Published in Nucleic Acids Res on July 01, 2006
MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A (2008) 6.38
Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet (2010) 2.54
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Definition of microRNAs that repress expression of the tumor suppressor gene FOXO1 in endometrial cancer. Cancer Res (2009) 2.32
eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. J Cell Biol (2008) 2.26
Function of alternative splicing. Gene (2012) 2.00
MicroRNA-126 regulates HOXA9 by binding to the homeobox. Mol Cell Biol (2008) 1.95
Human bocavirus can be cultured in differentiated human airway epithelial cells. J Virol (2009) 1.85
DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms. Proc Natl Acad Sci U S A (2009) 1.76
Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One (2011) 1.49
SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res (2010) 1.33
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics (2013) 1.32
Transterm: a database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res (2008) 1.27
Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk. J Clin Invest (2007) 1.25
Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron (2014) 1.13
Dopamine transporter gene variant affecting expression in human brain is associated with bipolar disorder. Neuropsychopharmacology (2011) 1.13
Increasing expression of microRNA 181 inhibits porcine reproductive and respiratory syndrome virus replication and has implications for controlling virus infection. J Virol (2012) 1.12
Cross-talk between miR-29 and transforming growth factor-betas in trabecular meshwork cells. Invest Ophthalmol Vis Sci (2011) 1.11
Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. Trends Genet (2014) 1.10
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res (2012) 1.06
The MicroRNA Biology of the Mammalian Nucleus. Mol Ther Nucleic Acids (2014) 1.05
Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion. J Am Coll Cardiol (2008) 1.05
RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res (2014) 1.04
MicroRNA-130a represses transcriptional activity of aquaporin 4 M1 promoter. J Biol Chem (2012) 0.95
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics (2011) 0.94
MicroRNA 181 suppresses porcine reproductive and respiratory syndrome virus (PRRSV) infection by targeting PRRSV receptor CD163. J Virol (2013) 0.93
Host cell transcriptome profile during wild-type and attenuated dengue virus infection. PLoS Negl Trop Dis (2013) 0.93
Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response. Cell Stress Chaperones (2013) 0.93
Murine models of chronic lymphocytic leukaemia: role of microRNA-16 in the New Zealand Black mouse model. Br J Haematol (2007) 0.92
MicroRNA 339 down-regulates μ-opioid receptor at the post-transcriptional level in response to opioid treatment. FASEB J (2012) 0.92
MicroRNAs 296 and 298 are imprinted and part of the GNAS/Gnas cluster and miR-296 targets IKBKE and Tmed9. RNA (2011) 0.91
Epigenetic regulation of miR-21 in colorectal cancer: ITGB4 as a novel miR-21 target and a three-gene network (miR-21-ITGΒ4-PDCD4) as predictor of metastatic tumor potential. Epigenetics (2013) 0.91
Human SP-A1 (SFTPA1) variant-specific 3' UTRs and poly(A) tail differentially affect the in vitro translation of a reporter gene. Am J Physiol Lung Cell Mol Physiol (2010) 0.91
microRNAs in circulation are altered in response to influenza A virus infection in humans. PLoS One (2013) 0.90
Intron 7 conserved sequence elements regulate the splicing of the SMN genes. Hum Genet (2009) 0.90
A possible role for miRNA silencing in disease phenotype variation in Swedish transthyretin V30M carriers. BMC Med Genet (2010) 0.90
The orthologue of the fruitfly sex behaviour gene fruitless in the mosquito Aedes aegypti: evolution of genomic organisation and alternative splicing. PLoS One (2013) 0.89
Lifespan profiles of Alzheimer's disease-associated genes and products in monkeys and mice. J Alzheimers Dis (2009) 0.89
In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions. Curr Genomics (2013) 0.88
Identification of splice variants, targeted microRNAs and functional single nucleotide polymorphisms of the BOLA-DQA2 gene in dairy cattle. DNA Cell Biol (2011) 0.88
Cellular microRNA miR-181b inhibits replication of mink enteritis virus by repression of non-structural protein 1 translation. PLoS One (2013) 0.87
Identification of miRNAs that specifically target tumor suppressive KLF6-FL rather than oncogenic KLF6-SV1 isoform. RNA Biol (2014) 0.87
An APOA5 3' UTR variant associated with plasma triglycerides triggers APOA5 downregulation by creating a functional miR-485-5p binding site. Am J Hum Genet (2014) 0.86
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource. Database (Oxford) (2014) 0.86
Genetic variation in the 3'-UTR of CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2, and UGT2B7: potential effects on regulation by microRNA and pharmacogenomics relevance. Front Genet (2014) 0.86
Peptide YY (PYY) gene polymorphisms in the 3'-untranslated and proximal promoter regions regulate cellular gene expression and PYY secretion and metabolic syndrome traits in vivo. J Clin Endocrinol Metab (2009) 0.84
