In 2005, Stamatoyannopoulos joined the Departments of Genome Sciences and Medicine at the
University of Washington. He later served as the
principal investigator leading the University's participation in the
ENCODE project and as director of the Northwest Reference Epigenome Mapping Center.[11] He was a member of the editorial board of
Genome Research and in 2009 was elected to the
American Society for Clinical Investigation.[10] In 2015, the
National Human Genome Research Institute awarded Dr. Stamatoyannopoulos $10 million to create a new Center of Excellence in Genomic Science, the Center for Photogenomics, with the focus of developing high speed imaging technology to replace traditional DNA sequencing methods.[12][13]
Stamatoyannopoulos is a member of the
ENCODE project, and in 2012 led the international ENCODE consortium in publishing a series of papers in
Nature which promoted the significance of regulatory regions within the genome.[6][14] His
ENCODE research provided the first detailed map of gene controlling regulatory DNA and a dictionary of the genome's programming language—instructions written within the DNA.[15]