Published in Nat Genet on April 19, 2009
Landscape of transcription in human cells. Nature (2012) 20.18
CpG islands and the regulation of transcription. Genes Dev (2011) 9.50
The impact of retrotransposons on human genome evolution. Nat Rev Genet (2009) 8.08
The functional role of long non-coding RNA in human carcinomas. Mol Cancer (2011) 6.37
The emergence of lncRNAs in cancer biology. Cancer Discov (2011) 6.32
Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem (2010) 5.99
Adaptive seeds tame genomic sequence comparison. Genome Res (2011) 4.96
Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011) 4.16
KAP1 controls endogenous retroviruses in embryonic stem cells. Nature (2010) 4.02
Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field. Gut (2010) 4.01
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics (2010) 3.84
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38
A comparative encyclopedia of DNA elements in the mouse genome. Nature (2014) 3.22
A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet (2011) 3.14
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell (2011) 3.10
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol (2010) 3.07
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) 3.00
Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet (2012) 2.92
Long non-coding RNAs in nervous system function and disease. Brain Res (2010) 2.53
Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet (2012) 2.52
Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res (2011) 2.51
LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet (2011) 2.42
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30
A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell (2012) 2.29
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell (2013) 2.28
Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet (2010) 2.27
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues. Epigenetics (2012) 2.17
LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? Trends Neurosci (2010) 2.12
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol (2011) 2.11
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease. Mod Pathol (2013) 1.95
Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma. Nat Med (2010) 1.93
Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell (2014) 1.83
Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. MBio (2010) 1.79
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet (2013) 1.70
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc (2012) 1.70
Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res (2011) 1.69
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57
Death by transposition - the enemy within? Bioessays (2013) 1.53
Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res (2010) 1.53
Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors. Mol Cancer (2010) 1.50
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol Biol (2012) 1.50
The Landscape of long noncoding RNA classification. Trends Genet (2015) 1.47
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res (2010) 1.45
Global methylation patterns in idiopathic pulmonary fibrosis. PLoS One (2012) 1.44
Exon-trapping mediated by the human retrotransposon SVA. Genome Res (2009) 1.44
The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet (2013) 1.41
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40
Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays (2011) 1.39
Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics Chromatin (2016) 1.38
Permutation and parametric bootstrap tests for gene-gene and gene-environment interactions. Ann Hum Genet (2011) 1.37
Hypomethylation of long interspersed nuclear element-1 (LINE-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis. Gut (2013) 1.37
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol (2010) 1.33
Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev (2014) 1.32
A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell (2012) 1.29
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol (2013) 1.28
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet (2014) 1.25
The complex transcriptional landscape of the anucleate human platelet. BMC Genomics (2013) 1.23
Inverted Alu dsRNA structures do not affect localization but can alter translation efficiency of human mRNAs independent of RNA editing. Nucleic Acids Res (2012) 1.21
SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol (2010) 1.20
Long-range function of an intergenic retrotransposon. Proc Natl Acad Sci U S A (2010) 1.20
Paraspeckle nuclear bodies--useful uselessness? Cell Mol Life Sci (2012) 1.19
Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms? PLoS Genet (2013) 1.19
Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PLoS One (2011) 1.18
Dark Matter RNA: Existence, Function, and Controversy. Front Genet (2012) 1.18
Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor. Genome Biol (2014) 1.17
Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet (2011) 1.17
A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle (2013) 1.16
Many LINE1 elements contribute to the transcriptome of human somatic cells. Genome Biol (2009) 1.15
Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol (2010) 1.14
Nuclear stress bodies. Cold Spring Harb Perspect Biol (2010) 1.14
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. Nucleic Acids Res (2010) 1.13
RNA dust: where are the genes? DNA Res (2010) 1.13
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol Biol Evol (2013) 1.11
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS Genet (2013) 1.11
Retrotransposons as regulators of gene expression. Science (2016) 1.09
