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Guocheng Yuan, PhD


  • 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.
  • Pulakanti K, Pinello L, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson J, Wang A, Yuan GC, Rao S.Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.Epigenetics. 2013 Dec;8(12):1303-20.
  • Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley G, Hochedlinger K, Kim J, Orkin SH.Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity.Mol Cell. 2014 Jan 9;53(1):32-48.
  • Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA.Chromatin signature of widespread monoallelic expression.Elife. 2013;2:e01256.
  • Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E.Modeling the dynamics of bivalent histone modifications.PLoS ONE. 2013;8(11):e77944.
  • Pinello L, Lo Bosco G, Yuan GC.Applications of alignment-free methods in epigenomics.Briefings In Bioinformatics. 2013 Nov 6.
  • Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH.An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level.Science. 2013 Oct 11;342(6155):253-7.
  • 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.
  • Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan GC, Frank DA.STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.Mol Cell Biol. 2013 Aug;33(15):2879-90.
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC.Passing messages between biological networks to refine predicted interactions.PLoS ONE. 2013;8(5):e64832.
  • 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 Interdisciplinary Reviews. Systems Biology And Medicine. 2012 Feb 17.
  • Pinello L, Lo Bosco G, Hanlon B, Yuan GC.A motif-independent metric for DNA sequence specificity.BMC Bioinformatics. 2011;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;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.
  • 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.
  • Liu Y, Shao Z, Yuan GC.Prediction of Polycomb target genes in mouse embryonic stem cells.Genomics. 2010 Jul;96(1):17-26.
  • 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.
  • 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.
  • 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.
  • 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.
  • Yuan GC.Targeted recruitment of histone modifications in humans predicted by genomic sequences.J Comput Biol. 2009 Feb;16(2):341-55.
  • 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.
  • 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.
  • Yuan GC, Liu JS.Genomic sequence is highly predictive of local nucleosome depletion.PLoS Comput Biol. 2008 Jan;4(1):e13.
  • 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.
  • 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.
  • 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.
  • Yuan GC, Nam K, Antonsen TM, Ott E, Guzdar PN.Power spectrum of passive scalars in two dimensional chaotic flows.Chaos. 2000 Mar;10(1):39-49.