Published in BMC Bioinformatics on March 01, 2007
MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
The impact of microRNAs on protein output. Nature (2008) 32.39
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA (2007) 6.44
DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res (2009) 5.23
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A (2008) 5.11
Spatial preferences of microRNA targets in 3' untranslated regions. BMC Genomics (2007) 4.99
The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol (2008) 4.88
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (2008) 4.53
Predicting effective microRNA target sites in mammalian mRNAs. Elife (2015) 4.30
Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics (2009) 3.21
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One (2008) 3.09
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol (2011) 2.82
Practical Aspects of microRNA Target Prediction. Curr Mol Med (2011) 2.64
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods (2013) 2.16
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res (2009) 1.98
Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell (2009) 1.92
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res (2010) 1.88
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res (2013) 1.59
Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2. Silence (2011) 1.53
MYCN-regulated microRNAs repress estrogen receptor-alpha (ESR1) expression and neuronal differentiation in human neuroblastoma. Proc Natl Acad Sci U S A (2010) 1.49
Got target? Computational methods for microRNA target prediction and their extension. Exp Mol Med (2010) 1.49
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res (2009) 1.44
TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics (2010) 1.43
Efficient use of accessibility in microRNA target prediction. Nucleic Acids Res (2010) 1.42
General rules for functional microRNA targeting. Nat Genet (2016) 1.39
Targeting of microRNA-142-3p in dendritic cells regulates endotoxin-induced mortality. Blood (2011) 1.39
Identifying miRNAs, targets and functions. Brief Bioinform (2012) 1.35
Towards computational prediction of microRNA function and activity. Nucleic Acids Res (2010) 1.32
MicroRNAs: molecular features and role in cancer. Front Biosci (Landmark Ed) (2012) 1.32
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32
miRTar: an integrated system for identifying miRNA-target interactions in human. BMC Bioinformatics (2011) 1.30
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics (2012) 1.28
MicroRNA networks in mouse lung organogenesis. PLoS One (2010) 1.28
The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics (2009) 1.27
MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res (2012) 1.27
MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA (2011) 1.26
The sufficient minimal set of miRNA seed types. Bioinformatics (2011) 1.25
Computational methods to identify miRNA targets. Semin Cell Dev Biol (2010) 1.21
Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics (2007) 1.21
Combined characterization of microRNA and mRNA profiles delineates early differentiation pathways of CD133+ and CD34+ hematopoietic stem and progenitor cells. Stem Cells (2011) 1.19
Involvement of microRNAs in physiological and pathological processes in the lung. Respir Res (2010) 1.17
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics (2009) 1.14
Inferring causative variants in microRNA target sites. Nucleic Acids Res (2011) 1.12
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol (2012) 1.10
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res (2010) 1.08
Reprogramming of the microRNA transcriptome mediates resistance to rapamycin. J Biol Chem (2013) 1.06
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
An evolutionary perspective of animal microRNAs and their targets. J Biomed Biotechnol (2009) 1.06
A systems genetic analysis of alcohol drinking by mice, rats and men: influence of brain GABAergic transmission. Neuropharmacology (2010) 1.05
Mapping a barbiturate withdrawal locus to a 0.44 Mb interval and analysis of a novel null mutant identify a role for Kcnj9 (GIRK3) in withdrawal from pentobarbital, zolpidem, and ethanol. J Neurosci (2009) 1.05
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Res (2014) 1.05
miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. Nat Commun (2015) 1.04
A two-step site and mRNA-level model for predicting microRNA targets. BMC Bioinformatics (2010) 1.04
The expression levels of microRNA-361-5p and its target VEGFA are inversely correlated in human cutaneous squamous cell carcinoma. PLoS One (2012) 1.04
Bioinformatic tools for microRNA dissection. Nucleic Acids Res (2015) 1.02
Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evol Dev (2010) 1.01
The Influence of 3'UTRs on MicroRNA Function Inferred from Human SNP Data. Comp Funct Genomics (2011) 1.00
MTar: a computational microRNA target prediction architecture for human transcriptome. BMC Bioinformatics (2010) 0.99
One decade of development and evolution of microRNA target prediction algorithms. Genomics Proteomics Bioinformatics (2012) 0.99
Large-scale screens of miRNA-mRNA interactions unveiled that the 3'UTR of a gene is targeted by multiple miRNAs. PLoS One (2013) 0.98
Advances in the techniques for the prediction of microRNA targets. Int J Mol Sci (2013) 0.97
Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One (2011) 0.96
miRNA target enrichment analysis reveals directly active miRNAs in health and disease. Nucleic Acids Res (2012) 0.96
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics (2013) 0.96
MicroRNA-mRNA interactions in a murine model of hyperoxia-induced bronchopulmonary dysplasia. BMC Genomics (2012) 0.95
Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. Bioessays (2015) 0.95
A study of miRNAs targets prediction and experimental validation. Protein Cell (2010) 0.95
MiR-200b/200c/429 subfamily negatively regulates Rho/ROCK signaling pathway to suppress hepatocellular carcinoma metastasis. Oncotarget (2015) 0.92
