Published in Proc Natl Acad Sci U S A on July 09, 2002
LIN-12/Notch activation leads to microRNA-mediated down-regulation of Vav in C. elegans. Science (2005) 4.28
Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res (2003) 3.99
Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol (2004) 3.47
Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc Natl Acad Sci U S A (2004) 3.39
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics (2005) 3.23
Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol (2005) 2.50
Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics (2003) 2.06
Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci U S A (2007) 1.98
A survey of motif discovery methods in an integrated framework. Biol Direct (2006) 1.94
Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. PLoS Comput Biol (2006) 1.88
Whole-genome analysis of temporal gene expression during foregut development. PLoS Biol (2004) 1.81
A common set of DNA regulatory elements shapes Drosophila appendages. Dev Cell (2013) 1.79
Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet (2012) 1.65
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res (2004) 1.52
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res (2004) 1.45
MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res (2004) 1.44
DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res (2008) 1.42
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol (2007) 1.38
Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput (2005) 1.33
Identification of genomic sites that bind the Drosophila suppressor of Hairy-wing insulator protein. Mol Cell Biol (2006) 1.31
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol (2008) 1.29
Identification of transcriptional targets of the dual-function transcription factor/phosphatase eyes absent. Dev Biol (2007) 1.23
cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Mol Cell Biol (2005) 1.23
An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Nucleic Acids Res (2008) 1.22
Using hexamers to predict cis-regulatory motifs in Drosophila. BMC Bioinformatics (2005) 1.16
Spalt mediates an evolutionarily conserved switch to fibrillar muscle fate in insects. Nature (2011) 1.13
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res (2008) 1.11
Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos Trans R Soc Lond B Biol Sci (2013) 1.06
Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02
Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors. Development (2010) 1.01
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol Biol (2007) 1.00
Genome-wide view of cell fate specification: ladybird acts at multiple levels during diversification of muscle and heart precursors. Genes Dev (2007) 0.98
Comparative analysis of regulatory motif discovery tools for transcription factor binding sites. Genomics Proteomics Bioinformatics (2007) 0.95
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PLoS One (2007) 0.95
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics (2007) 0.93
Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny. Proc Natl Acad Sci U S A (2010) 0.92
Genome-wide prediction, display and refinement of binding sites with information theory-based models. BMC Bioinformatics (2003) 0.92
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90
Drosophila Hey is a target of Notch in asymmetric divisions during embryonic and larval neurogenesis. Development (2010) 0.90
The Him gene reveals a balance of inputs controlling muscle differentiation in Drosophila. Curr Biol (2007) 0.89
Statistical detection of cooperative transcription factors with similarity adjustment. Bioinformatics (2009) 0.87
Notch regulates numb: integration of conditional and autonomous cell fate specification. Development (2010) 0.86
Ancestral and conserved cis-regulatory architectures in developmental control genes. Dev Biol (2011) 0.84
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. Nucleic Acids Res (2014) 0.83
Tools and methods for studying Notch signaling in Drosophila melanogaster. Methods (2014) 0.82
Identifying transcriptional cis-regulatory modules in animal genomes. Wiley Interdiscip Rev Dev Biol (2014) 0.82
Novel cis-regulatory modules control expression of the Hairy and Enhancer of Split-1 (HES1) transcription factor in myoblasts. J Biol Chem (2011) 0.82
Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. Nucleic Acids Res (2013) 0.82
Regulation of broad by the Notch pathway affects timing of follicle cell development. Dev Biol (2014) 0.81
Glycolysis supports embryonic muscle growth by promoting myoblast fusion. Proc Natl Acad Sci U S A (2013) 0.81
DISCOVER: a feature-based discriminative method for motif search in complex genomes. Bioinformatics (2009) 0.81
Regulation and functions of the lms homeobox gene during development of embryonic lateral transverse muscles and direct flight muscles in Drosophila. PLoS One (2010) 0.80
Muscle niche-driven Insulin-Notch-Myc cascade reactivates dormant Adult Muscle Precursors in Drosophila. Elife (2015) 0.80
Fast comparison of DNA sequences by oligonucleotide profiling. BMC Res Notes (2008) 0.80
Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function. Proc Natl Acad Sci U S A (2014) 0.79
Single-minded, Dmef2, Pointed, and Su(H) act on identified regulatory sequences of the roughest gene in Drosophila melanogaster. Dev Genes Evol (2005) 0.78
Recent computational approaches to understand gene regulation: mining gene regulation in silico. Curr Genomics (2007) 0.76
Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture. Curr Genomics (2005) 0.76
Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila. BMC Genomics (2003) 0.76
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. BMC Bioinformatics (2016) 0.75
Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density. PLoS One (2015) 0.75
Excessive Dpp signaling induces cardial apoptosis through dTAK1 and dJNK during late embryogenesis of Drosophila. J Biomed Sci (2011) 0.75
Tandem machine learning for the identification of genes regulated by transcription factors. BMC Bioinformatics (2005) 0.75
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. BMC Bioinformatics (2011) 0.75
