[HTML][HTML] Integrative analysis of 111 reference human epigenomes

…, A Milosavljevic, B Ren, JA Stamatoyannopoulos… - Nature, 2015 - nature.com
The reference human genome sequence set the stage for studies of genetic variation and
its association with human disease, but epigenomic studies lack a similar reference. To …

[HTML][HTML] The accessible chromatin landscape of the human genome

…, J Dekker, GE Crawford, JA Stamatoyannopoulos - Nature, 2012 - nature.com
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …

Systematic localization of common disease-associated variation in regulatory DNA

…, I Glass, SR Sunyaev, R Kaul, JA Stamatoyannopoulos - Science, 2012 - science.org
Genome-wide association studies have identified many noncoding variants associated with
common diseases and traits. We show that these variants are concentrated in regulatory …

The NIH roadmap epigenomics mapping consortium

BE Bernstein, JA Stamatoyannopoulos… - Nature …, 2010 - nature.com
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of
epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal …

The ENCODE (ENCyclopedia of DNA elements) project

…, G Stamatoyannopoulos, JA Stamatoyannopoulos… - Science, 2004 - scholarworks.bwise.kr
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 …

[HTML][HTML] Expanded encyclopaedias of DNA elements in the human and mouse genomes

…, RC Hardison, TR Gingeras, JA Stamatoyannopoulos… - Nature, 2020 - nature.com
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 these …

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

…, A Sidow, M Slattery, JA Stamatoyannopoulos… - Genome …, 2012 - genome.cshlp.org
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 …

[HTML][HTML] A comparative encyclopedia of DNA elements in the mouse genome

…, A Mortazavi, SM Weissman, JA Stamatoyannopoulos… - Nature, 2014 - nature.com
The laboratory mouse shares the majority of its protein-coding genes with humans, making
it the premier model organism in biomedical research, yet the two mammals differ in …

[HTML][HTML] Quantifying similarity between motifs

S Gupta, JA Stamatoyannopoulos, TL Bailey… - Genome biology, 2007 - Springer
… John A Stamatoyannopoulos … Where N o ja = N ja is the 'observed' count of letter a in column
j, and N e ja = N j N a /N is the 'expected' count of letter a at column j (Table 3 for definitions)…

[HTML][HTML] Guidelines for investigating causality of sequence variants in human disease

…, SM Leal, LA Pennacchio, JA Stamatoyannopoulos… - Nature, 2014 - nature.com
The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing
disease-causing sequence variants from the many potentially functional variants present in …