Published in Nucleic Acids Res on February 01, 2013
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
Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics (2014) 1.09
Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential. BMC Genomics (2015) 0.91
Characterization of human pseudogene-derived non-coding RNAs for functional potential. PLoS One (2014) 0.87
Pseudogenes in Human Cancer. Front Med (Lausanne) (2015) 0.81
Not so pseudo anymore: pseudogenes as therapeutic targets. Pharmacogenomics (2013) 0.80
Non-coding landscapes of colorectal cancer. World J Gastroenterol (2015) 0.80
VEGFR-1 Pseudogene Expression and Regulatory Function in Human Colorectal Cancer Cells. Mol Cancer Res (2015) 0.79
Differentially-Expressed Pseudogenes in HIV-1 Infection. Viruses (2015) 0.76
Post-transcriptional modulation of protein phosphatase PPP2CA and tumor suppressor PTEN by endogenous siRNA cleaved from hairpin within PTEN mRNA 3'UTR in human liver cells. Acta Pharmacol Sin (2016) 0.76
An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation. Oncotarget (2016) 0.75
Pseudogene BMI1P1 expression as a novel predictor for acute myeloid leukemia development and prognosis. Oncotarget (2016) 0.75
Expression of evolutionarily novel genes in tumors. Infect Agent Cancer (2016) 0.75
Protein-Coding Genes' Retrocopies and Their Functions. Viruses (2017) 0.75
The pseudogene derived long noncoding RNA DUXAP8 promotes gastric cancer cell proliferation and migration via epigenetically silencing PLEKHO1 expression. Oncotarget (2016) 0.75
MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
Human MicroRNA targets. PLoS Biol (2004) 34.51
The impact of microRNAs on protein output. Nature (2008) 32.39
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell (2007) 18.35
Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev (2003) 17.64
A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature (2010) 13.82
Divergent transcription from active promoters. Science (2008) 11.03
Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature (2008) 10.71
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature (2008) 10.11
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (2008) 8.62
An endogenous small interfering RNA pathway in Drosophila. Nature (2008) 7.88
RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res (2006) 7.39
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods (2006) 7.00
Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature (2008) 5.59
Strategies for silencing human disease using RNA interference. Nat Rev Genet (2007) 5.19
The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature (2008) 5.05
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res (2006) 4.80
A genome-wide survey of human pseudogenes. Genome Res (2003) 4.34
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol (2006) 4.30
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A (2006) 4.03
Vertebrate pseudogenes. FEBS Lett (2000) 3.93
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature (2003) 3.90
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res (2007) 3.05
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
miRNAs and apoptosis: RNAs to die for. Oncogene (2006) 2.80
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci (1999) 2.49
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res (2006) 2.27
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res (2008) 2.10
Mitotic regulation by NIMA-related kinases. Cell Div (2007) 1.88
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol (2009) 1.71
NONCODE v2.0: decoding the non-coding. Nucleic Acids Res (2007) 1.69
5-(N-ethyl-N-isopropyl)-amiloride enhances SMN2 exon 7 inclusion and protein expression in spinal muscular atrophy cells. Ann Neurol (2008) 1.60
A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet (2008) 1.57
Nek8, a NIMA family kinase member, is overexpressed in primary human breast tumors. Gene (2004) 1.52
A novel mitochondrial matrix serine/threonine protein phosphatase regulates the mitochondria permeability transition pore and is essential for cellular survival and development. Genes Dev (2007) 1.49
Identification of a human type II receptor for bone morphogenetic protein-4 that forms differential heteromeric complexes with bone morphogenetic protein type I receptors. J Biol Chem (1995) 1.47
The long and short of inverted repeat genes in animals: microRNAs, mirtrons and hairpin RNAs. Cell Cycle (2008) 1.38
Interaction of rhodamine 123 with living cells studied by flow cytometry. Cancer Res (1982) 1.32
Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics (2009) 1.26
What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH. PLoS One (2011) 1.20
Quantitative assay by flow cytometry of the mitochondrial membrane potential in intact cells. Biochim Biophys Acta (1998) 1.19
A novel nuclear interactor of ARF and MDM2 (NIAM) that maintains chromosomal stability. J Biol Chem (2006) 1.16
The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc Natl Acad Sci U S A (2006) 1.15
Increased rhodamine 123 uptake by carcinoma cells. Cancer Res (1985) 1.04
