Published in Nucleic Acids Res on November 27, 2012
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res (2015) 2.33
5' isomiR variation is of functional and evolutionary importance. Nucleic Acids Res (2014) 1.28
Global population-specific variation in miRNA associated with cancer risk and clinical biomarkers. BMC Med Genomics (2014) 1.13
Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res (2015) 1.09
Bias in microRNA functional enrichment analysis. Bioinformatics (2015) 1.07
Bioinformatic tools for microRNA dissection. Nucleic Acids Res (2015) 1.02
miRIAD-integrating microRNA inter- and intragenic data. Database (Oxford) (2014) 0.91
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. Nucleic Acids Res (2015) 0.91
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets. Database (Oxford) (2015) 0.88
miRspring: a compact standalone research tool for analyzing miRNA-seq data. Nucleic Acids Res (2013) 0.87
The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain. BMC Genomics (2015) 0.84
miTALOS v2: Analyzing Tissue Specific microRNA Function. PLoS One (2016) 0.84
Dysregulated miR-671-5p / CDR1-AS / CDR1 / VSNL1 axis is involved in glioblastoma multiforme. Oncotarget (2016) 0.83
Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches. Mol Cancer (2016) 0.82
Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing. RNA Biol (2014) 0.82
SMMRNA: a database of small molecule modulators of RNA. Nucleic Acids Res (2013) 0.82
Tiny giants of gene regulation: experimental strategies for microRNA functional studies. Wiley Interdiscip Rev Dev Biol (2016) 0.80
CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res (2016) 0.80
Targeted Regression of Hepatocellular Carcinoma by Cancer-Specific RNA Replacement through MicroRNA Regulation. Sci Rep (2015) 0.80
Macros in microRNA target identification: a comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification. RNA Biol (2014) 0.80
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Res (2016) 0.78
UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia (2017) 0.76
Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma. Epigenetics (2016) 0.76
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res (2017) 0.75
miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ (2015) 0.75
Evolutionary patterns of metazoan microRNAs reveal targeting principles in the let-7 and miR-10 families. Genome Res (2016) 0.75
Blood hsa-miR-122-5p and hsa-miR-885-5p levels associate with fatty liver and related lipoprotein metabolism-The Young Finns Study. Sci Rep (2016) 0.75
Epigenetic silencing of miR-19a-3p by cold atmospheric plasma contributes to proliferation inhibition of the MCF-7 breast cancer cell. Sci Rep (2016) 0.75
A Systematic Study of Dysregulated MicroRNA in Type 2 Diabetes Mellitus. Int J Mol Sci (2017) 0.75
CSmiRTar: Condition-Specific microRNA targets database. PLoS One (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res (2010) 25.85
The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res (2008) 8.97
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res (2010) 6.58
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res (2010) 5.72
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol (2011) 5.57
eVOC: a controlled vocabulary for unifying gene expression data. Genome Res (2003) 5.41
Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics (2007) 4.91
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res (2011) 4.54
The MeSH translation maintenance system: structure, interface design, and implementation. Stud Health Technol Inform (2004) 3.80
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2009) 2.90
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res (2011) 2.87
A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res (2010) 2.87
miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol (2012) 2.14
MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res (2010) 1.94
PMRD: plant microRNA database. Nucleic Acids Res (2009) 1.94
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res (2010) 1.70
Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One (2010) 1.31
RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinformatics (2009) 1.26
miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res (2011) 0.99
HOCTAR database: a unique resource for microRNA target prediction. Gene (2011) 0.96
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. BMC Plant Biol (2012) 0.80
The nuclear RNase III Drosha initiates microRNA processing. Nature (2003) 35.49
MicroRNA genes are transcribed by RNA polymerase II. EMBO J (2004) 20.65
MicroRNA maturation: stepwise processing and subcellular localization. EMBO J (2002) 19.47
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell (2006) 11.98
The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev (2004) 11.58
Human embryonic stem cells express a unique set of microRNAs. Dev Biol (2004) 8.87
Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol (2002) 8.81
Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell (2008) 8.32
Processing of intronic microRNAs. EMBO J (2007) 6.32
TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell (2009) 5.99
miR-29 miRNAs activate p53 by targeting p85 alpha and CDC42. Nat Struct Mol Biol (2008) 4.81
The role of PACT in the RNA silencing pathway. EMBO J (2006) 4.53
Posttranscriptional crossregulation between Drosha and DGCR8. Cell (2009) 3.54
Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res (2009) 3.44
miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res (2007) 2.59
Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature (2011) 2.49
Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res (2005) 2.48
Conserved MicroRNA miR-8/miR-200 and its target USH/FOG2 control growth by regulating PI3K. Cell (2009) 2.39
A p53/miRNA-34 axis regulates Snail1-dependent cancer cell epithelial-mesenchymal transition. J Cell Biol (2011) 2.19
The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol (2013) 2.12
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucleic Acids Res (2010) 2.12
Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell (2012) 2.09
ECgene: genome annotation for alternative splicing. Nucleic Acids Res (2005) 2.06
Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res (2006) 1.97
ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Res (2005) 1.95
p53 and microRNA-34 are suppressors of canonical Wnt signaling. Sci Signal (2011) 1.80
Crystal structure of human DGCR8 core. Nat Struct Mol Biol (2007) 1.74
Modifications of small RNAs and their associated proteins. Cell (2010) 1.69
LIN28A is a suppressor of ER-associated translation in embryonic stem cells. Cell (2012) 1.58
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol Cell (2012) 1.56
Structural and functional insights into Dom34, a key component of no-go mRNA decay. Mol Cell (2007) 1.54
Human cytomegalovirus microRNA miR-US4-1 inhibits CD8(+) T cell responses by targeting the aminopeptidase ERAP1. Nat Immunol (2011) 1.46
Clinical validity of the lung cancer biomarkers identified by bioinformatics analysis of public expression data. Cancer Res (2007) 1.38
ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res (2009) 1.36
Variants affecting exon skipping contribute to complex traits. PLoS Genet (2012) 1.24
Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation. EMBO Rep (2011) 1.24
Regulating the regulators: posttranslational modifications of RNA silencing factors. Cell (2009) 1.20
ChimerDB--a knowledgebase for fusion sequences. Nucleic Acids Res (2006) 1.20
Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing. Genes Chromosomes Cancer (2012) 1.19
miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res (2010) 1.15
In vitro and in vivo assays for the activity of Drosha complex. Methods Enzymol (2007) 1.12
Clinical validation of colorectal cancer biomarkers identified from bioinformatics analysis of public expression data. Clin Cancer Res (2011) 1.11
hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Res (2011) 1.08
A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers. PLoS One (2013) 1.08
TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol (2013) 1.05
ECgene: an alternative splicing database update. Nucleic Acids Res (2006) 1.05
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. Nucleic Acids Res (2004) 1.02
MRP9, an unusual truncated member of the ABC transporter superfamily, is highly expressed in breast cancer. Proc Natl Acad Sci U S A (2002) 1.00
Ahnak protein activates protein kinase C (PKC) through dissociation of the PKC-protein phosphatase 2A complex. J Biol Chem (2008) 0.98
Human UPF1 participates in small RNA-induced mRNA downregulation. Mol Cell Biol (2009) 0.93
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation. BMC Genomics (2008) 0.92
Gerontome: a web-based database server for aging-related genes and analysis pipelines. BMC Genomics (2010) 0.92
Retracted Cell adhesion-dependent control of microRNA decay. Mol Cell (2011) 0.89
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res (2006) 0.88
Bringing single-molecule spectroscopy to macromolecular protein complexes. Trends Biochem Sci (2012) 0.88
Positive feedback loop between Sox2 and Sox6 inhibits neuronal differentiation in the developing central nervous system. Proc Natl Acad Sci U S A (2014) 0.87
MicroRNA factory: RISC assembly from precursor microRNAs. Mol Cell (2012) 0.87
Down-regulation of Sox10 with specific small interfering RNA promotes transdifferentiation of Schwannoma cells into myofibroblasts. Differentiation (2006) 0.85
Genetic landscape of open chromatin in yeast. PLoS Genet (2013) 0.85
Cell cycle micromanagement in embryonic stem cells. Nat Genet (2008) 0.85
FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action. BMC Genomics (2013) 0.82
GARNET--gene set analysis with exploration of annotation relations. BMC Bioinformatics (2011) 0.81
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. Nucleic Acids Res (2011) 0.81
Dissection of the dimerization modes in the DJ-1 superfamily. Mol Cells (2012) 0.80
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs. Nucleic Acids Res (2005) 0.80
tsORFdb: theoretical small open reading frames (ORFs) database and massProphet: peptide mass fingerprinting (PMF) tool for unknown small functional ORFs. Biochem Biophys Res Commun (2010) 0.80
Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach. Biochem Biophys Res Commun (2013) 0.79
The effect of thiobarbituric acid on tyrosinase: inhibition kinetics and computational simulation. J Biomol Struct Dyn (2011) 0.79
Transcriptomic analysis of insulin-sensitive tissues from anti-diabetic drug treated ZDF rats, a T2DM animal model. PLoS One (2013) 0.79
Regulation of ApC/EBP mRNA by the Aplysia AU-rich element-binding protein, ApELAV, and its effects on 5-hydroxytryptamine-induced long-term facilitation. J Neurochem (2006) 0.79
The co-regulation mechanism of transcription factors in the human gene regulatory network. Nucleic Acids Res (2012) 0.79
Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. BMC Syst Biol (2013) 0.79
Inference of kinship coefficients from Korean SNP genotyping data. BMB Rep (2013) 0.78
Kinetics and molecular docking studies of an anti-diabetic complication inhibitor fucosterol from edible brown algae Eisenia bicyclis and Ecklonia stolonifera. Chem Biol Interact (2013) 0.78
A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials. J Comput Chem (2012) 0.78
VnD: a structure-centric database of disease-related SNPs and drugs. Nucleic Acids Res (2010) 0.78
Mixed-type inhibition of tyrosinase from Agaricus bisporus by terephthalic acid: computational simulations and kinetics. Protein J (2011) 0.78
Preparation and analysis of Drosha. Methods Mol Biol (2005) 0.76
VAMP2-NRG1 Fusion Gene is a Novel Oncogenic Driver of Non-Small-Cell Lung Adenocarcinoma. J Thorac Oncol (2015) 0.76
GS2PATH: a web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Bioinformation (2007) 0.75
Response to Comment on "Multiple repressive mechanisms in the hippocampus during memory formation". Science (2016) 0.75
gsGator: an integrated web platform for cross-species gene set analysis. BMC Bioinformatics (2014) 0.75
Kinetics and molecular docking studies of pimarane-type diterpenes as protein tyrosine phosphatase (PTP1B) inhibitors from Aralia continentalis roots. Arch Pharm Res (2013) 0.75