John Stamatoyannopoulos
Assistant Professor of Genome Sciences

The Stamatoyannopoulos lab combines classical molecular biology with high-throughput instrumentation and informatics to address basic questions about genome organization, evolution, and function. The information content of the human genome comprises not only the primary genome sequence, but the 2- and 3-dimensional organization of the genome within the living cell nucleus. Ultimately, we seek to understand the relationship between the physical structure of the living genome and its function – and how that function may go awry in disease.

Considerable emphasis is placed on development of novel high-throughput technologies for genomics applications including:

• Genome-scale mapping of chromatin structure and DNaseI hypersensitive sites
• Large-scale characterization of cis-regulatory sequences
• Profiling DNA methylation
• Identification of functional human regulatory variation

Major biological, physiological, and disease area emphases include:

• Chromatin ‘programming’ during development and differentiation
• Inherited variation in human gene regulation
• Regulatory genomics of:
• cancer
• inflammatory pathways and disorders
• diabetes and metabolic syndrome
• color vision
• Systems biology of gene regulation, mapping cis- and trans-regulatory networks
• Regulatory genetic modifiers of Mendelian disorders

Postdoctoral opportunities are currently available in both experimental and computational chromatin biology. See the Nature or Science career websites for more details.

Several projects are available for Graduate rotation students.

Publications:

The ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:782-3

Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. (2007) Identification of higher-order functional domains in the human genome. Genome Research 17:917-27.

Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos, JA. (2007) Widely distributed non-coding selection in the human genome.,Proc Nat'l Acad Sci USA 104:12410-5.

Schoenborn JR, Dorschner M, Sekimata M, Shnyreva M, Gilbertson D, Fitzpatrick D, Stamatoyannopoulos JA, Wilson CB. (2007) Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing Ifng transcription. Nature Immunology 8:732-42.

Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. (2006). Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3:511-8.

Noble WS, Kuehn S, Thurman R, Yu M, Stamatoyannopoulos JA. (2005). Predicting the in vivo signature of human gene regulatory sequences. Bioinformatics 21:i338-i343.

Dorschner MO, Hawrylycz M, Humbert R, Wallace JC, Shafer A, Mack J, Hall R, Goldy J, Kawamoto J, Sabo PJ, McArthur M, Stamatoyannopoulos JA. (2004). High-throughput localization of functional elements by quantitative chromatin profiling. Nature Methods 1:219-225 .

Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Shafer A, Kawamoto J, Mack J, Hall R, Kohli A, Li Q, McArthur M, Stamatoyannopoulos JA. (2004). Discovery of functional non-coding elements by digital analysis of chromatin structure. Proc. Nat’l. Acad. Sci. USA 101:16837-16842.

Sabo P, Humbert R, Hawrylycz M, Wallace J, Dorschner MO, Shafer A, McArthur M, Stamatoyannopoulos JA. (2004). Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Nat’l. Acad. Sci. USA 101:4537-42.

Stamatoyannopoulos, JA. (2004). The genomics of gene expression. Genomics84:449-457.

The ENCODE Project Consortium (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-40.