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. PNAS 2014 ; published ahead of print December 15, 2014, doi:10.1073/pnas.1408993111. [ paper ]
  • Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biology 2014. 15 (12), 525. [ paper ]
  • Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol. 2014 Nov 28;8(1):118. [Epub ahead of print] [ paper ]
  • 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. [ paper ]
  • Wu G, Cai J, Han Y, Chen J, Huang ZP, Chen C, Cai Y, Huang H, Yang Y, Liu Y, Xu Z, He D, Zhang X, Hu X, Pinello L, Zhong D, He F, Yuan GC, Wang DZ, Zeng C. LincRNA-p21 Regulates Neointima Formation, Vascular Smooth Muscle Cell Proliferation, Apoptosis and Atherosclerosis by Enhancing p53 Activity. Circulation. 2014 Oct 21;130(17):1452-65. [ paper ]
  • Pinello L, Lo Bosco G#, Yuan GC#. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May;15(3):419-30. [ paper ]
  • 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. [ paper ]
  • Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, Angeles AD, 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. Mol Cell. 2014 Jan 9;53(1):32-48. [ paper ]
  • 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. [ paper ] [ location of highly plastic regions (hg19) ]
  • Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA. Chromatin signature of widespread monoallelic expression. Elife. 2013 Dec 31;2(0):e01256. doi: 10.7554/eLife.01256. [ Paper ]
  • Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E. Modeling the Dynamics of Bivalent Histone Modifications. PLoS One. 2013 Nov 1;8(11):e77944. doi: 10.1371/journal.pone.0077944. [ paper ]
  • Pulakanti K*, Pinello L*, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblwai S, Peterson J, Wang A, Yuan GC#, Rao, S#. Enhancer Transcribed RNAs are produced from hypomethylated genomic regions in a Tet-dependent manner. Epigenetics. 2013 Dec;8(12):1303-20. [ paper ] [ Python code ]
  • 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 [ paper ] [ comment article ]
  • 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 [ paper ]
  • Meyer P, Siwo G, Zeevi D, Sharon E, Norel R; DREAM6 Promoter Prediction Consortium^, Segal E, Stolovitzky G.Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Res. 2013 Nov;23(11):1928-37. [ paper ]. ^(including Pinello L and Yuan GC)
  • Marco E, Dorn JF, Hsu P-H, Jaqaman K, Sorger PK, Danuser G. S. cerevisiae Chromosomes Biorient via Gradual Resolution of Syntely between S Phase and Anaphase. Cell. 2013. Volume 154, Issue 5, 29 August 2013, Pages 959-961. [paper]
  • 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) 2879-2890. [paper]
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE. 2013 8(5): e64832. doi:10.1371/journal.pone.0064832 [paper] [Software] [F1000 review ].
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul;102(1):1-7. [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. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):297-309. [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) protein. J Biol Chem. 2011 Sep 2;286(35):30462-70. [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 DF. 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. [ paper ]
  • 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. [ paper ]
  • 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. [ paper ]
  • 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. [ paper ]
  • 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. [ paper ]
  • Haller, G, Yuan G. Lagrangian coherent structures and mixing in two-dimensional turbulence. Physica D 2000;147(3-4):352-370. [ paper ]
  • 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. [ paper ]
  • Yuan GC, Yorke JA. Collapsing of chaos in one dimensional maps. Physica D 2000;36(1-2):18-30. [ paper ]
  • 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. [ paper ]
  • Yuan G, Hunt BR. Optimal orbits of hyperbolic systems. Nonlinearity 1999;12(4):1207-1224. [ paper ]