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Guocheng Yuan, PhD

Publications

  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC.A tiered hidden Markov model characterizes multi-scale chromatin states.Genomics. 2013 Apr 6.
    23570996
  • 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.
    23512661
  • 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.
    23041383
  • Pinello L, Lo Bosco G, Hanlon B, Yuan GC.A motif-independent metric for DNA sequence specificity.BMC Bioinformatics. 2011;12:408.
    22017798
  • 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.
    21757720
  • Larson JL, Yuan GC.Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model.BMC Bioinformatics. 2010;11:557.
    21073706
  • 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.
    20837710
  • 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.Mol Cell. 2010 Jul 30;39(2):222-33.
    20670891
  • Liu Y, Shao Z, Yuan GC.Prediction of Polycomb target genes in mouse embryonic stem cells.Genomics. 2010 Jul;96(1):17-26.
    20353814
  • Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick RM.Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis.Proc Natl Acad Sci U S A. 2010 May 4;107(18):8486-91.
    20404177
  • Lantermann AB, Straub T, Strålfors A, Yuan GC, Ekwall K, Korber P.Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.Nat Struct Mol Biol. 2010 Feb;17(2):251-7.
    20118936
  • Shen X, Kim W, Fujiwara Y, Simon MD, 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.
    20064376
  • 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.Mol Cell Biol. 2009 Jun;29(11):2960-81.
    19307305
  • Yuan GC.Targeted recruitment of histone modifications in humans predicted by genomic sequences.J Comput Biol. 2009 Feb;16(2):341-55.
    19193151
  • Di Ges V, Lo Bosco G, Pinello L, Yuan GC, Corona DF.A multi-layer method to study genome-scale positions of nucleosomes.Genomics. 2009 Feb;93(2):140-5.
    18951969
  • 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.
    19026780
  • Yuan GC, Liu JS.Genomic sequence is highly predictive of local nucleosome depletion.PLoS Comput Biol. 2008 Jan;4(1):e13.
    18225943
  • 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 Res. 2007 Jun;17(6):928-39.
    17568008
  • Yuan GC, Ma P, Zhong W, Liu JS.Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae.Genome Biol. 2006;7(8):R70.
    16884527
  • 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 Jul 22;309(5734):626-30.
    15961632