Published in RNA on October 01, 2004
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42
Human MicroRNA targets. PLoS Biol (2004) 34.51
Principles of microRNA-target recognition. PLoS Biol (2005) 23.70
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
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miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res (2008) 8.97
The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2005) 8.60
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RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res (2006) 7.39
microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol (2005) 6.77
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics (2007) 6.21
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res (2007) 5.67
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci U S A (2008) 5.29
MicroRNA 21 promotes glioma invasion by targeting matrix metalloproteinase regulators. Mol Cell Biol (2008) 5.21
MiRNA-directed regulation of VEGF and other angiogenic factors under hypoxia. PLoS One (2006) 4.29
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell (2013) 4.28
Distinctive microRNA signature of acute myeloid leukemia bearing cytoplasmic mutated nucleophosmin. Proc Natl Acad Sci U S A (2008) 4.26
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol (2007) 4.19
RNA editing of human microRNAs. Genome Biol (2006) 4.16
MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes Dev (2007) 4.01
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MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J Clin Invest (2012) 3.46
A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nat Cell Biol (2009) 3.44
miRU: an automated plant miRNA target prediction server. Nucleic Acids Res (2005) 3.24
Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics (2009) 3.21
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
Molecular architecture of a miRNA-regulated 3' UTR. RNA (2008) 3.11
MicroRNA-132-mediated loss of p120RasGAP activates the endothelium to facilitate pathological angiogenesis. Nat Med (2010) 2.99
Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res (2006) 2.90
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics (2008) 2.88
An alternative mode of microRNA target recognition. Nat Struct Mol Biol (2012) 2.77
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival. J Exp Med (2008) 2.68
Mammalian microRNAs: a small world for fine-tuning gene expression. Mamm Genome (2006) 2.64
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol (2008) 2.61
Retracted The human angiotensin II type 1 receptor +1166 A/C polymorphism attenuates microRNA-155 binding. J Biol Chem (2007) 2.60
MIR-206 regulates connexin43 expression during skeletal muscle development. Nucleic Acids Res (2006) 2.59
Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet (2007) 2.58
Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. Mol Genet Metab (2007) 2.52
The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog (2012) 2.45
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev (2007) 2.44
Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms. Nat Methods (2009) 2.32
Virus-encoded microRNAs. Virology (2011) 2.28
LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker. Nat Med (2012) 2.24
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods (2013) 2.16
MicroRNA regulation of cyclooxygenase-2 during embryo implantation. Proc Natl Acad Sci U S A (2007) 2.16
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics (2006) 2.08
miR-29 modulates Wnt signaling in human osteoblasts through a positive feedback loop. J Biol Chem (2010) 2.05
Modulation of mismatch repair and genomic stability by miR-155. Proc Natl Acad Sci U S A (2010) 2.05
Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. EMBO J (2011) 2.03
MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res (2010) 1.94
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res (2012) 1.94
Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol (2013) 1.90
Identification of microRNA-93 as a novel regulator of vascular endothelial growth factor in hyperglycemic conditions. J Biol Chem (2010) 1.89
Host-virus interaction: a new role for microRNAs. Retrovirology (2006) 1.88
A set of differentially expressed miRNAs, including miR-30a-5p, act as post-transcriptional inhibitors of BDNF in prefrontal cortex. Hum Mol Genet (2008) 1.87
MicroRNA-298 and microRNA-328 regulate expression of mouse beta-amyloid precursor protein-converting enzyme 1. J Biol Chem (2008) 1.86
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles. Mol Microbiol (2008) 1.83
The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet (2010) 1.83
MicroRNA regulation of human protein protein interaction network. RNA (2007) 1.82
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS One (2011) 1.80
The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS One (2008) 1.78
The microRNA miR-8 is a conserved negative regulator of Wnt signaling. Proc Natl Acad Sci U S A (2008) 1.76
Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. J Virol (2010) 1.71
Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One (2008) 1.71
MicroRNA-21 orchestrates high glucose-induced signals to TOR complex 1, resulting in renal cell pathology in diabetes. J Biol Chem (2011) 1.70
Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci U S A (2010) 1.69
MicroRNA-29c is a signature microRNA under high glucose conditions that targets Sprouty homolog 1, and its in vivo knockdown prevents progression of diabetic nephropathy. J Biol Chem (2011) 1.68
Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res (2008) 1.66
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res (2011) 1.64
Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a. Proc Natl Acad Sci U S A (2009) 1.64
TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res (2008) 1.64
MicroRNA regulation of IFN-beta protein expression: rapid and sensitive modulation of the innate immune response. J Immunol (2010) 1.61
Modulation of LMP2A expression by a newly identified Epstein-Barr virus-encoded microRNA miR-BART22. Neoplasia (2009) 1.59
MicroRNA-135b promotes cancer progression by acting as a downstream effector of oncogenic pathways in colon cancer. Cancer Cell (2014) 1.59
MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res (2010) 1.58
Regulation of ABCG2 expression at the 3' untranslated region of its mRNA through modulation of transcript stability and protein translation by a putative microRNA in the S1 colon cancer cell line. Mol Cell Biol (2008) 1.58
Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res (2006) 1.56
Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput Biol (2006) 1.55
Upregulation of miR-23a-27a-24-2 cluster induces caspase-dependent and -independent apoptosis in human embryonic kidney cells. PLoS One (2009) 1.54
The role of microRNAs in cancer. Yale J Biol Med (2006) 1.54
miR-1915 and miR-1225-5p regulate the expression of CD133, PAX2 and TLR2 in adult renal progenitor cells. PLoS One (2013) 1.52
Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell (2014) 1.51
