John Stamatoyannopoulos

Associate Professor of Genome Sciences and Medicine

phone (Foege office): (206) 685-2672 | fax: (206) 267-1094
phone (Elliott lab office): (206) 267-1098
Foege S-310A, Box 355065
jstam [ a t ]

Dr. Stamatoyannopoulos' laboratory focuses on how the human genome encodes transcriptional regulatory programs that unfold during development and differentiation, and how defects in these programs underlie common diseases.  

Research areas:

Ongoing efforts in the Stamatoyannopoulos lab:

  • To understand how and where regulatory information is encoded within the human genome, from individual nucleotides to genome-scale patterns of regulatory DNA activation

  • To define and analyze transcription factor regulatory networks

  • To map and determine the functional consequences of disease-associated non-coding variation in regulatory DNA

  • To define the genomic regulatory mechanisms underlying the genesis and perpetuation of cancer

  • To create next-generation technologies for visualizing and analyzing the living regulatory genome

Selected Publications:

The accessible chromatin landscape of the human genome.  Nature 489:75-82, 2012.

Systematic localization of common disease-associated variation in regulatory DNA. Science  337:1190-5, 2012.

Circuitry and dynaomics of human transcription factor regulatory networks.  Cell 150:1274-86, 2012.

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.  Cell 154:888-903, 2013.

Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature 489:83-90, 2012.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.  Science 346:1007-12, 2014.

Exonic transcription factor binding directs codon choice and impacts protein evolution.  Science 342:1367-72, 2013.

An expansive human cis-regulatory lexicon encoded in transcription factor footprints.  Nature 489:83-90, 2012.

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.  Nature Methods, 11:66-72, 2013.