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Open AccessA new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species
Comparative analyses between traditional model organisms, such as the fruit fly Drosophila melanogaster, and more recent model organisms, such as the red flour beetle Tribolium castaneum, have provided a wealth o...
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Article
Open AccessReporter gene assays and chromatin-level assays define substantially non-overlap** sets of enhancer sequences
Transcriptional enhancers are essential for gene regulation, but how these regulatory elements are best defined remains a significant unresolved question. Traditional definitions rely on activity-based criteri...
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Article
Open AccessPeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map
The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 ...
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Article
Open AccessComputational enhancer prediction: evaluation and improvements
Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods f...
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CRM Discovery Beyond Model Insects
Although the number of sequenced insect genomes numbers in the hundreds, little is known about gene regulatory sequences in any species other than the well-studied Drosophila melanogaster. We provide here a detai...
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Insect Regulatory Genomics
Insects are the most diverse and ecologically important group of animals in the animal kingdom, with more than a million species described to date. Whole-genome sequencing, which has revolutionized many areas ...
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Article
Open AccessErroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules
Cis-regulatory modules are bound by transcription factors to regulate gene expression. Characterizing these DNA sequences is central to understanding gene regulatory networks and gaining insight into mechanisms o...
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Article
Open AccessGenome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland
The ETS transcription factor Elf5 (also known as ESE-2) is highly expressed in the mammary gland and plays an important role in its development and differentiation. Indeed studies in mice have illustrated an e...
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Article
Open AccessPreferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for...
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Article
Open AccessComplex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster
The promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating tempora...
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Open AccessComputational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a ...
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Article
Open AccessLarge-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Transcriptional cis-regulatory modules (for example, enhancers) play a critical role in regulating gene expression. While many individual regulatory elements have been characterized, they have never been analyzed...
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Article
(Re)modeling the transcriptional enhancer
Transcriptional cis-regulatory modules have a fundamental role in regulating eukaryotic gene expression. A new study shows how computational modeling can test hypotheses about how regulatory elements function,...
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Open AccessPreferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
As more methods are developed to analyze RNA-profiling data, assessing their performance using control datasets becomes increasingly important.
