Learn More
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described(More)
Transposable elements are viewed as 'selfish genetic elements', yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up(More)
A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active(More)
y These authors contributed equally to this work. zAuthors are listed in the descending order based on their microattributions credits in the Zebrafish GenomeWiki database. §Authors provided technical assistance for creating and maintaining the database and related infrastructure. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail(More)
y These authors contributed equally to this work. zAuthors are listed in the descending order based on their microattributions credits in the Zebrafish GenomeWiki database. §Authors provided technical assistance for creating and maintaining the database and related infrastructure. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail(More)
Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target(More)
  • 1