Cardiac insulin resistance and microRNA modulators. Exp Diabetes Res (2011) 0.84
Stabilization of human interferon-α1 mRNA by its antisense RNA. Cell Mol Life Sci (2012) 0.84
Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. Front Plant Sci (2011) 0.82
The two faces of miR-29. J Cardiovasc Med (Hagerstown) (2015) 0.81
MicroRNA miR-320a and miR-140 inhibit mink enteritis virus infection by repression of its receptor, feline transferrin receptor. Virol J (2014) 0.81
Respiratory syncytial virus infection alters surfactant protein A expression in human pulmonary epithelial cells by reducing translation efficiency. Am J Physiol Lung Cell Mol Physiol (2009) 0.80
Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol (2008) 0.80
Natural history of SLC11 genes in vertebrates: tales from the fish world. BMC Evol Biol (2011) 0.79
Endoplasmic Reticulum Stress Induced Synthesis of a Novel Viral Factor Mediates Efficient Replication of Genotype-1 Hepatitis E Virus. PLoS Pathog (2016) 0.79
Myeloid-derived miR-223 regulates intestinal inflammation via repression of the NLRP3 inflammasome. J Exp Med (2017) 0.79
Pancreatic cancer risk variant in LINC00673 creates a miR-1231 binding site and interferes with PTPN11 degradation. Nat Genet (2016) 0.79
CDKN2B expression in adipose tissue of familial combined hyperlipidemia patients. J Lipid Res (2013) 0.79
Genetic variations creating microRNA target sites in the FXN 3'-UTR affect frataxin expression in Friedreich ataxia. PLoS One (2013) 0.79
Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes. Nucleic Acids Res (2012) 0.78
Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies. Hum Mol Genet (2015) 0.78
NF-YC complexity is generated by dual promoters and alternative splicing. J Biol Chem (2009) 0.78
Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant. PLoS One (2012) 0.77
Optimization of mRNA design for protein expression in the crustacean Daphnia magna. Mol Genet Genomics (2014) 0.77
A transcribed ultraconserved noncoding RNA, Uc.173, is a key molecule for the inhibition of lead-induced neuronal apoptosis. Oncotarget (2016) 0.77
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts. PeerJ (2016) 0.77
MicroRNA target prediction: theory and practice. Mol Genet Genomics (2014) 0.77
c-myc in whitefish (Coregonus lavaretus): structure, expression, and insights into possible posttranscriptional regulatory mechanism. Fish Physiol Biochem (2015) 0.76
Cloning of aquaporin-1 of the blue crab, Callinectes sapidus: its expression during the larval development in hyposalinity. Aquat Biosyst (2012) 0.76
Overexpression of FGF9 in colon cancer cells is mediated by hypoxia-induced translational activation. Nucleic Acids Res (2013) 0.76
Human heart rate: heritability of resting and stress values in twin pairs, and influence of genetic variation in the adrenergic pathway at a microribonucleic acid (microrna) motif in the 3'-UTR of cytochrome b561 [corrected]. J Am Coll Cardiol (2013) 0.76
Delayed glial clearance of degenerating axons in aged Drosophila is due to reduced PI3K/Draper activity. Nat Commun (2016) 0.76
Phosphorylation of elongation factor-2 kinase differentially regulates the enzyme's stability under stress conditions. Biochem Biophys Res Commun (2012) 0.75
Genetic Analysis of Natural Variation in Antirrhinum Scent Profiles Identifies BENZOIC ACID CARBOXYMETHYL TRANSFERASE As the Major Locus Controlling Methyl Benzoate Synthesis. Front Plant Sci (2017) 0.75
GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism. PLoS One (2016) 0.75
CCM3/SERPINI1 bidirectional promoter variants in patients with cerebral cavernous malformations: a molecular and functional study. BMC Med Genet (2016) 0.75
A novel regulatory network among LncRpa, CircRar1, MiR-671 and apoptotic genes promotes lead-induced neuronal cell apoptosis. Arch Toxicol (2016) 0.75
The alpaca melanocortin 1 receptor: gene mutations, transcripts, and relative levels of expression in ventral skin biopsies. ScientificWorldJournal (2015) 0.75
Genome-wide association study for hereditary ataxia in the Parson Russell Terrier and DNA-testing for ataxia-associated mutations in the Parson and Jack Russell Terrier. BMC Vet Res (2016) 0.75
Double hit of NEMO gene in preeclampsia. PLoS One (2017) 0.75
Polymorphisms in lncRNA PTENP1 and the Risk of Gastric Cancer in a Chinese Population. Dis Markers (2017) 0.75
LncRNA AFAP1-AS Functions as a Competing Endogenous RNA to Regulate RAP1B Expression by sponging miR-181a in the HSCR. Int J Med Sci (2017) 0.75
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders. Sci Rep (2017) 0.75
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.85
Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet (2002) 16.29
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
Gene regulation by riboswitches. Nat Rev Mol Cell Biol (2004) 7.00
Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc Natl Acad Sci U S A (1996) 5.53
RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res (2001) 4.96
GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res (2001) 3.71
ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res (2006) 3.60
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res (2005) 2.80
PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res (2003) 2.18
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res (2005) 2.12
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA (2005) 1.97
Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res (2004) 1.47
Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res (2006) 1.44
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics (2004) 1.35
Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. Trends Genet (1999) 1.25
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Res (2005) 1.08
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
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
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
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
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
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
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
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
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
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
dbSNO: a database of cysteine S-nitrosylation. Bioinformatics (2012) 1.07
SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS One (2011) 1.04
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res (2010) 1.03
Computational identification of riboswitches based on RNA conserved functional sequences and conformations. RNA (2009) 1.02
Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells. PLoS One (2011) 0.99
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics (2013) 0.96
Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants. PLoS One (2010) 0.94
FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res (2009) 0.94
RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res (2006) 0.93
A novel role of CPEB3 in regulating EGFR gene transcription via association with Stat5b in neurons. Nucleic Acids Res (2010) 0.92
Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma. Nucleic Acids Res (2013) 0.92
A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res Notes (2009) 0.91
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database (Oxford) (2014) 0.90
CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication. Mol Microbiol (2014) 0.90
Identifying the combination of genetic factors that determine susceptibility to cervical cancer. IEEE Trans Inf Technol Biomed (2004) 0.89
N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J Comput Chem (2010) 0.88
The activation of directional stem cell motility by green light-emitting diode irradiation. Biomaterials (2012) 0.87
Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. PLoS One (2011) 0.86
Characterization and prediction of mRNA polyadenylation sites in human genes. Med Biol Eng Comput (2011) 0.85
The repetitive sequence database and mining putative regulatory elements in gene promoter regions. J Comput Biol (2002) 0.85
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. BMC Genomics (2014) 0.84
Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis. J Microbiol Immunol Infect (2012) 0.83
Mining putative regulatory elements in promoter regions of Saccharomyces cerevisiae. In Silico Biol (2002) 0.83
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. J Comput Aided Mol Des (2013) 0.81
Functional analyses of endometriosis-related polymorphisms in the estrogen synthesis and metabolism-related genes. PLoS One (2012) 0.80
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. BMC Genomics (2015) 0.79
Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data. IEEE Trans Inf Technol Biomed (2006) 0.79
YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43. PLoS One (2013) 0.79
Identifying discriminative amino acids within the hemagglutinin of human influenza A H5N1 virus using a decision tree. IEEE Trans Inf Technol Biomed (2008) 0.78
Database to dynamically aid probe design for virus identification. IEEE Trans Inf Technol Biomed (2006) 0.78
A new method for post Genome-Wide Association Study (GWAS) analysis of colorectal cancer in Taiwan. Gene (2012) 0.77
Identifying cancer highly-expressed membrane receptors for targeted drug delivery. Int J Bioinform Res Appl (2012) 0.76
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. Database (Oxford) (2013) 0.76
RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling. BMC Genomics (2006) 0.76
A probabilistic method to correlate ion pairs with protein thermostability. Appl Bioinformatics (2004) 0.76
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res (2006) 0.75
i-Genome: a database to summarize oligonucleotide data in genomes. BMC Genomics (2004) 0.75
Computing motif correlations in proteins. J Comput Chem (2003) 0.75
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures. J Comput Chem (2006) 0.75
MRA Images Identification of the Artery Blood Vessel of the Knee with SOM LVQ Neural Networks as Auxiliary. Conf Proc IEEE Eng Med Biol Soc (2005) 0.75
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. J Comput Chem (2006) 0.75
Editorial. Comput Biol Chem (2015) 0.75
Guest Editorial for the 13th Asia Pacific Bioinformatics Conference. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75