Selected publications

  1. Blinka S, Reimer MH Jr, Pulakanti K, Pinello L, Yuan GC, Rao S. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. Methods Mol Biol. 2017;1468:91-109. [ paper ].
  2. Lizotte PH, Ivanova EV, Awad MM, Jones RE, Keogh L, Liu H, Dries R, Almonte C, Herter-Sprie GS, Santos A, Feeney NB, Paweletz CP, Kulkarni MM, Bass AJ, Rustgi AK, Yuan GC, Kufe DW, Jänne PA, Hammerman PS, Sholl LM, Hodi FS, Richards WG, Bueno R, English JM, Bittinger MA, Wong KK, Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes. JCI Insight. 2016 Sep 8;1(14):e89014.[ paper ].
  3. Kim TH*, Saadatpour A*, Guo G, Saxena M, Cavazza A, Desai N, Jadhav U, Jiang L, Rivera MN, Orkin SH, Yuan GC#, Shivdasani RA#. Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5+ Intestinal Stem Cells. Cell Rep. 2016 Aug 23;16(8):2053-60. [ paper ].
  4. Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE#, Yuan GC#. CRISPResso: sequencing analysis toolbox for CRISPR-Cas9 genome editing. Nat Biotechnol. 2016 Jul 12;34(7):695-7. [ paper ].
  5. Jiang L, Chen H, Pinello L, Yuan GC. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biol. 2016 Jul 1;17(1):144. [ paper ].
  6. Ni J, Ramkissoon SH, Xie S, Goel S, Stover DG, Guo H, Luu V, Marco E, Ramkissoon LA, Kang YJ, Hayashi M, Nguyen QD, Ligon AH, Du R, Claus EB, Alexander BM, Yuan GC, Wang ZC, Iglehart JD, Krop IE, Roberts TM, Winer EP, Lin NU, Ligon KL, Zhao JJ. Combination inhibition of PI3K and mTORC1 yields durable remissions in mice bearing orthotopic patient-derived xenografts of HER2-positive breast cancer brain metastases. Nat Med. 2016 Jul;22(7):723-6.[ paper ].
  7. Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA. Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Cell. 2016 Jun 2;165(6):1389-400. [ paper ].
  8. Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC. Robust lineage reconstruction from high-dimensional single-cell data. Nucleic Acids Res. 2016 Aug 19;44(14):e122. [ paper ].
  9. Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev S, Hessner MJ; Milanovich S, Yuan GC, Rao S. The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing. Epigenetics Chromatin. 2016 Apr 15;9:14. [ paper ].
  10. Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature. 2016 Mar 3;531(7592):53-8. [ paper ].
  11. Guo G*, Pinello L*, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC#, Orkin SH#. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. Cell Rep. 2016 Feb 2;14(4):956-65. [ paper ].
  12. Huang J, Liu X, Li D, Shao Z, Cao H, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH, Xu J. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Dev Cell. 2016 Jan 11;36(1):9-23. [ paper ].
  13. Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, Chen ZH, Goldklang MP, Yuan GC, Moore SC, Demeo DL, Rouault TA, D'Armiento JM, Schon EA, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AM. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med. 2016 Feb;22(2):163-74. [ paper ]
  14. Wu JN*, Pinello L*, Yissachar E, Wischhusen JW, Yuan GC, Roberts CW. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin. 2015 Dec 2;8:53. [ paper ].
  15. Saadatpour A, Lai S, Guo G#, Yuan GC#. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015 Oct;31(10):576-86. Review. [ paper ]

  16. Canver MC*, Smith EC*, Sher F*, Pinello L*, Sanjana NE*, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12;527(7577):192-7. [ paper ] [ ScienceDaily News ]
  17. Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks.Genome Biol. 2015 Aug 14;16(1):162. [ paper ]
  18. Hu T, Yeh JE, Pinello L, Jacob J, Chakravarthy S, Yuan GC, Chopra R, Frank DA. Impact of the N-terminal domain of STAT3 in STAT3-dependent transcriptional activity. Mol Cell Biol. 2015 Oct;35(19):3284-300. [ paper ]
  19. Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. BMC Bioinformatics. 2015 Apr 11;16:115. [ paper ]

  20. Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med. 2015 Feb 14;7(1):12. [ paper ]
  21. Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH. Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions. Mol Cell. 2015 Jan 22;57(2):304-16. [ paper ]
  22. 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. [ paper ]

  23. 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. [ paper ]

  24. 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. [ paper ]
  25. 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 ]
  26. 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 ]
  27. Pinello L, Lo Bosco G#, Yuan GC#. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May;15(3):419-30. [ paper ]
  28. 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 ]
  29. 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. 2014 Jan 9;53(1):32-48. [ paper ]
  30. 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) ]
  31. 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 ]
  32. 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 ]
  33. 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 ]
  34. 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. 2013 Oct 11;342(6155):253-7. [ paper ] [ comment article ]
  35. 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 ]
  36. 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)
  37. 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]
  38. 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 ].
  39. 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. (cover article) [paper]
  40. 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]
  41. 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]
  42. 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].
  43. Yuan GC. Linking genome to epigenome. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):297-309. [paper]
  44. Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation status. PLoS ONE. 2012. 7(2): e31414. doi:10.1371/journal.pone.0031414 [paper]
  45. 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].
  46. 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]
  47. 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]
  48. 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].
  49. 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]
  50. 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]
  51. 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]
  52. 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]
  53. 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]
  54. 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]
  55. 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]
  56. Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol 2009 Feb;16(2):341-355.[paper]
  57. 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]
  58. 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]
  59. 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]
  60. 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]
  61. Yuan GC*, Ma P*, Zhong W, Liu JS. Statistical assessment of the global impact of histone acetylation on gene expression in Saccharomyces cerevisiae. Genome Biol. 2006;7(8):R70. [paper]
  62. 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

  63. 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 ]
  64. 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 ]
  65. 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 ]
  66. 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 ]
  67. 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 ]
  68. Haller, G, Yuan G. Lagrangian coherent structures and mixing in two-dimensional turbulence. Physica D 2000;147(3-4):352-370. [ paper ]
  69. 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 ]
  70. Yuan GC, Yorke JA. Collapsing of chaos in one dimensional maps. Physica D 2000;36(1-2):18-30. [ paper ]
  71. 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 ]
  72. Yuan G, Hunt BR. Optimal orbits of hyperbolic systems. Nonlinearity 1999;12(4):1207-1224. [ paper ]