Published in J Cell Biochem on April 01, 2005
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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol (2012) 3.52
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A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer. Genes Dev (2006) 2.76
Selective transcription in response to an inflammatory stimulus. Cell (2010) 2.75
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Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet (2012) 1.68
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The role of transposable elements in the regulation of IFN-lambda1 gene expression. Proc Natl Acad Sci U S A (2009) 1.24
cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Mol Cell Biol (2005) 1.23
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PLoS One (2009) 1.13
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet (2012) 1.10
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell (2012) 1.07
A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep (2014) 1.05
Evolutionary origins of transcription factor binding site clusters. Mol Biol Evol (2011) 1.05
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A closer look at the eve stripe 2 enhancers of Drosophila and Themira. PLoS Genet (2008) 1.04
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Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biol (2007) 0.99
Localization of the cis-enhancer element for mouse type X collagen expression in hypertrophic chondrocytes in vivo. J Bone Miner Res (2009) 0.99
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Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
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Functional anatomy of distant-acting mammalian enhancers. Philos Trans R Soc Lond B Biol Sci (2013) 0.91
Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet (2011) 0.91
Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet (2014) 0.91
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res (2015) 0.91
General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda. Nucleic Acids Res (2007) 0.90
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res (2014) 0.90
Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules. PLoS Genet (2012) 0.90
The untranslated exon B of human surfactant protein A2 mRNAs is an enhancer for transcription and translation. Am J Physiol Lung Cell Mol Physiol (2011) 0.89
Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis. Development (2009) 0.88
Investigating the transcriptional control of cardiovascular development. Circ Res (2015) 0.87
Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philos Trans R Soc Lond B Biol Sci (2013) 0.87
Analysis of functional importance of binding sites in the Drosophila gap gene network model. BMC Genomics (2015) 0.87
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res (2013) 0.86
Deciphering the genome's regulatory code: the many languages of DNA. Bioessays (2010) 0.85
Formation of regulatory modules by local sequence duplication. PLoS Comput Biol (2011) 0.85
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. Bioinformatics (2012) 0.85
Ancestral and conserved cis-regulatory architectures in developmental control genes. Dev Biol (2011) 0.84
Dramatic changes in transcription factor binding over evolutionary time. Genome Biol (2010) 0.84
Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. Bioinformatics (2013) 0.84
Association of C1QB gene polymorphism with schizophrenia in Armenian population. BMC Med Genet (2011) 0.84
Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet (2016) 0.84
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. Genome Res (2016) 0.83
Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics (2009) 0.83
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. Nucleic Acids Res (2014) 0.83
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A competition mechanism for a homeotic neuron identity transformation in C. elegans. Dev Cell (2015) 0.82
Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Rep (2015) 0.82
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution. Cell (2016) 0.82
Sequence-based model of gap gene regulatory network. BMC Genomics (2014) 0.81
Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA. Development (2013) 0.81
HOT DNAs: a novel class of developmental enhancers. Genes Dev (2012) 0.80
ChIPs and regulatory bits. Nat Biotechnol (2010) 0.79
How to tune an enhancer. Proc Natl Acad Sci U S A (2016) 0.79
Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. Brief Funct Genomics (2012) 0.79
The Lineage-Specific Transcription Factor PU.1 Prevents Polycomb-Mediated Heterochromatin Formation at Macrophage-Specific Genes. Mol Cell Biol (2015) 0.78
Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Res (2016) 0.78
Viral enhancer mimicry of host innate-immune promoters. PLoS Pathog (2014) 0.78
metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PLoS Comput Biol (2016) 0.78
The epigenomics of schizophrenia, in the mouse. Am J Med Genet B Neuropsychiatr Genet (2017) 0.77
Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence. PLoS Genet (2015) 0.77
Learning the transcriptional regulatory code. Mol Syst Biol (2009) 0.76
A comparison of midline and tracheal gene regulation during Drosophila development. PLoS One (2014) 0.76
Genome-wide errant targeting by Hairy. Elife (2015) 0.76
Synthetic promoters in planta. Planta (2015) 0.75
An enhancer-blocking element regulates the cell-specific expression of alcohol dehydrogenase 7. Gene (2014) 0.75
Genome-wide identification of hypoxia-induced enhancer regions. PeerJ (2015) 0.75
Assessing constraints on the path of regulatory sequence evolution. Philos Trans R Soc Lond B Biol Sci (2013) 0.75
Enhanceosome transcription factors preferentially dimerize with high mobility group proteins. BMC Syst Biol (2016) 0.75
TrFAST: a tool to predict signaling pathway-specific transcription factor binding sites. Genomics Proteomics Bioinformatics (2012) 0.75
A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes. PLoS Genet (2016) 0.75
Conserved Cis-Regulatory Modules Control Robustness in Msx1 Expression at Single-Cell Resolution. Genome Biol Evol (2015) 0.75
Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol (2016) 0.75
GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays. G3 (Bethesda) (2015) 0.75
Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration. Mol Biol Evol (2016) 0.75
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. Elife (2017) 0.75
An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. Front Genet (2017) 0.75