An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. Front Genet (2017) 0.75
The genome sequence of Drosophila melanogaster. Science (2000) 74.32
Notch signaling: cell fate control and signal integration in development. Science (1999) 28.83
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56
Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A (2001) 6.39
Suppressor of hairless directly activates transcription of enhancer of split complex genes in response to Notch receptor activity. Genes Dev (1995) 4.47
GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques (2000) 3.98
The suppressor of hairless protein participates in notch receptor signaling. Cell (1994) 3.81
The Bearded box, a novel 3' UTR sequence motif, mediates negative post-transcriptional regulation of Bearded and Enhancer of split Complex gene expression. Development (1997) 3.75
The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development (1998) 3.52
Recognition sequence of a highly conserved DNA binding protein RBP-J kappa. Nucleic Acids Res (1994) 3.36
Groucho/TLE family proteins and transcriptional repression. Gene (2000) 3.31
The neurogenic suppressor of hairless DNA-binding protein mediates the transcriptional activation of the enhancer of split complex genes triggered by Notch signaling. Genes Dev (1995) 3.24
Suppressor of Hairless, the Drosophila homolog of the mouse recombination signal-binding protein gene, controls sensory organ cell fates. Cell (1992) 2.95
The Drosophila rhomboid gene mediates the localized formation of wing veins and interacts genetically with components of the EGF-R signaling pathway. Genes Dev (1993) 2.08
Discrete enhancer elements mediate selective responsiveness of enhancer of split complex genes to common transcriptional activators. Dev Biol (1999) 2.07
The Notch signalling pathway is required for Enhancer of split bHLH protein expression during neurogenesis in the Drosophila embryo. Development (1994) 2.07
Comparative analysis of the human and mouse Hey1 promoter: Hey genes are new Notch target genes. Biochem Biophys Res Commun (2000) 2.06
Repression by suppressor of hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo. Genes Dev (2000) 1.87
A genomewide survey of basic helix-loop-helix factors in Drosophila. Proc Natl Acad Sci U S A (2000) 1.72
Structure and regulation of a complex locus: the cut gene of Drosophila. Genetics (1995) 1.71
A notch-independent activity of suppressor of hairless is required for normal mechanoreceptor physiology. Cell (2000) 1.70
Cells with persistent twist expression are the embryonic precursors of adult muscles in Drosophila. Development (1991) 1.64
Regulation of Drosophila neurogenesis by RNA:RNA duplexes? Cell (1998) 1.62
The myogenic regulatory gene Mef2 is a direct target for transcriptional activation by Twist during Drosophila myogenesis. Genes Dev (1998) 1.56
The enhancer of split complex of Drosophila includes four Notch-regulated members of the bearded gene family. Development (2000) 1.43
Molecular analysis of the neurogenic locus Enhancer of split of Drosophila melanogaster. EMBO J (1987) 1.42
Antagonism of notch signaling activity by members of a novel protein family encoded by the bearded and enhancer of split gene complexes. Development (2000) 1.25
Muscle pattern diversification in Drosophila: the story of imaginal myogenesis. Bioessays (1999) 1.16
The mesoderm determinant snail collaborates with related zinc-finger proteins to control Drosophila neurogenesis. EMBO J (1999) 1.16
Synergy between suppressor of Hairless and Notch in regulation of Enhancer of split m gamma and m delta expression. Mol Cell Biol (1997) 1.11
Distinct expression patterns of different enhancer of split bHLH genes during embryogenesis of Drosophila melanogaster. Dev Genes Evol (1999) 1.02
Dynamic expression of Drosophila TRAF1 during embryogenesis and larval development. Mech Dev (2001) 0.97
Specificity of CNS and PNS regulatory subelements comprising pan-neural enhancers of the deadpan and scratch genes is achieved by repression. Development (1995) 0.92
Cell-type specific modular regulation of derailed in the Drosophila nervous system. Mech Dev (1999) 0.81
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
KCNQ potassium channel mutations cause cardiac arrhythmias in Drosophila that mimic the effects of aging. Proc Natl Acad Sci U S A (2007) 3.30
New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP. Biotechniques (2004) 2.82
Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling. Genes Dev (2002) 2.77
Default repression and Notch signaling: Hairless acts as an adaptor to recruit the corepressors Groucho and dCtBP to Suppressor of Hairless. Genes Dev (2002) 1.87
Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A (2011) 1.60
Genetic programs activated by proneural proteins in the developing Drosophila PNS. Dev Cell (2005) 1.54
Lateral inhibition in proneural clusters: cis-regulatory logic and default repression by Suppressor of Hairless. Development (2005) 1.41
GenePalette: a universal software tool for genome sequence visualization and analysis. Dev Biol (2004) 1.35
Upd/Jak/STAT signaling represses wg transcription to allow initiation of morphogenetic furrow in Drosophila eye development. Dev Biol (2007) 0.97
Complex interplay of three transcription factors in controlling the tormogen differentiation program of Drosophila mechanoreceptors. Dev Biol (2009) 0.96
A major role for zygotic hunchback in patterning the Nasonia embryo. Development (2005) 0.95
Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules. PLoS Genet (2012) 0.90
An ancient transcriptional regulatory linkage. Dev Biol (2005) 0.88
Notch regulates numb: integration of conditional and autonomous cell fate specification. Development (2010) 0.86
Identification of hunchback cis-regulatory DNA conferring temporal expression in neuroblasts and neurons. Gene Expr Patterns (2011) 0.85
Ancestral and conserved cis-regulatory architectures in developmental control genes. Dev Biol (2011) 0.84
Both inhibition and activation of Notch signaling rely on a conserved Neuralized-binding motif in Bearded proteins and the Notch ligand Delta. Dev Biol (2009) 0.84