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 these programs relate to common physiological traits and diseases.  The lab develops and applies genome-scale molecular and computational methodologies and technologies to a variety of cell and experimental paradigms.

Research areas:

Major ongoing efforts in the Stamatoyannopoulos lab are:

  • To create comprehensive atlases of regulatory DNA in the human and mouse genomes, and to define the occupancy of regulatory DNA by DNA binding proteins at nucleotide resolution;

  • To map and analyze transcription factor regulatory networks;

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

  • To understand, at a fundamental level, how regulatory information is encoded within the human genome, from individual nucleotides to chromosomal patterns of regulatory DNA actuation

  • To define the process by which a normal cell, with a normal genome, commits to malignant transformation

Selected Publications:

Stergachis AB et al. (2013).  Exonic transcription factor binding directs codon choice and impacts protein evolution.  Science 342:1367-72.

Vierstra J et al. (2013).  Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.  Nature Methods, 11:66-72.

Stergachis AB, Neph S et al.  (2013).  Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.  Cell 154:888-903

Mercer TR et al.  (2013).  DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements.  Nature Genetics 45:852-9

Neph SJ, Viertstra J et al.  (2012).  An expansive human cis-regulatory lexicon encoded in transcription factor footprints.  Nature 489:83-90.

Thurman RT, Rynes E., et al., (2012) The accessible chromatin landscape of the human genome.  Nature 489:75-82.

Maurano MT et al.  (2012). Systematic localization of common disease-associated variation in regulatory DNA. Science  337:1190-5.

Neph SJ. Stergachis AB et al.  (2012).  Circuitry and dynaomics of human transcription factor regulatory networks.  Cell 150:1274-86.

John S, Sabo PJ et al. (2011).  Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.  Nature Genetics, 43:264-8.