Published in Bioessays on April 01, 2009
MicroRNA control of bone formation and homeostasis. Nat Rev Endocrinol (2012) 2.05
The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol (2011) 1.84
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics (2011) 1.33
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics (2010) 1.26
IL-10-induced microRNA-187 negatively regulates TNF-α, IL-6, and IL-12p40 production in TLR4-stimulated monocytes. Proc Natl Acad Sci U S A (2012) 1.24
A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS One (2012) 1.23
miRNA-transcription factor interactions: a combinatorial regulation of gene expression. Mol Genet Genomics (2013) 1.21
MicroRNA regulatory networks in human adipose tissue and obesity. Nat Rev Endocrinol (2015) 1.20
Vitamin D receptor signaling mechanisms: integrated actions of a well-defined transcription factor. Steroids (2012) 1.18
Biological robustness and the role of microRNAs: a network perspective. Curr Top Dev Biol (2012) 1.14
miRNAs give worms the time of their lives: small RNAs and temporal control in Caenorhabditis elegans. Dev Dyn (2010) 1.14
MicroRNAs: new regulators of Toll-like receptor signalling pathways. Biomed Res Int (2014) 1.11
Prediction of Associations between microRNAs and Gene Expression in Glioma Biology. PLoS One (2011) 1.10
Bioinformatic tools for microRNA dissection. Nucleic Acids Res (2015) 1.02
Gene-centered regulatory networks. Brief Funct Genomics (2009) 0.98
A curated database of miRNA mediated feed-forward loops involving MYC as master regulator. PLoS One (2011) 0.97
Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells. J Cell Biochem (2012) 0.95
A regulatory circuit comprising GATA1/2 switch and microRNA-27a/24 promotes erythropoiesis. Nucleic Acids Res (2013) 0.93
Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma. BMC Genomics (2012) 0.92
MicroRNAs in the regulation of TLR and RIG-I pathways. Cell Mol Immunol (2012) 0.92
A comprehensive analysis of GATA-1-regulated miRNAs reveals miR-23a to be a positive modulator of erythropoiesis. Nucleic Acids Res (2013) 0.91
The negative feedback-loop between the oncomir Mir-24-1 and menin modulates the Men1 tumorigenesis by mimicking the "Knudson's second hit". PLoS One (2012) 0.89
Transcription factor binding sites are highly enriched within microRNA precursor sequences. Biol Direct (2011) 0.88
A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes. PLoS Comput Biol (2014) 0.88
SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research. PLoS One (2012) 0.87
Chronological changes in microRNA expression in the developing human brain. PLoS One (2013) 0.86
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. BMC Syst Biol (2012) 0.86
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. BMC Syst Biol (2012) 0.85
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) (2013) 0.85
MicroRNA profiling of Sendai virus-infected A549 cells identifies miR-203 as an interferon-inducible regulator of IFIT1/ISG56. J Virol (2013) 0.81
Involvement of microRNA families in cancer. Nucleic Acids Res (2012) 0.81
An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury. BMC Genomics (2013) 0.81
cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. BMC Syst Biol (2013) 0.81
Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks. BMC Syst Biol (2012) 0.80
Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation. Oncotarget (2016) 0.79
miR-58 family and TGF-β pathways regulate each other in Caenorhabditis elegans. Nucleic Acids Res (2015) 0.79
Identification of cis-regulatory modules encoding temporal dynamics during development. BMC Genomics (2014) 0.79
Genome-wide uncovering of STAT3-mediated miRNA expression profiles in colorectal cancer cell lines. Biomed Res Int (2014) 0.79
Functional characteristics of a double negative feedback loop mediated by microRNAs. Cogn Neurodyn (2013) 0.78
Co-activation of microRNAs by Zelda is essential for early Drosophila development. Development (2014) 0.78
E2F1-miR-20a-5p/20b-5p auto-regulatory feedback loop involved in myoblast proliferation and differentiation. Sci Rep (2016) 0.78
Targeting noncoding RNAs in disease. J Clin Invest (2017) 0.78
VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription. Epigenetics (2015) 0.77
Regulatory network analysis of microRNAs and genes in imatinib-resistant chronic myeloid leukemia. Funct Integr Genomics (2016) 0.77
Analysis of miRNA, mRNA, and TF interactions through network-based methods. EURASIP J Bioinform Syst Biol (2015) 0.76
Regulatory networks in retinal ischemia-reperfusion injury. BMC Genet (2015) 0.76
Important miRs of pathways in different tumor types. PLoS Comput Biol (2013) 0.76
A role for fibrocytes in peritoneal fibrosis? Perit Dial Int (2012) 0.76
Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures. Proteome Sci (2012) 0.76
A step-by-step microRNA guide to cancer development and metastasis. Cell Oncol (Dordr) (2017) 0.75
A local genetic algorithm for the identification of condition-specific microRNA-gene modules. ScientificWorldJournal (2013) 0.75
Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. RNA (2016) 0.75
An evolutionarily biased distribution of miRNA sites toward regulatory genes with high promoter-driven intrinsic transcriptional noise. BMC Evol Biol (2014) 0.75
FSTVAL: a new web tool to validate bulk flanking sequence tags. Plant Methods (2012) 0.75
Effect of Dynamic Interaction between microRNA and Transcription Factor on Gene Expression. Biomed Res Int (2016) 0.75
HIC1 and miR-23~27~24 clusters form a double-negative feedback loop in breast cancer. Cell Death Differ (2016) 0.75
Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics (2017) 0.75
Redundant and incoherent regulations of multiple phenotypes suggest microRNAs' role in stability control. Genome Res (2017) 0.75
The co-regulatory networks of tumor suppressor genes, oncogenes, and miRNAs in colorectal cancer. Genes Chromosomes Cancer (2017) 0.75
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The genome sequence of Drosophila melanogaster. Science (2000) 74.32
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
Genome sequence of the nematode C. elegans: a platform for investigating biology. Science (1998) 61.48
Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
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
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet (2008) 32.08
c-Myc-regulated microRNAs modulate E2F1 expression. Nature (2005) 31.81
Lethality and centrality in protein networks. Nature (2001) 29.64
The large-scale organization of metabolic networks. Nature (2000) 27.57
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature (2003) 26.58
A synthetic oscillatory network of transcriptional regulators. Nature (2000) 24.58
Construction of a genetic toggle switch in Escherichia coli. Nature (2000) 24.02
Principles of microRNA-target recognition. PLoS Biol (2005) 23.70
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
Dicer is essential for mouse development. Nat Genet (2003) 15.87
Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell (2005) 15.38
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
Network motifs: theory and experimental approaches. Nat Rev Genet (2007) 15.04
Selective blockade of microRNA processing by Lin28. Science (2008) 14.39
The TRANSFAC system on gene expression regulation. Nucleic Acids Res (2001) 13.63
Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24
Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet (2004) 12.97
A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature (2003) 12.93
Engineering stability in gene networks by autoregulation. Nature (2000) 12.88
Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A (2003) 12.50
MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16
Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev (2006) 11.04
microRNA target predictions in animals. Nat Genet (2006) 10.76
A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res (2007) 9.61
A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell (2005) 9.22
Transcription regulation and animal diversity. Nature (2003) 9.22
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
A MicroRNA feedback circuit in midbrain dopamine neurons. Science (2007) 8.33
The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci U S A (2005) 8.33
Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci U S A (2007) 7.93
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science (2004) 7.75
Genomics of microRNA. Trends Genet (2006) 7.75
Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature (2002) 7.60
Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science (2007) 7.15
Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11
RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell (2007) 7.06
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81
Post-transcriptional regulation of microRNA expression. RNA (2006) 6.76
DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct (2000) 6.61
Aberrant T cell differentiation in the absence of Dicer. J Exp Med (2005) 6.58
Transcription of eukaryotic protein-coding genes. Annu Rev Genet (2000) 6.12
RNA regulation: a new genetics? Nat Rev Genet (2004) 5.97
The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell (2005) 5.90
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell (2007) 5.67
Canalization of development by microRNAs. Nat Genet (2006) 5.46
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33
MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature (2004) 5.31
T cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer. J Exp Med (2005) 5.26
An E2F/miR-20a autoregulatory feedback loop. J Biol Chem (2006) 5.20
The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat Genet (2003) 4.97
Dicer function is essential for lung epithelium morphogenesis. Proc Natl Acad Sci U S A (2006) 4.87
Direct regulation of an oncogenic micro-RNA cluster by E2F transcription factors. J Biol Chem (2006) 4.57
miR-148 targets human DNMT3b protein coding region. RNA (2008) 4.56
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J (2006) 4.34
Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31
Translational control by the 3'-UTR: the ends specify the means. Trends Biochem Sci (2003) 4.00
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science (2002) 3.93
The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev Biol (2003) 3.92
A gene-centered C. elegans protein-DNA interaction network. Cell (2006) 3.84
MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl Acad Sci U S A (2005) 3.69
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A (2004) 3.60
Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev (2007) 3.56
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46
The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell (2008) 2.19
Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15
MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun (2006) 1.88
The pha-4 gene is required to generate the pharyngeal primordium of Caenorhabditis elegans. Development (1994) 1.85
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics (2007) 1.83
MicroRNA regulation of human protein protein interaction network. RNA (2007) 1.82
microRNA miR-14 acts to modulate a positive autoregulatory loop controlling steroid hormone signaling in Drosophila. Genes Dev (2007) 1.80
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev (2008) 1.42
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet (2003) 4.09
A gene-centered C. elegans protein-DNA interaction network. Cell (2006) 3.84
A first version of the Caenorhabditis elegans Promoterome. Genome Res (2004) 3.29
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
A gateway-compatible yeast one-hybrid system. Genome Res (2004) 3.23
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc (2008) 1.89
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics (2007) 1.83
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res (2011) 1.62
MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development (2002) 1.57
Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell (2013) 1.51
A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol (2011) 1.49
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods (2007) 1.49
C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech Ageing Dev (2006) 1.44
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev (2008) 1.42
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods (2011) 1.41
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol (2010) 1.40
Using networks to measure similarity between genes: association index selection. Nat Methods (2013) 1.30
C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab (2005) 1.28
EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics (2007) 1.26
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol Cell (2013) 1.21
Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet (2011) 1.20
Gateway-compatible yeast one-hybrid screens. CSH Protoc (2006) 1.18
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods (2011) 1.12
Enhanced Y1H assays for Arabidopsis. Nat Methods (2011) 1.10
Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res (2013) 1.06
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res (2009) 1.01
Gene-centered regulatory networks. Brief Funct Genomics (2009) 0.98
Transcription factor functionality and transcription regulatory networks. Mol Biosyst (2008) 0.96
Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol (2002) 0.95
lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics (2005) 0.90
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) (2013) 0.85
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res (2013) 0.84
Gene-centered yeast one-hybrid assays. Methods Mol Biol (2012) 0.81
RNA Interference in Caenorhabditis elegans. Curr Protoc Mol Biol (2015) 0.79
Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6. BMC Dev Biol (2014) 0.77
A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. Gene (2011) 0.75
Getting an edge on human disease. Mol Syst Biol (2009) 0.75
Genomics in 2011: challenges and opportunities. Genome Biol (2011) 0.75
Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits. Cell (2014) 0.75