Selected publications

  • Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE. 2013 (in press)
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 [paper]
  • 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# and Li Z#. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes & Development. 2013 27: 683-698 [paper]
  • 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. [paper]
  • Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model to quantitatively compare ChIP-Seq data sets. Genome Biology 2012, 13:R16 (16 March 2012). (highly accessed) [paper] [Software page].
  • Yuan GC. Linking genome to epigenome. WIREs Systems Biology and Medicine.2012 Feb 17. doi: 10.1002/wsbm.1165. [Epub ahead of print] [paper]
  • Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation status. PLoS ONE. 2012. 7(2): e31414. doi:10.1371/journal.pone.0031414 [paper]
  • Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12:408. [paper] [Software].
  • Van Rechem C, Black JC, Abbas TA, 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). J Biol Chem. 2011 Jul 8. [Epub ahead of print] [paper]
  • Yuan GC. Prediction of epigenetic target sites by using genomic DNA sequence. in Handbook of Research on Computational and Systems Biology (eds. Limin Liu et al.) Chapter 8, 2011 [paper]
  • Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12;11:557. (highly accessed) [paper] [Software].
  • Rao S, Shao Z, Roumiantsev S, McDonald LT, Yuan GC, Orkin SH. Differential roles of sall4 isoforms in embryonic stem cell pluripotency. Molecular and Cellular Biololgy. 2010 Nov;30(22):5364-80. Epub 2010 Sep 13. [paper]
  • Fang R, Barbera AJ, Xu Y, Rutenberg M, Leonor T, Bi Q, Lan F, Mei P, Yuan GC, Lian C, Peng J, Cheng D, Sui G, Kaiser UB, Shi Y, Shi YG. Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Molecular Cell. 2010 Jul 30;39(2):222-33. [paper]
  • Liu Y*, Shao Z*, Yuan GC. Prediction of Polycomb target plasticity in mouse embryonic stem cells. Genomics. 2010 Jul;96(1):17-26. (cover article) [paper]
  • 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 USA. 2010 May 4;107(18):8486-91.[paper]
  • Lantermann AB, Straub T, Strålfors A, Yuan GC, Eckwall K, Korber P. Schizosaccharomyces pombegenome-wide nucleosome mapping reveals positioning mechanisms distinct from Saccharomyces cerevisiae. Nature Structural and Molecular Biology 2010 Feb;17(2):251-7. [paper]
  • 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. [paper]
  • Wippo CJ, Krstulovic BS, Ertel F, Musladin S, Blaschke D, Stürzl S, Yuan GC, Hörz W, Korber P, Barbaric S. Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Molecular and Cellular Biology 2009 June;29(11): 2960-81.[paper]
  • Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol 2009 Feb;16(2):341-355.[paper]
  • Di Gesù V, Lo Bosco G, Pinello L, Yuan GC, Corona DFV.? A multi-layer method to study genome-scale positions of nucleosomes. Genomics 2009 Feb;93(2):140-145.[paper]
  • 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. Mol Cell 2008 Nov 21;32(4):491-502.[paper]
  • Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol 2008 Jan;4(1):e13. doi:10.1371/journal.pcbi.0040013.eor [paper] [MATLAB code]
  • Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research 2007 Jun;17(6):928-39.[paper]
  • Yuan GC*, Ma P*, Zhong W, Liu JS. Statistical assessment of the global impact of histone acetylation on gene expression in Saccharomyces cerevisiae. Genome Biology 2006;7:R70. [paper]
  • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. Cerevisiae. Science 2005;309(5734):626-630.[paper] [MATLAB code]

    *co-first authors; #co-senior authors

    Prior work

  • Yang SC, Cai M, Kalnay E, Rienecker M, Yuan G, Toth Z. ENSO bred vectors in coupled ocean-atmosphere General Circulation Models. Journal of Climate 2006;19(8):1422-1436.
  • Yuan GC, Lozier MS, Pratt LJ, Jones CKRT, Helfrich KR. Estimating the predictability of an oceanic time series using linear and nonlinear methods. Journal of Geophysical Research 2004;109(C08):C08002.
  • Yuan GC, Pratt LJ, Jones CKRT. Cross-jet Lagrangian transport and mixing in a 2 1/2 layer model. Journal of Physical Oceanography 2004;34(9):1991-2005.
  • Yuan GC, Pratt LJ, Jones CKRT. Barrier destruction and Lagrangian predictability at depth in a meandering jet. Dynamics of Atmospheres and Oceans 2002;35(1):41-61.
  • Yuan GC, Yorke JA, Carroll TL, Ott E, Pecora LM. Testing whether two chaotic one dimensional processes are dynamically identical. Physical Review Letters 2000;85(20):4265-4268.
  • Haller, G, Yuan G. Lagrangian coherent structures and mixing in two-dimensional turbulence. Physica D 2000;147(3-4):352-370.
  • Yuan GC, Yorke JA. An open set of maps for which every point is absolutely nonshadowable. Proceedings of the American Mathematical Society 2000;128(3):909-918.
  • Yuan GC, Yorke JA. Collapsing of chaos in one dimensional maps. Physica D 2000;36(1-2):18-30.
  • Yuan GC, Nam K, Antonsen TM Jr, Ott E, Guzdar PN. Power spectrum of passive scalars in two dimensional chaotic flows. CHAOS 2000;10(1) (Focus issue: chaotic kinetics and transport):39-49.
  • Yuan G, Hunt BR. Optimal orbits of hyperbolic systems. Nonlinearity 1999;12(4):1207-1224.