Published in Gene on July 04, 2005
Transcription factor binding and modified histones in human bidirectional promoters. Genome Res (2007) 2.40
Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics (2007) 1.79
The ets-related transcription factor GABP directs bidirectional transcription. PLoS Genet (2007) 1.67
Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res (2007) 1.36
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet (2014) 1.25
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res (2010) 1.10
The dual lives of bidirectional promoters. Biochim Biophys Acta (2012) 0.99
Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription. Nucleic Acids Res (2010) 0.97
The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species. Genome Res (2012) 0.95
Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol (2008) 0.92
Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci (2014) 0.91
Farm animal genomics and informatics: an update. Nucleic Acids Res (2005) 0.90
Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes. BMC Genomics (2009) 0.85
Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system. BMC Genomics (2007) 0.85
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? BMC Syst Biol (2012) 0.84
Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicing. BMC Mol Biol (2009) 0.84
Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair. BMC Mol Biol (2009) 0.82
Orientation, distance, regulation and function of neighbouring genes. Hum Genomics (2009) 0.82
Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression. J Mol Biol (2014) 0.79
Beyond the histone tale: HP1α deregulation in breast cancer epigenetics. Cancer Biol Ther (2015) 0.77
Regulatory dissection of the CBX5 and hnRNPA1 bi-directional promoter in human breast cancer cells reveals novel transcript variants differentially associated with HP1α down-regulation in metastatic cells. BMC Cancer (2016) 0.77
Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana. Genetics (2010) 0.76
Overlapping of genes in the human genome. Int J Biomed Sci (2007) 0.75
Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression. PLoS Genet (2016) 0.75
Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. DNA Res (2017) 0.75
Big data: The future of biocuration. Nature (2008) 10.81
Mapping human genetic diversity in Asia. Science (2009) 7.40
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
CIBEX: center for information biology gene expression database. C R Biol (2004) 6.16
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res (2006) 6.02
DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res (2009) 5.89
Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet (2004) 5.49
The genome sequence and structure of rice chromosome 1. Nature (2002) 4.99
MMP9 induction by vascular endothelial growth factor receptor-1 is involved in lung-specific metastasis. Cancer Cell (2002) 4.93
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A (2002) 4.22
The dynamic genome of Hydra. Nature (2010) 4.00
Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses. Virology (2002) 3.79
DDBJ progress report. Nucleic Acids Res (2010) 3.34
DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res (2008) 3.24
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Res (2011) 3.05
Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell (2011) 3.03
Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature (2010) 2.91
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res (2006) 2.90
Glycoproteomic probes for fluorescent imaging of fucosylated glycans in vivo. Proc Natl Acad Sci U S A (2006) 2.70
Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS). DNA Res (2006) 2.51
DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res (2006) 2.50
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol (2013) 2.28
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol (2003) 2.19
The origin and evolution of porcine reproductive and respiratory syndrome viruses. Mol Biol Evol (2005) 2.09
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res (2003) 2.07
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol (2004) 2.07
Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol (2011) 2.04
A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades. Proc Natl Acad Sci U S A (2002) 2.02
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics (2010) 1.96
Rate of evolution in brain-expressed genes in humans and other primates. PLoS Biol (2007) 1.87
FGFR-related gene nou-darake restricts brain tissues to the head region of planarians. Nature (2002) 1.80
Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics (2007) 1.79
Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med (2011) 1.78
Targeted deletion of MMP-2 attenuates early LV rupture and late remodeling after experimental myocardial infarction. Am J Physiol Heart Circ Physiol (2003) 1.74
Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration. Dev Biol (2009) 1.62
The evolutionary position of nematodes. BMC Evol Biol (2002) 1.60
A crucial role for matrix metalloproteinase 2 in osteocytic canalicular formation and bone metabolism. J Biol Chem (2006) 1.52
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res (2007) 1.52
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A (2003) 1.43
MMP-2 and MMP-9 synergize in promoting choroidal neovascularization. FASEB J (2003) 1.42
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res (2008) 1.39
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res (2005) 1.39
Origin and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs. Proc Natl Acad Sci U S A (2003) 1.38
A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva. Dev Dyn (2007) 1.38
Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. Genetics (2006) 1.37
Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Hum Mol Genet (2005) 1.36
Deficiency of gelatinase a suppresses smooth muscle cell invasion and development of experimental intimal hyperplasia. Circulation (2003) 1.35
Contribution of host MMP-2 and MMP-9 to promote tumor vascularization and invasion of malignant keratinocytes. FASEB J (2004) 1.34
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res (2006) 1.34
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res (2007) 1.32
Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One (2012) 1.31
Evolution of complex structures: minicollagens shape the cnidarian nematocyst. Trends Genet (2008) 1.29
SALAD database: a motif-based database of protein annotations for plant comparative genomics. Nucleic Acids Res (2009) 1.29
Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene (2005) 1.27
Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene (2006) 1.26
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
The expression of neural-specific genes reveals the structural and molecular complexity of the planarian central nervous system. Mech Dev (2002) 1.23
High-mobility group box 1 is involved in the initial events of early loss of transplanted islets in mice. J Clin Invest (2010) 1.21
Stroma-derived matrix metalloproteinase (MMP)-2 promotes membrane type 1-MMP-dependent tumor growth in mice. Cancer Res (2007) 1.21
H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Res (2006) 1.20
Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci U S A (2010) 1.20
Large human islets secrete less insulin per islet equivalent than smaller islets in vitro. Islets (2011) 1.20
Mutations in two matrix metalloproteinase genes, MMP-2 and MT1-MMP, are synthetic lethal in mice. Oncogene (2004) 1.19
Independent domestication of Asian rice followed by gene flow from japonica to indica. Mol Biol Evol (2011) 1.19
Evolution of gap junctions: the missing link? Curr Biol (2004) 1.19
Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis. Genetics (2004) 1.19
Improving efficacy of clinical islet transplantation with iodixanol-based islet purification, thymoglobulin induction, and blockage of IL-1β and TNF-α. Cell Transplant (2011) 1.18
Detection of apoptosis during planarian regeneration by the expression of apoptosis-related genes and TUNEL assay. Gene (2004) 1.17
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res (2009) 1.16
Reduced retinal angiogenesis in MMP-2-deficient mice. Invest Ophthalmol Vis Sci (2003) 1.14