurogenesis. Cell (2008) 14.50
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature (2005) 6.95
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development (2004) 5.47
A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (2004) 5.38
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Functional profiling of a human cytomegalovirus genome. Proc Natl Acad Sci U S A (2003) 5.21
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res (2002) 4.92
Light-regulated transcriptional networks in higher plants. Nat Rev Genet (2007) 4.82
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature (2008) 4.71
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell (2007) 4.13
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med (2005) 3.26
The COP9 signalosome. Annu Rev Cell Dev Biol (2003) 3.25
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
COP1 - from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol (2005) 3.01
A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev (2007) 3.01
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol (2012) 2.97
The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev (2003) 2.97
Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res (2003) 2.90
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Resolving new memories: a critical look at the dentate gyrus, adult neurogenesis, and pattern separation. Neuron (2011) 2.84
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res (2011) 2.82
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
One-year treatment with exenatide improves beta-cell function, compared with insulin glargine, in metformin-treated type 2 diabetic patients: a randomized, controlled trial. Diabetes Care (2009) 2.75