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Guo-Cheng Yuan, Ph.D.

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Biography
2008 - 2010
Claudia Adams Barr Award
2010 - 2011
Career Incubator Award

Overview
We develop computational method to analyze and integrate various data-types. Our long-term goal is to characterize the structure and dynamics of gene regulatory networks in order to mechanistic insights into the maintenance of cell-type identity. We apply this knowledge to investigate the etiology of cancer and other diseases.

Current research topics involving new statistical methodologies include: 1) targeting mechanisms for epigenetic factors; 2) multi-level spatial organization of chromatin states; 3) gene regulatory network reconstruction; 4) single cell level gene expression;.

Application areas include: 1) role of epigenetics in cancer and other diseases. 2) cancer pathways and networks; 3) stem cells maintenance and cell differentiation

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Dong R, Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinformatics. 2020 Apr 25; 21(1):158. PMID: 32334526.
    Citations:    
  2. McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S, Wucherpfennig K, Yuan GC, de Sauvage FJ, Turley SJ, Shivdasani RA. Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient. Cell Stem Cell. 2020 Mar 05; 26(3):391-402.e5. PMID: 32084389.
    Citations:    
  3. de Andrade LF, Lu Y, Luoma A, Ito Y, Pan D, Pyrdol JW, Yoon CH, Yuan GC, Wucherpfennig KW. Discovery of specialized NK cell populations infiltrating human melanoma metastases. JCI Insight. 2019 12 05; 4(23). PMID: 31801909.
    Citations:    
  4. Akerberg BN, Gu F, VanDusen NJ, Zhang X, Dong R, Li K, Zhang B, Zhou B, Sethi I, Ma Q, Wasson L, Wen T, Liu J, Dong K, Conlon FL, Zhou J, Yuan GC, Zhou P, Pu WT. A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. Nat Commun. 2019 10 28; 10(1):4907. PMID: 31659164.
    Citations:    
  5. Zhu Q, Liu N, Orkin SH, Yuan GC. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol. 2019 09 09; 20(1):192. PMID: 31500663.
    Citations:    
  6. Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, McLane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, Yuan GC, Young RA, George RE. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature. 2019 08; 572(7771):676-680. PMID: 31391581.
    Citations:    
  7. Tracy S, Yuan GC, Dries R. RESCUE: imputing dropout events in single-cell RNA-sequencing data. BMC Bioinformatics. 2019 Jul 12; 20(1):388. PMID: 31299886.
    Citations:    
  8. Sethi I, Cai Z, Roberts TM, Yuan GC. Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110ß Inhibitor KIN-193. Cancer Res. 2019 09 01; 79(17):4524-4531. PMID: 31292159.
    Citations:    
  9. Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC. Accurate estimation of cell-type composition from gene expression data. Nat Commun. 2019 07 05; 10(1):2975. PMID: 31278265.
    Citations:    
  10. Joyce CE, Saadatpour A, Ruiz-Gutierrez M, Bolukbasi OV, Jiang L, Thomas DD, Young S, Hofmann I, Sieff CA, Myers KC, Whangbo J, Libermann TA, Nusbaum C, Yuan GC, Shimamura A, Novina CD. TGFß signaling underlies hematopoietic dysfunction and bone marrow failure in Shwachman-Diamond Syndrome. J Clin Invest. 2019 06 18; 129(9):3821-3826. PMID: 31211692.
    Citations:    
  11. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019 04 23; 10(1):1903. PMID: 31015418.
    Citations:    
  12. Krajewska M, Dries R, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nat Commun. 2019 04 15; 10(1):1757. PMID: 30988284.
    Citations:    
  13. Grootjans J, Krupka N, Hosomi S, Matute JD, Hanley T, Saveljeva S, Gensollen T, Heijmans J, Li H, Limenitakis JP, Ganal-Vonarburg SC, Suo S, Luoma AM, Shimodaira Y, Duan J, Shih DQ, Conner ME, Glickman JN, Fuhler GM, Palm NW, de Zoete MR, van der Woude CJ, Yuan GC, Wucherpfennig KW, Targan SR, Rosenstiel P, Flavell RA, McCoy KD, Macpherson AJ, Kaser A, Blumberg RS. Epithelial endoplasmic reticulum stress orchestrates a protective IgA response. Science. 2019 03 01; 363(6430):993-998. PMID: 30819965.