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat (2010) 1.51
Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res (2012) 1.51
A common polymorphism in serotonin receptor 1B mRNA moderates regulation by miR-96 and associates with aggressive human behaviors. Mol Psychiatry (2008) 1.50
Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res (2008) 1.50
Got target? Computational methods for microRNA target prediction and their extension. Exp Mol Med (2010) 1.49
Human cytomegalovirus microRNA miR-US4-1 inhibits CD8(+) T cell responses by targeting the aminopeptidase ERAP1. Nat Immunol (2011) 1.46
Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA (2005) 1.46
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A (2011) 1.46
The interleukin 13 (IL-13) pathway in human macrophages is modulated by microRNA-155 via direct targeting of interleukin 13 receptor alpha1 (IL13Ralpha1). J Biol Chem (2010) 1.44
West Nile virus encodes a microRNA-like small RNA in the 3' untranslated region which up-regulates GATA4 mRNA and facilitates virus replication in mosquito cells. Nucleic Acids Res (2011) 1.44
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res (2009) 1.44
Mouse miRNA-709 directly regulates miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system. Cell Res (2011) 1.44
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59
Prediction of mammalian microRNA targets. Cell (2003) 53.70
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (2001) 44.16
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
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MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell (2003) 22.14
Specificity of microRNA target selection in translational repression. Genes Dev (2004) 21.14
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
Prediction of plant microRNA targets. Cell (2002) 19.20
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet (2002) 17.20
The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell (1997) 12.87
Identification of Drosophila MicroRNA targets. PLoS Biol (2003) 12.72
The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell (2000) 10.92
The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev Cell (2003) 6.86
Computational identification of microRNA targets. Dev Biol (2004) 6.84
The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev Cell (2003) 6.74
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Developmental functions of the Distal-less/Dlx homeobox genes. Development (2002) 3.89
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Discovery of genes with highly restricted expression patterns in the Drosophila wing disc using DNA oligonucleotide microarrays. Development (2003) 1.84
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Short-range cell interactions and cell survival in the Drosophila wing. Dev Cell (2002) 1.57
GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88
RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics (2005) 3.20
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics (2004) 2.73
Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics (2006) 2.66
PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (2002) 2.43
Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf (2003) 2.33
Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 1.91
GenAlyzer: interactive visualization of sequence similarities between entire genomes. Bioinformatics (2004) 1.85
Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.79
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics (2005) 1.74
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Nucleic Acids Res (2007) 1.74
Reduction of postoperative pulmonary complications after lung surgery using a fast track clinical pathway. Eur J Cardiothorac Surg (2008) 1.56
The effects of thoracic epidural anesthesia on hepatic blood flow in patients under general anesthesia. Anesth Analg (2009) 1.48
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics (2008) 1.43
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Evaluating the predictability of conformational switching in RNA. Bioinformatics (2004) 1.30
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics (2010) 1.24
Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol (2006) 1.23
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021. BMC Genomics (2013) 1.21
Locomotif: from graphical motif description to RNA motif search. Bioinformatics (2007) 1.10
Effective ambiguity checking in biosequence analysis. BMC Bioinformatics (2005) 1.06
A prospective randomized trial comparing traditional and fast-track patient care in elective open infrarenal aneurysm repair. World J Surg (2009) 1.05
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KnotInFrame: prediction of -1 ribosomal frameshift events. Nucleic Acids Res (2008) 1.02
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics (2011) 1.01
RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res (2003) 1.00
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. Nucleic Acids Res (2004) 0.99
Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics (2005) 0.97
Shape based indexing for faster search of RNA family databases. BMC Bioinformatics (2008) 0.96
mkESA: enhanced suffix array construction tool. Bioinformatics (2009) 0.94
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics (2012) 0.93
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics (2006) 0.93
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91
Alignment of minisatellite maps based on run-length encoding scheme. J Bioinform Comput Biol (2009) 0.91
The role of periaqueductal gray and cingulate cortex during suppression of pain in complex regional pain syndrome. Clin J Pain (2011) 0.90
Prospective randomized controlled trial to evaluate "fast-track" elective open infrarenal aneurysm repair. Langenbecks Arch Surg (2008) 0.89
Faster computation of exact RNA shape probabilities. Bioinformatics (2010) 0.88
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Bioinformatics (2009) 0.86
RNA secondary structure analysis using the RNAshapes package. Curr Protoc Bioinformatics (2009) 0.86
Validation of a raw data-based synchronization signal (kymogram) for phase-correlated cardiac image reconstruction. Eur Radiol (2007) 0.84
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server. Brief Bioinform (2008) 0.82
Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics (2010) 0.81
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics (2005) 0.81
Thermodynamic matchers for the construction of the cuckoo RNA family. RNA Biol (2015) 0.79
Abstract shape analysis of RNA. Methods Mol Biol (2014) 0.78
A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis. PLoS One (2013) 0.77
WAMI: a web server for the analysis of minisatellite maps. BMC Evol Biol (2010) 0.77
Introduction to RNA secondary structure comparison. Methods Mol Biol (2014) 0.76
The BRaliBase dent-a tale of benchmark design and interpretation. Brief Bioinform (2017) 0.75
Surprises in approximating Levenshtein distances. J Theor Biol (2006) 0.75