Latent regulatory potential of human-specific repetitive elements. Mol Cell (2012) 1.08
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res (2010) 1.08
Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res (2014) 1.07
The Microprocessor controls the activity of mammalian retrotransposons. Nat Struct Mol Biol (2013) 1.07
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA (2014) 1.06
Promoter architecture of mouse olfactory receptor genes. Genome Res (2011) 1.06
Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals. Microb Ecol (2013) 1.06
Mobile elements in the human genome: implications for disease. Genome Med (2012) 1.02
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PLoS Comput Biol (2012) 1.02
SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res (2012) 1.01
Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics (2014) 1.01
Is sequencing enlightenment ending the dark age of the transcriptome? Nat Methods (2009) 1.01
The role of transposable elements in health and diseases of the central nervous system. J Neurosci (2013) 1.01
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol (2013) 1.00
Chromatin structure and transposable elements in organismal aging. Front Genet (2013) 1.00
Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res (2011) 0.99
Untangling the web: the diverse functions of the PIWI/piRNA pathway. Mol Reprod Dev (2013) 0.98
Functional transcriptomics in the post-ENCODE era. Genome Res (2013) 0.98
A repetitive elements perspective in Polycomb epigenetics. Front Genet (2012) 0.97
Endogenous retroviruses and the development of cancer. J Immunol (2014) 0.97
L1 retrotransposons, cancer stem cells and oncogenesis. FEBS J (2013) 0.97
The human genome browser at UCSC. Genome Res (2002) 168.23
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Open source clustering software. Bioinformatics (2004) 23.17
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Antisense transcription in the mammalian transcriptome. Science (2005) 15.69
Alu repeats and human genomic diversity. Nat Rev Genet (2002) 12.40
Mobile elements: drivers of genome evolution. Science (2004) 11.78
Controlling elements and the gene. Cold Spring Harb Symp Quant Biol (1956) 11.42
Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature (2008) 10.71
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature (2008) 10.11
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature (2009) 6.88
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature (2007) 5.57
Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature (2004) 5.15
L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol (2006) 4.80
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
A role for TFIIIC transcription factor complex in genome organization. Cell (2006) 4.03
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell (2004) 3.85
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res (2000) 3.78
Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol Cell Biol (1990) 3.58
Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev (2005) 3.50
Alu element-mediated gene silencing. EMBO J (2008) 3.22
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nat Genet (2001) 3.05
Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol (2001) 2.88
Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science (2007) 2.70
The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J (2006) 2.55
Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics (2002) 2.49
RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet (2006) 2.22
Progress in understanding the biology of the human mutagen LINE-1. Hum Mutat (2007) 2.17
LINE-1 retrotransposition in human embryonic stem cells. Hum Mol Genet (2007) 2.13
L1 retrotransposition can occur early in human embryonic development. Hum Mol Genet (2007) 2.04
Transcriptional interference: an unexpected layer of complexity in gene regulation. J Cell Sci (2007) 2.02
Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proc Natl Acad Sci U S A (2005) 1.88
Evolutionary impact of human Alu repetitive elements. Curr Opin Genet Dev (2004) 1.68
Current topics in genome evolution: molecular mechanisms of new gene formation. Cell Mol Life Sci (2007) 1.62
RNA at the steering wheel. Genome Biol (2006) 1.57
Useful 'junk': Alu RNAs in the human transcriptome. Cell Mol Life Sci (2007) 1.50
RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. Genome Res (2000) 1.50
L1 antisense promoter drives tissue-specific transcription of human genes. J Biomed Biotechnol (2006) 1.49
Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat Genet (2001) 1.35
Human cis natural antisense transcripts initiated by transposable elements. Trends Genet (2008) 1.35
High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques (2009) 1.16
Long L1 insertions in human gene introns specifically reduce the content of corresponding primary transcripts. Genetica (2006) 1.13
Inducible and cell type-specific expression of VL30 U3 subgroups correlate with their enhancer design. J Virol (1994) 0.99
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
Signatures of mutational processes in human cancer. Nature (2013) 21.63
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol (2003) 12.34
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature (2012) 8.31
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res (2002) 6.61
HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA. Science (2009) 6.59
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res (2008) 6.43
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature (2011) 6.21
Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity (2012) 6.18
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02