    Citations:    
  14. Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas. Cell Rep. 2018 11 06; 25(6):1436-1445.e3. PMID: 30404000.
    Citations:    Fields:    
  15. Zhu Q, Shah S, Dries R, Cai L, Yuan GC. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nat Biotechnol. 2018 Oct 29. PMID: 30371680.
    Citations:    
  16. Guo Y, Jardin BD, Zhou P, Sethi I, Akerberg BN, Toepfer CN, Ai Y, Li Y, Ma Q, Guatimosim S, Hu Y, Varuzhanyan G, VanDusen NJ, Zhang D, Chan DC, Yuan GC, Seidman CE, Seidman JG, Pu WT. Hierarchical and stage-specific regulation of murine cardiomyocyte maturation by serum response factor. Nat Commun. 2018 09 21; 9(1):3837. PMID: 30242271.
    Citations:    Fields:    Translation:AnimalsCells
  17. Glass K, Thibault D, Guo F, Mitchel JA, Pham B, Qiu W, Li Y, Jiang Z, Castaldi PJ, Silverman EK, Raby B, Park JA, Yuan GC, Zhou X. Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke. Sci Rep. 2018 08 24; 8(1):12750. PMID: 30143676.
    Citations:    Fields:    
  18. Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics. 2018 06 01; 34(11):1930-1933. PMID: 29360936.
    Citations:    Fields:    
  19. Tsoucas D, Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biol. 2018 05 10; 19(1):58. PMID: 29747686.
    Citations:    Fields:    Translation:AnimalsCells
  20. Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc. 2018 05; 13(5):946-986. PMID: 29651054.
    Citations: 1     Fields:    
  21. Ferrari de Andrade L, Tay RE, Pan D, Luoma AM, Ito Y, Badrinath S, Tsoucas D, Franz B, May KF, Harvey CJ, Kobold S, Pyrdol JW, Yoon C, Yuan GC, Hodi FS, Dranoff G, Wucherpfennig KW. Antibody-mediated inhibition of MICA and MICB shedding promotes NK cell-driven tumor immunity. Science. 2018 Mar 30; 359(6383):1537-1542. PMID: 29599246.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  22. Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell. 2018 04 05; 173(2):430-442.e17. PMID: 29606353.
    Citations: 4     Fields:    
  23. Huang J, Li K, Cai W, Liu X, Zhang Y, Orkin SH, Xu J, Yuan GC. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun. 2018 03 05; 9(1):943. PMID: 29507293.
    Citations: 1     Fields:    Translation:HumansCells
  24. Jiang L, Tsoucas D, Yuan GC. Assessing Inequality in Transcriptomic Data. Cell Syst. 2018 Feb 28; 6(2):149-150. PMID: 29494801.
    Citations:    Fields:    
  25. Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma AM, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu XS, Wucherpfennig KW. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science. 2018 02 16; 359(6377):770-775. PMID: 29301958.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  26. Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. J Allergy Clin Immunol. 2018 04; 141(4):1250-1258. PMID: 28736268.
    Citations:    Fields:    
  27. Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell. 2017 07 06; 21(1):65-77.e5. PMID: 28648363.
    Citations: 16     Fields:    Translation:AnimalsCells
  28. Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 05 08; 18(1):84. PMID: 28482897.
    Citations: 20     Fields:    Translation:HumansAnimals
  29. Adeegbe DO, Liu Y, Lizotte PH, Kamihara Y, Aref AR, Almonte C, Dries R, Li Y, Liu S, Wang X, Warner-Hatten T, Castrillon J, Yuan GC, Poudel-Neupane N, Zhang H, Guerriero JL, Han S, Awad MM, Barbie DA, Ritz J, Jones SS, Hammerman PS, Bradner J, Quayle SN, Wong KK. Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-Small Cell Lung Cancer. Cancer Discov. 2017 08; 7(8):852-867. PMID: 28408401.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  30. Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nat Commun. 2017 04 07; 8:15011. PMID: 28387224.
