All vertebrates possess anatomical features not seen in their closest living relatives, the
protochordates (tunicates and amphioxus). Some of these features depend on develop mental …

Phylogenetic analyses and sequence surveys of developmental regulator gene families
indicate that two large-scale gene duplications, most likely genome duplications, occurred in …

We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements
in the human genome sequence. The pilot phase of the Project is focused on a specified …

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq)
has become a valuable and widely used approach for mapping the genomic location of …

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes;
the ensemble of these binding events forms a regulatory network, constituting the wiring …

Comparisons of orthologous genomic DNA sequences can be used to characterize regions
that have been subject to purifying selection and are enriched for functional elements. We …

Molecular interactions between protein complexes and DNA mediate essential gene-regulatory
functions. Uncovering such interactions by chromatin immunoprecipitation coupled with …

To compare entire genomes from different species, biologists increasingly need alignment
methods that are efficient enough to handle long sequences, and accurate enough to …

The development of Next Generation Sequencing technologies, capable of sequencing
hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to …