It is well established that the vast majority of human RNA transcripts do not encode for
proteins and that non-coding RNAs regulate cell physiology and shape cellular functions. A …

Networks of regulatory enhancers dictate distinct cell identities and cellular responses to
diverse signals by instructing precise spatiotemporal patterns of gene expression. However …

Functional genomics assays based on high-throughput sequencing greatly expand our
ability to understand the genome. Here, we define the ENCODE blacklist-a comprehensive …

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The
identification of TF–target regulatory relationships is a key step for revealing functions of TFs …

Self-organizing maps (SOMs) are popular tools for grouping and visualizing data in many
areas of science. This paper describes recent changes in package kohonen, implementing …

Twenty-nine years following the breakthrough discovery that a single-gene mutation of daf-2
doubles Caenorhabditis elegans lifespan, it remains unclear where this insulin/IGF-1 …

Abstract The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of
creating a comprehensive catalog of functional elements in the human genome. This phase …

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly
distinctive genomes that have been sculpted by two whole-genome duplications. Here we …

Next-generation sequencing (NGS) technologies using DNA, RNA, or methylation
sequencing have impacted enormously on the life sciences. NGS is the choice for large …

Genome function is dynamically regulated in part by chromatin, which consists of the
histones, non-histone proteins and RNA molecules that package DNA. Studies in …