Yuan Lab website
We develop computational biology methodologies for genomic data analysis and integration, with the aim to understand systems-level gene regulatory mechanisms. Since virtually all the cells in a living organism share the same genome, epigenetic information provides an essential role in regulating cell-type specific gene regulation. Our long-term goal is to systematically investigate the structure and dynamics the gene regulatory network and its role in maintenance of cell-type specificity. To this end, we have developed integrated approaches to identify the chromatin state organization, to determine the targeting mechanism for epigenetic factors, and to reconstruct the gene regulatory network from integration of multiple data-types. We have applied these approaches to stem cells and cancer biology. We actively participate in the ENCODE consortium. We collaborate closely with a number of basic scientists and clinical physicians at Harvard and affiliated hospitals. Our research is mainly funded by NHGRI and NHLBI.
1999 Ph.D., Applied Mathematics, University of Maryland at College Park
1994 M.A., Applied Mathematics, Peking University, China
1992 B.S., Applied Mathematics, Peking University, China
Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Apr 6.
Baena E, Shao Z, Linn DE, Glass K, Hamblen MJ, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho FJ, Bronson RT, Mucci LA, Loda M, Yuan GC, Orkin SH, Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev. 2013 Mar 15;27(6):683-98.
Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S,
Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell. 2012 Oct 16;23(4):796-811.
Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol. 2012 Mar 16;13(3):R16.
Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation stages. PLoS One. 2012;7(2):e31414.
Yuan GC. Linking genome to epigenome. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):297-309.
Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12:408.
Van Rechem C, Black JC, Abbas T, Allen A, Rinehart CA, Yuan GC, Dutta A, Whetstine JR. The SKP1-Cul1-F-box and leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A) protein. J Biol Chem. 2011 Sep 2;286(35):30462-70.
Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12;11:557.
Rao S, Zhen S, Roumiantsev S, McDonald LT, Yuan GC, Orkin SH. Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol. 2010 Nov;30(22):5364-80.