The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Umap and Bismap: quantifying genome and methylome mappability

(2018) Mehran Karimzadeh et al.   NUCLEIC ACIDS RESEARCH

Deciphering ENCODE

(2016) Adam G. Diehl et al.   TRENDS IN GENETICS

Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases

(2014) Wentian Li et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA