Selected Publications:

Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5643-50.

Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol. 2014 Dec 3;15(12):525.

Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, George RE. CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer. Cell. 2014 Nov 20;159(5):1126-39.

Riddell J, Gazit R, Garrison BS, Guo G, Saadatpour A , Mandal PK, Ebina W, Volchkov P, Yuan GC, Orkin SH, Rossi DJ. Reprogramming Committed Murine Blood Cells to Induced Hematopoietic Stem Cells with Defined Factors. Cell. 2014 Apr 24;157(3):549-64.

Pinello L, Xu J, Orkin SH, Yuan GC. Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns.Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):E344-53.

Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo P, Vierstra J, Voit R, Yuan GC, Porteus M, Stamatoyannopoulos JA, Lettre G, Orkin SH. An adult-stage erythroid enhancer of BCL11A determines fetal hemoglobin level. Science 11 October 2013: Vol. 342 no. 6155 pp. 253-257

Guo G, Luc S, Marco E, Lin TW, Peng C, Kerenyi MA, Beyaz S, Kim W, Xu J, Das PP, Neff T, Zou K, Yuan GC, Orkin SH. Mapping Cellular Hierarchy by Single-Cell Analysis of the Cell Surface Repertoire. Cell Stem Cell. 2013 Oct 3;13(4):492-505

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE. 2013 8(5): e64832.

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.

Yuan GC. Linking genome to epigenome. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):297-309

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.

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