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res (2012) 0.92
Optimal use of conservation and accessibility filters in microRNA target prediction. PLoS One (2012) 0.92
Timescales and bottlenecks in miRNA-dependent gene regulation. Mol Syst Biol (2013) 0.91
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res (2014) 0.91
Brain expression quantitative trait locus mapping informs genetic studies of psychiatric diseases. Neurosci Bull (2011) 0.90
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics (2010) 0.89
"Seed-Milarity" confers to hsa-miR-210 and hsa-miR-147b similar functional activity. PLoS One (2012) 0.89
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets. Database (Oxford) (2015) 0.88
Hsa-miRNA-765 as a key mediator for inhibiting growth, migration and invasion in fulvestrant-treated prostate cancer. PLoS One (2014) 0.87
Interactions between cancer cells and normal cells via miRNAs in extracellular vesicles. Cell Mol Life Sci (2015) 0.87
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. PLoS One (2014) 0.87
Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro Oncol (2013) 0.87
Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. PLoS Comput Biol (2013) 0.86
Detection of novel 3' untranslated region extensions with 3' expression microarrays. BMC Genomics (2010) 0.86
Rational design of micro-RNA-like bifunctional siRNAs targeting HIV and the HIV coreceptor CCR5. Mol Ther (2010) 0.85
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Res (2015) 0.85
MicroRNA-276a functions in ellipsoid body and mushroom body neurons for naive and conditioned olfactory avoidance in Drosophila. J Neurosci (2013) 0.85
A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet (2016) 0.85
MicroRNA-centric measurement improves functional enrichment analysis of co-expressed and differentially expressed microRNA clusters. BMC Genomics (2012) 0.84
Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Res (2014) 0.83
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res (2014) 0.83
Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis. Nucleic Acids Res (2012) 0.83
Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region. PLoS One (2012) 0.83
Molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer) myostatin gene. BMC Genomics (2008) 0.82
A microRNA negative feedback loop downregulates vesicle transport and inhibits fear memory. Elife (2016) 0.82
Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data. Front Genet (2012) 0.82
Seq and CLIP through the miRNA world. Genome Biol (2014) 0.81
Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Syst Biol (2011) 0.81
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
Prediction of mammalian microRNA targets. Cell (2003) 53.70
Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95
Identification of novel genes coding for small expressed RNAs. Science (2001) 44.44
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (2001) 44.16
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
Human MicroRNA targets. PLoS Biol (2004) 34.51
An extensive class of small RNAs in Caenorhabditis elegans. Science (2001) 34.17
Silencing of microRNAs in vivo with 'antagomirs'. Nature (2005) 32.56
Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A (2002) 32.26
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
RAS is regulated by the let-7 microRNA family. Cell (2005) 30.24
MicroRNAs modulate hematopoietic lineage differentiation. Science (2003) 30.05
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Principles of microRNA-target recognition. PLoS Biol (2005) 23.70
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
miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A (2005) 21.51
Specificity of microRNA target selection in translational repression. Genes Dev (2004) 21.14
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14
Fast and effective prediction of microRNA/target duplexes. RNA (2004) 18.10
Vertebrate microRNA genes. Science (2003) 17.42
Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet (2002) 17.20
Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol Cancer Res (2003) 17.13
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
MicroRNA expression in zebrafish embryonic development. Science (2005) 15.52
Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell (2005) 15.38
Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of Drosophila MicroRNA targets. PLoS Biol (2003) 12.72
Identification of virus-encoded microRNAs. Science (2004) 12.56
The colorectal microRNAome. Proc Natl Acad Sci U S A (2006) 11.59
The small RNA profile during Drosophila melanogaster development. Dev Cell (2003) 11.46
MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell (2005) 9.01
Human embryonic stem cells express a unique set of microRNAs. Dev Biol (2004) 8.87
TOR controls translation initiation and early G1 progression in yeast. Mol Biol Cell (1996) 8.03
Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11
Computational identification of microRNA targets. Dev Biol (2004) 6.84
microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol (2005) 6.77
Diversity of microRNAs in human and chimpanzee brain. Nat Genet (2006) 6.57
Numerous microRNPs in neuronal cells containing novel microRNAs. RNA (2003) 6.28
Incorporating structure to predict microRNA targets. Proc Natl Acad Sci U S A (2005) 5.68
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res (2006) 5.23
RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA (2005) 4.91
Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev (2005) 4.34
The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation. Nat Cell Biol (2006) 4.31
Medaka--a model organism from the far East. Nat Rev Genet (2002) 3.55
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res (2006) 2.58
Architecture of a validated microRNA::target interaction. Chem Biol (2004) 2.36
The bantam gene regulates Drosophila growth. Genetics (2002) 1.62