MicroRNA fate upon targeting with anti-miRNA oligonucleotides as revealed by an improved Northern-blot-based method for miRNA detection. RNA (2011) 1.02
Identification of novel ARF binding proteins by two-hybrid screening. Cell Cycle (2006) 1.02
Evolution of nitric oxide synthase regulatory genes by DNA inversion. Mol Biol Evol (2002) 0.97
Epigenetic alteration of the SOCS1 gene in chronic myeloid leukaemia. Br J Haematol (2003) 0.96
Subcellular and functional proteomic analysis of the cellular responses induced by Helicobacter pylori. Mol Cell Proteomics (2006) 0.86
Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures. BMC Genomics (2007) 0.83
miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res (2010) 5.72
MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. Hepatology (2009) 4.36
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J Clin Invest (2012) 3.46
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res (2007) 3.05
Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science (2013) 2.99
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res (2007) 2.69
Modulation of KCNQ1 alternative splicing regulates cardiac IKs and action potential repolarization. Heart Rhythm (2013) 2.61
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res (2006) 2.43
Deregulated expression of the PER1, PER2 and PER3 genes in breast cancers. Carcinogenesis (2005) 2.31
Flow-Dependent Regulation of Kruppel-Like Factor 2 Is Mediated by MicroRNA-92a. Circulation (2011) 2.29
dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res (2006) 2.28
Adjuvant immunotherapy with whole-cell lysate dendritic cells vaccine for glioblastoma multiforme: a phase II clinical trial. World Neurosurg (2011) 2.24
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics (2009) 2.22
TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. Cell Rep (2012) 2.20
Determinants of bilateral audiometric notches in noise-induced hearing loss. Laryngoscope (2013) 2.04
Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(∗)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. Mol Cell (2011) 2.01
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol (2011) 1.95
miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4. Cancer Res (2012) 1.77
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
Deregulated expression of sprouty2 and microRNA-21 in human colon cancer: Correlation with the clinical stage of the disease. Cancer Biol Ther (2011) 1.72
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res (2012) 1.71
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics (2008) 1.68
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res (2011) 1.64
5-(N-ethyl-N-isopropyl)-amiloride enhances SMN2 exon 7 inclusion and protein expression in spinal muscular atrophy cells. Ann Neurol (2008) 1.60
DNA methylation of the Trip10 promoter accelerates mesenchymal stem cell lineage determination. Biochem Biophys Res Commun (2010) 1.52
Caffeic Acid phenethyl ester inhibits oral cancer cell metastasis by regulating matrix metalloproteinase-2 and the mitogen-activated protein kinase pathway. Evid Based Complement Alternat Med (2012) 1.47
microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng (2010) 1.44
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics (2013) 1.32
RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res (2008) 1.31
miRTar: an integrated system for identifying miRNA-target interactions in human. BMC Bioinformatics (2011) 1.30
Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. J Clin Invest (2013) 1.30
Disturbance of circadian gene expression in hepatocellular carcinoma. Mol Carcinog (2008) 1.27
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res (2008) 1.26
Sterol regulatory element binding protein 2 activation of NLRP3 inflammasome in endothelium mediates hemodynamic-induced atherosclerosis susceptibility. Circulation (2013) 1.25
Abnormal expression of period 1 (PER1) in endometrial carcinoma. J Pathol (2005) 1.25
Human papillomavirus 16/18 E6 oncoprotein is expressed in lung cancer and related with p53 inactivation. Cancer Res (2007) 1.23
Let-7b is a novel regulator of hepatitis C virus replication. Cell Mol Life Sci (2012) 1.22
ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res (2006) 1.21
Toll-like receptor 4 gene C119A but not Asp299Gly polymorphism is associated with ischemic stroke among ethnic Chinese in Taiwan. Atherosclerosis (2005) 1.21
CASP3 gene single-nucleotide polymorphism (rs72689236) and Kawasaki disease in Taiwanese children. J Hum Genet (2010) 1.19
Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem (2009) 1.16
Incorporating support vector machine for identifying protein tyrosine sulfation sites. J Comput Chem (2009) 1.16
Targeted methylation of two tumor suppressor genes is sufficient to transform mesenchymal stem cells into cancer stem/initiating cells. Cancer Res (2011) 1.15
The F-box protein Fbxo7 interacts with human inhibitor of apoptosis protein cIAP1 and promotes cIAP1 ubiquitination. Biochem Biophys Res Commun (2006) 1.14
Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res (2013) 1.14
A systematic review of microRNA expression profiling studies in human gastric cancer. Cancer Med (2014) 1.14
Association of O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation with p53 mutation occurrence in non-small cell lung cancer with different histology, gender, and smoking status. Ann Surg Oncol (2008) 1.13
Mutational, epigenetic and expressional analyses of caveolin-1 gene in breast cancers. Int J Mol Med (2004) 1.13
Genotypic and phenotypic characterization of a putative tumor susceptibility gene, GNMT, in liver cancer. Cancer Res (2003) 1.12
A polymorphic -844T/C in FasL promoter predicts survival and relapse in non-small cell lung cancer. Clin Cancer Res (2011) 1.09
JunB gene expression is inactivated by methylation in chronic myeloid leukemia. Blood (2002) 1.07
dbSNO: a database of cysteine S-nitrosylation. Bioinformatics (2012) 1.07
4beta-Hydroxywithanolide E from Physalis peruviana (golden berry) inhibits growth of human lung cancer cells through DNA damage, apoptosis and G2/M arrest. BMC Cancer (2010) 1.06
SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS One (2011) 1.04
Association of high levels of Jagged-1 and Notch-1 expression with poor prognosis in head and neck cancer. Ann Surg Oncol (2010) 1.04
Expression of hepcidin and other iron-regulatory genes in human hepatocellular carcinoma and its clinical implications. J Cancer Res Clin Oncol (2009) 1.03
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res (2010) 1.03
High-resolution melting: applications in genetic disorders. Clin Chim Acta (2012) 1.03
Antiproliferative effects of goniothalamin on Ca9-22 oral cancer cells through apoptosis, DNA damage and ROS induction. Mutat Res (2012) 1.03
Fast simultaneous detection of K-RAS mutations in colorectal cancer. BMC Cancer (2009) 1.02
Serine protease inhibitor (SERPIN) B1 promotes oral cancer cell motility and is over-expressed in invasive oral squamous cell carcinoma. Oral Oncol (2009) 1.02
Computational identification of riboswitches based on RNA conserved functional sequences and conformations. RNA (2009) 1.02
A phase I/II clinical trial investigating the adverse and therapeutic effects of a postoperative autologous dendritic cell tumor vaccine in patients with malignant glioma. J Clin Neurosci (2011) 1.02
Association of RS2200733 but not RS10033464 on 4q25 with atrial fibrillation based on the recessive model in a Taiwanese population. Cardiology (2010) 1.01
Downregulation of circadian clock genes in chronic myeloid leukemia: alternative methylation pattern of hPER3. Cancer Sci (2006) 1.01
Amiloride modulates alternative splicing in leukemic cells and resensitizes Bcr-AblT315I mutant cells to imatinib. Cancer Res (2011) 1.01
Detecting Epstein-Barr virus DNA from peripheral blood mononuclear cells in adult patients with systemic lupus erythematosus in Taiwan. Med Microbiol Immunol (2004) 1.01
MicroRNA-21-mediated regulation of Sprouty2 protein expression enhances the cytotoxic effect of 5-fluorouracil and metformin in colon cancer cells. Int J Mol Med (2012) 1.01
Induction of apoptosis by 11-dehydrosinulariolide via mitochondrial dysregulation and ER stress pathways in human melanoma cells. Mar Drugs (2012) 1.00
Disturbance of circadian gene expression in breast cancer. Virchows Arch (2009) 0.99
Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells. PLoS One (2011) 0.99
Fenofibrate exhibits a high potential to suppress the formation of squamous cell carcinoma in an oral-specific 4-nitroquinoline 1-oxide/arecoline mouse model. Biochim Biophys Acta (2010) 0.98
Orai1/CRACM1 overexpression suppresses cell proliferation via attenuation of the store-operated calcium influx-mediated signalling pathway in A549 lung cancer cells. Biochim Biophys Acta (2011) 0.98
Gender difference in the prognostic role of interleukin 6 in oral squamous cell carcinoma. PLoS One (2012) 0.97
Subamolide E from Cinnamomum subavenium induces sub-G1 cell-cycle arrest and caspase-dependent apoptosis and reduces the migration ability of human melanoma cells. J Agric Food Chem (2011) 0.97
Effect of TIMP-1 and MMP in pterygium invasion. Invest Ophthalmol Vis Sci (2010) 0.97
Human papilloma virus 16 E6 oncoprotein associated with p53 inactivation in colorectal cancer. World J Gastroenterol (2012) 0.97
Obtusilactone A and (-)-sesamin induce apoptosis in human lung cancer cells by inhibiting mitochondrial Lon protease and activating DNA damage checkpoints. Cancer Sci (2010) 0.97
Decreased expression of thrombomodulin is correlated with tumor cell invasiveness and poor prognosis in nonsmall cell lung cancer. Mol Carcinog (2010) 0.96
Epigenetic alteration of the SOCS1 gene in chronic myeloid leukaemia. Br J Haematol (2003) 0.96
Novel heteroplasmic frameshift and missense somatic mitochondrial DNA mutations in oral cancer of betel quid chewers. Genes Chromosomes Cancer (2003) 0.96
The effect of hydroxyurea in spinal muscular atrophy cells and patients. J Neurol Sci (2007) 0.96
Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer. BMC Cancer (2006) 0.96