    Citations: 2     Fields:    Translation:HumansCells
  31. Guo Y, VanDusen NJ, Zhang L, Gu W, Sethi I, Guatimosim S, Ma Q, Jardin BD, Ai Y, Zhang D, Chen B, Guo A, Yuan GC, Song LS, Pu WT. Analysis of Cardiac Myocyte Maturation Using CASAAV, a Platform for Rapid Dissection of Cardiac Myocyte Gene Function In Vivo. Circ Res. 2017 Jun 09; 120(12):1874-1888. PMID: 28356340.
    Citations: 14     Fields:    Translation:AnimalsCells
  32. Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017 Apr; 49(4):625-634. PMID: 28218758.
    Citations: 13     Fields:    Translation:HumansCells
  33. Tu S, Yuan GC, Shao Z. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Sci Rep. 2017 01 31; 7:41669. PMID: 28139710.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  34. Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res. 2017 03; 27(3):386-401. PMID: 28128194.
    Citations: 2     Fields:    Translation:AnimalsCells
  35. Tsoucas D, Yuan GC. Recent progress in single-cell cancer genomics. Curr Opin Genet Dev. 2017 Feb; 42:22-32. PMID: 28126650.
    Citations: 7     Fields:    Translation:Humans
  36. Blinka S, Reimer MH, 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. PMID: 27662872.
    Citations: 2     Fields:    Translation:AnimalsCells
  37. Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, Orkin SH, Winau F. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol. 2017 02; 18(2):184-195. PMID: 27992400.
    Citations: 9     Fields:    Translation:AnimalsCells
  38. 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 09 08; 1(14):e89014. PMID: 27699239.
    Citations: 14     Fields:    Translation:HumansCells
  39. 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 08 23; 16(8):2053-2060. PMID: 27524622.
    Citations: 7     Fields:    Translation:AnimalsCells
  40. Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 07 12; 34(7):695-7. PMID: 27404874.
    Citations: 43     Fields:    Translation:HumansAnimalsCells
  41. 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 07 01; 17(1):144. PMID: 27368803.
    Citations: 24     Fields:    Translation:AnimalsCells
  42. 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 07; 22(7):723-6. PMID: 27270588.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  43. Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC. Robust lineage reconstruction from high-dimensional single-cell data. Nucleic Acids Res. 2016 08 19; 44(14):e122. PMID: 27207878.
    Citations: 6     Fields:    Translation:Animals
  44. 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 02; 165(6):1389-1400. PMID: 27212235.
    Citations: 16     Fields:    Translation:AnimalsCells
  45. 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; 9:14. PMID: 27087855.
    Citations: 3     Fields:    
  46. 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. Nature. 2016 Mar 03; 531(7592):53-8. PMID: 26935695.
    Citations: 64     Fields:    Translation:HumansAnimalsCells
  47. 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 02; 14(4):956-965. PMID: 26804902.
    Citations: 13     Fields:    Translation:AnimalsCells
  48. 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. PMID: 26766440.
    Citations: 39     Fields:    Translation:HumansCells
  49. 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. PMID: 26752519.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  50. Wu JN, Pinello L, Yissachar E, Wischhusen JW, Yuan GC, Roberts CWM. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin. 2015; 8:53. PMID: 26633995.
    Citations: 2     Fields:    
  51. Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015 Oct; 31(10):576-586. PMID: 26450340.
    Citations: 20     Fields:    Translation:Humans
  52. 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. PMID: 26375006.
    Citations: 123     Fields:    Translation:HumansAnimalsCells
  53. Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol. 2015 Aug 14; 16:162. PMID: 26272203.
    Citations: 24     Fields:    Translation:HumansCells
  54. 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. PMID: 26169829.
    Citations: 5     Fields:    Translation:AnimalsCells
  55. 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. PMID: 25888305.
    Citations: 12     Fields:    Translation:Humans
  56. 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; 7(1):12. PMID: 25763110.
    Citations: 12     Fields:    
  57. 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):304-316. PMID: 25578878.
    Citations: 26     Fields:    Translation:HumansCells
  58. 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. PMID: 25512504.
    Citations: 56     Fields:    Translation:HumansAnimalsCells
  59. Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol. 2014 Dec 03; 15(12):525. PMID: 25517911.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  60. 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; 8:118. PMID: 25431000.
    Citations: 11     Fields:    Translation:Humans
  61. 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):1126-1139. PMID: 25416950.
    Citations: 91     Fields:    Translation:HumansAnimalsCells
  62. 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):1452-1465. PMID: 25156994.
