Alan P. Boyle

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

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

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis -elements where transcription factors bind. Here we demonstrate that data from...

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate t...

Architecture of the human regulatory network derived from ENCODE data

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 th...