| review article | Q7318358 |
| scholarly article | Q13442814 |
| P50 | author | Kushal Suryamohan | Q51733962 |
| P2093 | author name string | Marc S Halfon | |
| P2860 | cites work | Highly conserved non-coding sequences are associated with vertebrate development | Q21092819 |
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| Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm | Q21563555 | ||
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| Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo | Q24530508 | ||
| Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | Q24534193 | ||
| TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes | Q24538709 | ||
| Sequence logos: a new way to display consensus sequences | Q24598387 | ||
| REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila | Q24607002 | ||
| UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions | Q24607175 | ||
| FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system | Q24609505 | ||
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| Global mapping of protein-DNA interactions in vivo by digital genomic footprinting | Q37157318 | ||
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| Hox gene evolution: multiple mechanisms contributing to evolutionary novelties | Q37982757 | ||
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| Genomic approaches towards finding cis-regulatory modules in animals | Q38019305 | ||
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| Multiple layers of complexity in cis-regulatory regions of developmental genes | Q38042890 | ||
| Chromatin looping and organization at developmentally regulated gene loci | Q38135369 | ||
| Enhancer biology and enhanceropathies | Q38193691 | ||
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| Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo | Q38304339 | ||
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| Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). | Q38355701 | ||
| The Drosophila anatomy ontology | Q38442731 | ||
| Cluster-Buster: Finding dense clusters of motifs in DNA sequences. | Q39804240 | ||
| Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer | Q39846861 | ||
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| Homotypic regulatory clusters in Drosophila. | Q34994285 | ||
| Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. | Q35004175 | ||
| A model for all genomes: the role of transcription factories | Q35009288 | ||
| Combinatorial binding predicts spatio-temporal cis-regulatory activity | Q35011328 | ||
| Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster | Q35033165 | ||
| Widespread misinterpretable ChIP-seq bias in yeast | Q35071005 | ||
| Rapid evolutionary rewiring of a structurally constrained eye enhancer | Q35127076 | ||
| FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells | Q35128053 | ||
| The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity | Q35153238 | ||
| Integrating diverse datasets improves developmental enhancer prediction | Q35195359 | ||
| A cis-regulatory map of the Drosophila genome. | Q35229726 | ||
| Discriminative prediction of mammalian enhancers from DNA sequence. | Q35581580 | ||
| Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. | Q35617204 | ||
| Large-scale discovery of enhancers from human heart tissue | Q35635739 | ||
| ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments | Q35676599 | ||
| Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting | Q35748712 | ||
| Evolutionary origins of transcription factor binding site clusters | Q35753857 | ||
| Applied bioinformatics for the identification of regulatory elements | Q35766840 | ||
| In silico representation and discovery of transcription factor binding sites | Q35895069 | ||
| Comparative genomics | Q35918528 | ||
| Unsupervised pattern discovery in human chromatin structure through genomic segmentation | Q35923331 | ||
| Enhancers: emerging roles in cell fate specification | Q35931823 | ||
| A brief review of computational gene prediction methods. | Q36131382 | ||
| i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules | Q36180297 | ||
| Importance of low affinity Elf-1 sites in the regulation of lymphoid-specific inducible gene expression | Q36365913 | ||
| Complex effects of nucleotide variants in a mammalian cis-regulatory element. | Q36436964 | ||
| DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila | Q36504410 | ||
| Computational identification of transcriptional regulatory elements in DNA sequence | Q36541365 | ||
| ChromHMM: automating chromatin-state discovery and characterization | Q36625108 | ||
| Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses | Q36672362 | ||
| Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs | Q36673507 | ||
| Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. | Q36701644 | ||
| Evaluation of methods for modeling transcription factor sequence specificity | Q36941693 | ||
| VISTA Enhancer Browser--a database of tissue-specific human enhancers | Q24676452 | ||
| Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo | Q24794169 | ||
| Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila | Q24796663 | ||
| Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura | Q24801531 | ||
| Human-zebrafish non-coding conserved elements act in vivo to regulate transcription | Q24816250 | ||
| Enhancer RNAs and regulated transcriptional programs | Q26865277 | ||
| Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome | Q28131828 | ||
| Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase | Q28140783 | ||
| DNA binding sites: representation and discovery | Q28144459 | ||
| Scanning Human Gene Deserts for Long-Range Enhancers | Q28210571 | ||
| ChIP-seq accurately predicts tissue-specific activity of enhancers | Q28235102 | ||
| Histone modifications at human enhancers reflect global cell-type-specific gene expression | Q28238467 | ||
| Gene Regulation for Higher Cells: A Theory | Q28256064 | ||
| A transcription factor collective defines cardiac cell fate and reflects lineage history | Q28258920 | ||
| High-resolution mapping and characterization of open chromatin across the genome | Q28266995 | ||
| ChIP-Seq identification of weakly conserved heart enhancers | Q28291198 | ||
| Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project | Q28301622 | ||
| Single-copy nuclear genes resolve the phylogeny of the holometabolous insects | Q28752290 | ||
| Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities | Q29301030 | ||
| A unique chromatin signature uncovers early developmental enhancers in humans | Q29614327 | ||
| Identifying DNA and protein patterns with statistically significant alignments of multiple sequences | Q29615307 | ||