    Citations: 75     Fields:    Translation:HumansAnimalsCells
  63. 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. PMID: 24766805.
    Citations: 104     Fields:    Translation:AnimalsCells
  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. PMID: 24395799.
    Citations: 25     Fields:    Translation:HumansCells
  65. 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:e01256. PMID: 24381246.
    Citations: 26     Fields:    Translation:HumansCells
  66. 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 01 09; 53(1):32-48. PMID: 24361252.
    Citations: 33     Fields:    Translation:AnimalsCells
  67. Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May; 15(3):419-30. PMID: 24197932.
    Citations: 2     Fields:    Translation:Humans
  68. Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E. Modeling the dynamics of bivalent histone modifications. PLoS One. 2013; 8(11):e77944. PMID: 24223747.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  69. 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. PMID: 24135681.
    Citations: 21     Fields:    Translation:AnimalsCells
  70. 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. PMID: 24115442.
    Citations: 159     Fields:    Translation:HumansAnimalsCells
  71. 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 03; 13(4):492-505. PMID: 24035353.
    Citations: 79     Fields:    Translation:HumansAnimalsCells
  72. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832. PMID: 23741402.
    Citations: 23     Fields:    Translation:AnimalsCells
  73. 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. PMID: 23716595.
    Citations: 30     Fields:    Translation:HumansCells
  74. 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. PMID: 23570996.
    Citations: 3     Fields:    Translation:HumansCells
  75. 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. PMID: 23512661.
    Citations: 44     Fields:    Translation:HumansAnimalsCells
  76. 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. PMID: 23041383.
    Citations: 74     Fields:    Translation:HumansCells
  77. 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. PMID: 22424423.
    Citations: 90     Fields:    Translation:HumansCells
  78. Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation stages. PLoS One. 2012; 7(2):e31414. PMID: 22363642.
    Citations: 3     Fields:    Translation:HumansCells
  79. Yuan GC. Linking genome to epigenome. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun; 4(3):297-309. PMID: 22344857.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  80. Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21; 12:408. PMID: 22017798.
    Citations: 4     Fields:    Translation:HumansCells
  81. 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 02; 286(35):30462-70. PMID: 21757720.
    Citations: 29     Fields:    Translation:HumansCells
  82. Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12; 11:557. PMID: 21073706.
    Citations: 10     Fields:    Translation:AnimalsCells
  83. 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. PMID: 20837710.
    Citations: 52     Fields:    Translation:HumansAnimalsCells
  84. 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. PMID: 20670891.
    Citations: 74     Fields:    Translation:HumansCells
  85. 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 04; 107(18):8486-91. PMID: 20404177.
    Citations: 51     Fields:    Translation:Cells
  86. Liu Y, Shao Z, Yuan GC. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics. 2010 Jul; 96(1):17-26. PMID: 20353814.
    Citations: 14     Fields:    Translation:AnimalsCells
  87. 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. PMID: 20118936.
    Citations: 108     Fields:    Translation:AnimalsCells
  88. 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. PMID: 20064376.
    Citations: 183     Fields:    Translation:HumansAnimalsCells
  89. 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. PMID: 19307305.
    Citations: 20     Fields:    Translation:AnimalsCells
  90. Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol. 2009 Feb; 16(2):341-55. PMID: 19193151.
    Citations: 7     Fields:    Translation:HumansCells
  91. 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. PMID: 19026780.
    Citations: 297     Fields:    Translation:AnimalsCells
  92. 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):140-5. PMID: 18951969.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  93. Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol. 2008 Jan; 4(1):e13. PMID: 18225943.
    Citations: 78     Fields:    Translation:HumansAnimalsCells
  94. 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. PMID: 17568008.
    Citations: 21     Fields:    Translation:HumansCells
  95. 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. PMID: 16884527.
    Citations: 12     Fields:    Translation:AnimalsCells
  96. 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. PMID: 15961632.
    Citations: 512     Fields:    Translation:AnimalsCells
  97. Yuan GC, Yorke JA, Carroll TL, Ott E, Pecora LM. Testing whether two chaotic one dimensional processes are dynamically identical Phys Rev Lett. 2000 Nov 13; 85(20):4265-8. PMID: 11060614.
    Citations:    Fields:    
  98. 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. PMID: 12779361.
    Citations:    Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.