Identification of a genetic cluster influencing memory performance and hippocampal activity in humans. Proc Natl Acad Sci U S A (2006) 1.38
SPA: a probabilistic algorithm for spliced alignment. PLoS Genet (2006) 1.37
Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics (2005) 1.33
Effect of rapamycin on mouse chronic lymphocytic leukemia and the development of nonhematopoietic malignancies in Emu-TCL1 transgenic mice. Cancer Res (2006) 1.26
Identification of microRNAs from different tissues of chicken embryo and adult chicken. FEBS Lett (2006) 1.18
Inhibition of BMP2-induced, TAK1 kinase-mediated neurite outgrowth by Smad6 and Smad7. Genes Cells (2001) 1.00
A role for CaMKII in T cell memory. Cell (2000) 0.93
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The small RNA profile during Drosophila melanogaster development. Dev Cell (2003) 11.46
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75
Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (2008) 4.53
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res (2003) 4.07
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods (2011) 4.06
MicroRNAs 103 and 107 regulate insulin sensitivity. Nature (2011) 3.98
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol (2008) 3.98
miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Natl Acad Sci U S A (2009) 3.89
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35
A probabilistic method to detect regulatory modules. Bioinformatics (2003) 3.24
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One (2008) 3.09
miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods (2009) 3.03
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res (2006) 2.96
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics (2005) 2.76
SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res (2006) 2.30
PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp (2010) 2.23
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods (2013) 2.16
MicroRNA activity is suppressed in mouse oocytes. Curr Biol (2010) 2.15
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol (2008) 2.09
Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep (2012) 2.07
Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype. Am J Pathol (2008) 2.03
Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol (2014) 1.98
Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol (2010) 1.98
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res (2009) 1.98
Computational analysis of small RNA cloning data. Methods (2008) 1.96
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res (2010) 1.88
Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming. Cancer Cell (2013) 1.85
The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet (2010) 1.83
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res (2002) 1.78
Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc Natl Acad Sci U S A (2002) 1.78
Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends Genet (2009) 1.73
Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA (2007) 1.61
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res (2013) 1.59
A simple physical model predicts small exon length variations. PLoS Genet (2006) 1.59
The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion. Genome Res (2009) 1.56
Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. J Clin Invest (2014) 1.54
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res (2012) 1.54
Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. Breast Cancer Res (2013) 1.49
Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes (2012) 1.44
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res (2009) 1.44
Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1. J Virol (2007) 1.38
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res (2014) 1.37
SPA: a probabilistic algorithm for spliced alignment. PLoS Genet (2006) 1.37
Virus-encoded microRNAs: novel regulators of gene expression. Trends Microbiol (2006) 1.36
Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathog (2011) 1.33
Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS One (2013) 1.33
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Res (2003) 1.31
Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathog (2009) 1.28
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. Nat Struct Mol Biol (2013) 1.26
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res (2012) 1.22
MicroRNA-7a regulates pancreatic β cell function. J Clin Invest (2014) 1.18
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics (2010) 1.14
MicroRNA-221-222 regulate the cell cycle in mast cells. J Immunol (2009) 1.14
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics (2012) 1.14
Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res (2007) 1.11
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol (2012) 1.10
Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Mol Biol Cell (2008) 1.09
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res (2010) 1.08
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. BMC Genomics (2010) 1.07
Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol Evol (2010) 1.06
MicroRNA binding sites in the coding region of mRNAs: extending the repertoire of post-transcriptional gene regulation. Bioessays (2014) 1.05
The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism. Mol Cell Biol (2012) 1.02
The types and prevalence of alternative splice forms. Curr Opin Struct Biol (2006) 1.00
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing. Nucleic Acids Res (2010) 0.99
PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA (2011) 0.99
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. Genome Biol (2013) 0.99
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC Microbiol (2013) 0.98
The evolution of domain-content in bacterial genomes. Biol Direct (2008) 0.97
Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. J Cell Sci (2014) 0.96
MicroRNA-194 is a target of transcription factor 1 (Tcf1, HNF1α) in adult liver and controls expression of frizzled-6. Hepatology (2012) 0.95