| The long-range interaction landscape of gene promoters | Q29615403 | ||
| A map of the cis-regulatory sequences in the mouse genome | Q29615404 | ||
| In vivo enhancer analysis of human conserved non-coding sequences | Q29616554 | ||
| Identification of functional elements and regulatory circuits by Drosophila modENCODE | Q29617551 | ||
| The NIH Roadmap Epigenomics Mapping Consortium | Q29619856 | ||
| Automated protein-DNA interaction screening of Drosophila regulatory elements | Q30442866 | ||
| Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition | Q30476628 | ||
| JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles | Q30486475 | ||
| kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets | Q30648830 | ||
| SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. | Q30702540 | ||
| MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules | Q30837902 | ||
| CLARE: Cracking the LAnguage of Regulatory Elements | Q31044057 | ||
| Practical strategies for discovering regulatory DNA sequence motifs | Q33242798 | ||
| Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data | Q33287630 | ||
| KIRMES: kernel-based identification of regulatory modules in euchromatic sequences | Q33434261 | ||
| Computational methods for the detection of cis-regulatory modules | Q33460920 | ||
| Genome-wide discovery of human heart enhancers | Q33523952 | ||
| Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites | Q33524650 | ||
| Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers | Q33526988 | ||
| Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers | Q33549139 | ||
| Function-based identification of mammalian enhancers using site-specific integration | Q33559746 | ||
| Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. | Q33644434 | ||
| Regulation of gene expression via the core promoter and the basal transcriptional machinery. | Q33695416 | ||
| Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. | Q33698455 | ||
| Assessing computational methods of cis-regulatory module prediction | Q33769725 | ||
| Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities | Q33881396 | ||
| Evidence for stabilizing selection in a eukaryotic enhancer element. | Q33890254 | ||
| Conserved noncoding sequences are reliable guides to regulatory elements. | Q33916564 | ||
| Genome-wide quantitative enhancer activity maps identified by STARR-seq | Q34035127 | ||
| Expression of a β-globin gene is enhanced by remote SV40 DNA sequences | Q34055192 | ||
| De novo discovery of a tissue-specific gene regulatory module in a chordate | Q34056053 | ||
| An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes | Q34070737 | ||
| Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules | Q34083301 | ||
| Nuclease hypersensitive sites in chromatin | Q34164152 | ||
| Massively parallel functional dissection of mammalian enhancers in vivo | Q34174436 | ||
| Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay | Q34174445 | ||
| Alignment-free sequence comparison-a review | Q34180455 | ||
| Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution | Q34239260 | ||
| Barcoded DNA-tag reporters for multiplex cis-regulatory analysis | Q34259835 | ||
| Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters | Q34276083 | ||
| Modification of enhancer chromatin: what, how, and why? | Q34331930 | ||
| Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules | Q34335532 | ||
| A CRISPR view of development | Q34342877 | ||
| High-throughput functional testing of ENCODE segmentation predictions. | Q34350068 | ||
| Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. | Q34354921 | ||
| What is a hidden Markov model? | Q34356820 | ||
| Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos | Q34357459 | ||
| Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position | Q34375601 | ||
| Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? | Q34391887 | ||
| Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution | Q34423553 | ||
| Evidence for deep regulatory similarities in early developmental programs across highly diverged insects | Q34443568 | ||
| What are DNA sequence motifs? | Q34566348 | ||
| Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling | Q34649230 | ||
| A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system | Q34760479 | ||
| Molecular mechanisms of selector gene function and evolution | Q34801972 | ||
| Extensive low-affinity transcriptional interactions in the yeast genome | Q34881942 | ||
| Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model | Q39860941 | ||
| Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. | Q39935609 | ||
| Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance | Q40607315 | ||
| Common themes in the function of transcription and splicing enhancers | Q41477035 | ||
| The hardwiring of development: organization and function of genomic regulatory systems. | Q41486875 | ||
| HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature | Q41766976 | ||
| Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins | Q41836932 | ||
| ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy | Q41849576 | ||
| Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression | Q41995414 | ||
| Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse | Q42594046 | ||
| Modeling the specificity of protein-DNA interactions | Q42738475 | ||
| Evolution of transcriptional enhancers and animal diversity. | Q42909090 | ||
| Genome-scale functional characterization of Drosophila developmental enhancers in vivo | Q44998927 | ||
| ChIP-seq: welcome to the new frontier | Q47597783 | ||
| A statistical model for locating regulatory regions in genomic DNA. | Q48050889 | ||
| Enhancer loops appear stable during development and are associated with paused polymerase. | Q50647626 | ||
| Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. | Q50775300 | ||
| A probabilistic method to detect regulatory modules. | Q50792656 | ||
| Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. | Q51827112 | ||
| Promoter prediction analysis on the whole human genome. | Q51984804 | ||
| Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors. | Q52163714 | ||
| Identification of regulatory regions which confer muscle-specific gene expression. | Q52242949 | ||
| Quantification of insect genome divergence | Q56625465 | ||
| (Re)modeling the transcriptional enhancer | Q79151093 | ||
| P433 | issue | 2 | |
| P304 | page(s) | 59-84 | |
| P577 | publication date | 2014-12-29 | |
| P1433 | published in | Wiley interdisciplinary reviews. Developmental biology | Q26842107 |
| P1476 | title | Identifying transcriptional cis-regulatory modules in animal genomes | |
| P478 | volume | 4 |
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