Published in Science on May 03, 2002
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
Genome regulation by long noncoding RNAs. Annu Rev Biochem (2012) 11.70
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell (2010) 8.66
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
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The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J (2005) 7.10
Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell (2006) 7.06
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res (2005) 6.08
Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81
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RNA processing and its regulation: global insights into biological networks. Nat Rev Genet (2010) 5.34
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature (2009) 4.96
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
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Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
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Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc Natl Acad Sci U S A (2002) 4.26
The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet (2009) 4.19
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85
ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol (2005) 3.83
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The ENCODE Project at UC Santa Cruz. Nucleic Acids Res (2006) 3.57
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 3.49
Noncoding RNA in development. Mamm Genome (2008) 3.42
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A (2007) 3.35
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res (2004) 3.30
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21
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Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res (2003) 3.03
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res (2003) 2.97
Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2004) 2.94
What would you do if you could sequence everything? Nat Biotechnol (2008) 2.89
Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A (2002) 2.87
Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A (2005) 2.85
RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res (2005) 2.84
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res (2007) 2.72
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev (2005) 2.64
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet (2013) 2.46
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res (2002) 2.40
An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res (2005) 2.39
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res (2007) 2.39
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci U S A (2005) 2.30
Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev (2009) 2.30
The function of non-coding RNAs in genomic imprinting. Development (2009) 2.21
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol (2004) 2.21
A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A (2009) 2.18
Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res (2004) 2.17
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Classification of human chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes. Am J Hum Genet (2007) 2.06
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol (2007) 2.03
SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA (2011) 2.03
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res (2008) 2.01
Characterization of brain neurons that express enzymes mediating neurosteroid biosynthesis. Proc Natl Acad Sci U S A (2006) 2.01
MicroRNA and 3T3-L1 pre-adipocyte differentiation. RNA (2006) 2.00
Noncoding RNA and Polycomb recruitment. RNA (2013) 2.00
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res (2006) 1.95
Activation of receptor activator of NF-kappaB ligand gene expression by 1,25-dihydroxyvitamin D3 is mediated through multiple long-range enhancers. Mol Cell Biol (2006) 1.92
Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res (2002) 1.89
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arterioscler Thromb Vasc Biol (2014) 1.87
Brain expressed microRNAs implicated in schizophrenia etiology. PLoS One (2007) 1.85
Identification of novel functional TBP-binding sites and general factor repertoires. EMBO J (2007) 1.77
Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic Acids Res (2004) 1.75
The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J (2006) 1.73
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res (2005) 1.71
DNA-methyltransferase 1 mRNA is selectively overexpressed in telencephalic GABAergic interneurons of schizophrenia brains. Proc Natl Acad Sci U S A (2003) 1.71
Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Res (2006) 1.68
Organismal complexity, protein complexity, and gene duplicability. Proc Natl Acad Sci U S A (2003) 1.67
Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol (2004) 1.67
Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol (2003) 1.66
Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci U S A (2006) 1.66
Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci U S A (2005) 1.64
A facilitated tracking and transcription mechanism of long-range enhancer function. Nucleic Acids Res (2007) 1.60
The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol (2004) 1.56
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem Sci (2013) 1.55
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85
Landscape of transcription in human cells. Nature (2012) 20.18
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
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
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
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med (2006) 14.33
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Large-scale genotyping of complex DNA. Nat Biotechnol (2003) 10.00
Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59
Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods (2004) 9.52
Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Genetic variation in an individual human exome. PLoS Genet (2008) 6.68
Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet (2006) 6.20
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res (2005) 6.08
Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A (2002) 4.45
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
The dynamic genome of Hydra. Nature (2010) 4.00
Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci U S A (2003) 3.31
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol (2007) 2.90
Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A (2005) 2.85
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (2010) 2.76
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A (2003) 2.64
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res (2008) 2.62
TUF love for "junk" DNA. Cell (2006) 2.59
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A (2009) 2.57
The transcriptional diversity of 25 Drosophila cell lines. Genome Res (2010) 2.47
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res (2005) 2.39
Evaluation of non-formalin tissue fixation for molecular profiling studies. Am J Pathol (2002) 2.38
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas. Proc Natl Acad Sci U S A (2005) 2.38
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 2.18
MyD88 primes macrophages for full-scale activation by interferon-gamma yet mediates few responses to Mycobacterium tuberculosis. J Exp Med (2003) 2.10
Multiple testing methods for ChIP-Chip high density oligonucleotide array data. J Comput Biol (2006) 2.08
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet (2011) 2.07
Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data. Breast Cancer Res (2006) 2.03
Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion. Cancer Res (2010) 2.01
Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Dev Dyn (2002) 2.01
Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc Natl Acad Sci U S A (2011) 1.89
Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A (2011) 1.89
KRAS mutation is associated with lung metastasis in patients with curatively resected colorectal cancer. Clin Cancer Res (2011) 1.87
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci U S A (2003) 1.79
The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer (2005) 1.70
Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66
Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res (2004) 1.63
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet (2010) 1.53
Ancient noncoding elements conserved in the human genome. Science (2006) 1.53
Cancer Molecular Analysis Project: weaving a rich cancer research tapestry. Cancer Cell (2002) 1.53
A preliminary transcriptome map of non-small cell lung cancer. Cancer Res (2002) 1.42
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40
SMAD2, SMAD3 and SMAD4 mutations in colorectal cancer. Cancer Res (2012) 1.39