Selected Publications:

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE. 2013 (in press)

Xu J, Shao Z, Glass K, Bauer DE, Pinello L, van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan GC, Orkin SH. Combinatorial Assembly of Developmental Stage Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis. Developmental Cell. 2012 Oct 16;23(4):796-811.

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model to quantitatively compare ChIP-Seq data sets. 2012 Mar 16;13(3):R16.

Larson JL, Yuan GC. A hidden Markov model for detecting multi-gene chromatin domains. BMC Bioinformatics. 2010 Nov 12;11:557.

Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick R. Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis.  Proceedings of the National Academy of Sciences 2010 May 4;107(18):8486-91.

Liu Y, Shao Z, Yuan GC. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics. 2010 Jul;96(1):17-26. Epub 2010 Mar 29

Shen X, Kim W, Fujiwara Y, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates Polycomb activity and self-renewal versus differentiation of stem cells. Cell 2009 Dec 24;139(7):1303-14.

Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH, EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Molecular Cell 2008. Nov 21;32(4):491-502.

Yuan, G.C. and J.S. Liu, Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology 2008 Jan;4(1):e13.

Yuan, G.C., Y.-J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler, and O.J. Rando, Genome-scale Identification of Nucleosome Positions in S. Cerevisiae, Science, 2005, 309(5734), p.626