Photo of Guo-Cheng Yuan, PhD

Guo-Cheng Yuan, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 582-8532


gcyuan@jimmy.harvard.edu

Photo of Guo-Cheng Yuan, PhD

Dana-Farber Cancer Institute
Phone: (617) 582-8532


gcyuan@jimmy.harvard.edu

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Guo-Cheng Yuan, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Associate Professor, Biostatistics, Harvard T.H. Chan School Of Public Health

DF/HCC PROGRAM AFFILIATION

Research Abstract

We develop computational biology methodologies for genomic data analysis and integration, with the aim to understand systems-level gene regulatory mechanisms. Since virtually all the cells in a living organism share the same genome, epigenetic information provides an essential role in regulating cell-type specific gene expression patterns. Our long-term goal is to systematically investigate the structure and dynamics of the gene regulatory network and its role in maintenance of cell-type specificity. To this end, we have developed integrated approaches to identify the chromatin state organization, to determine the targeting mechanism for epigenetic factors, and to reconstruct the gene regulatory network from integration of multiple data-types. We have applied these approaches to stem cells and cancer biology. We actively participate in the ENCODE consortium. We collaborate closely with a number of basic scientists and clinical physicians at Harvard and affiliated hospitals.

Publications from Harvard Catalyst Profiles

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  • Yu F, Sankaran VG, Yuan GC. CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis. Bioinformatics 2021. PubMed
  • Heckler M, Ali LR, Clancy-Thompson E, Qiang L, Ventre KS, Lenehan P, Roehle K, Luoma A, Boelaars K, Peters V, McCreary J, Boschert T, Wang ES, Suo S, Marangoni F, Mempel TR, Long HW, Wucherpfennig KW, Dougan M, Gray NS, Yuan GC, Goel S, Tolaney SM, Dougan SK. Inhibition of CDK4/6 promotes CD8 T-cell memory formation. 2021. PubMed
  • Dries R, Zhu Q, Dong R, Eng CL, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George RE, Pierson N, Cai L, Yuan GC. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol 2021; 22:78. PubMed
  • Cartwright ANR, Suo S, Badrinath S, Kumar S, Melms J, Luoma A, Bagati A, Saadatpour A, Izar B, Yuan GC, Wucherpfennig KW. Immunosuppressive Myeloid Cells Induce Nitric Oxide-Dependent DNA Damage and p53 Pathway Activation in CD8 T Cells. Cancer Immunol Res 2021. PubMed
  • Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the γ-globin promoters controls hemoglobin switching. Nat Genet 2021; 53:511-520. PubMed
  • Kai Y, Li BE, Zhu M, Li GY, Chen F, Han Y, Cha HJ, Orkin SH, Cai W, Huang J, Yuan GC. Mapping the evolving landscape of super-enhancers during cell differentiation. Genome Biol 2021; 22:269. PubMed
  • Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun 2021; 12:6241. PubMed
  • Cai W, Huang J, Zhu Q, Li BE, Seruggia D, Zhou P, Nguyen M, Fujiwara Y, Xie H, Yang Z, Hong D, Ren P, Xu J, Pu WT, Yuan GC, Orkin SH. Enhancer dependence of cell-type-specific gene expression increases with developmental age. Proc Natl Acad Sci U S A 2020; 117:21450-21458. PubMed
  • Luoma AM, Suo S, Williams HL, Sharova T, Sullivan K, Manos M, Bowling P, Hodi FS, Rahma O, Sullivan RJ, Boland GM, Nowak JA, Dougan SK, Dougan M, Yuan GC, Wucherpfennig KW. Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy. Cell 2020. PubMed
  • Dong R, Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinformatics 2020; 21:158. PubMed
  • 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; 26:391-402.e5. PubMed
  • Chen J, Liang X, Zhang S, Wang S, Garcia SP, Yan P, Yu H, Li Z, Liu L, Zhang F, Wei W, Le H, Zhang Y, Yuan GC, Chen S, Chen Y, Sun K, Pu WT, Zhang B. Two faces of bivalent domain regulate VEGFA responsiveness and angiogenesis. Cell Death Dis 2020; 11:75. PubMed
  • Zhang H, Christensen CL, Dries R, Oser MG, Deng J, Diskin B, Li F, Pan Y, Zhang X, Yin Y, Papadopoulos E, Pyon V, Thakurdin C, Kwiatkowski N, Jani K, Rabin AR, Castro DM, Chen T, Silver H, Huang Q, Bulatovic M, Dowling CM, Sundberg B, Leggett A, Ranieri M, Han H, Li S, Yang A, Labbe KE, Almonte C, Sviderskiy VO, Quinn M, Donaghue J, Wang ES, Zhang T, He Z, Velcheti V, Hammerman PS, Freeman GJ, Bonneau R, Kaelin WG, Sutherland KD, Kersbergen A, Aguirre AJ, Yuan GC, Rothenberg E, Miller G, Gray NS, Wong KK. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer. Cancer Cell 2019. PubMed
  • 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. PubMed
  • Zhu Q, Liu N, Orkin SH, Yuan GC. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol 2019; 20:192. PubMed
  • Sethi I, Cai Z, Roberts TM, Yuan GC. Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110β Inhibitor KIN-193. Cancer Res 2019; 79:4524-4531. PubMed
  • Hu X, Xiang D, Xie Y, Tao L, Zhang Y, Jin Y, Pinello L, Wan Y, Yuan GC, Li Z. LSD1 suppresses invasion, migration and metastasis of luminal breast cancer cells via activation of GATA3 and repression of TRIM37 expression. Oncogene 2019. PubMed
  • 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; 572:676-680. PubMed
  • Tracy S, Yuan GC, Dries R. RESCUE: imputing dropout events in single-cell RNA-sequencing data. BMC Bioinformatics 2019; 20:388. PubMed
  • Joyce CE, Saadatpour A, Ruiz-Gutierrez M, Bolukbasi OV, Jiang L, Thomas DD, Young S, Hofmann I, Sieff C, Myers KC, Whangbo J, Libermann TA, Nusbaum C, Yuan GC, Shimamura A, Novina CD. TGFβ signaling underlies hematopoietic dysfunction and bone marrow failure in Shwachman-Diamond Syndrome. J Clin Invest 2019. PubMed
  • Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. iScience 2019; 14:226-240. PubMed
  • Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature 2019; 568:235-239. PubMed
  • 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; 363:993-998. PubMed
  • Wang S, Chen J, Garcia SP, Liang X, Zhang F, Yan P, Yu H, Wei W, Li Z, Wang J, Le H, Han Z, Luo X, Day DS, Stevens SM, Zhang Y, Park PJ, Liu ZJ, Sun K, Yuan GC, Pu WT, Zhang B. A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA. Genome Res 2019; 29:193-207. PubMed
  • 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; 10:1903. PubMed
  • 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; 10:1757. PubMed
  • 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; 10:2975. PubMed
  • Barros-Silva JD, Linn DE, Steiner I, Guo G, Ali A, Pakula H, Ashton G, Peset I, Brown M, Clarke NW, Bronson RT, Yuan GC, Orkin SH, Li Z, Baena E. Single-Cell Analysis Identifies LY6D as a Marker Linking Castration-Resistant Prostate Luminal Cells to Prostate Progenitors and Cancer. Cell Rep 2018; 25:3504-3518.e6. PubMed
  • 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; 25:1436-1445.e3. PubMed
  • 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. PubMed
  • 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; 8:12750. PubMed
  • 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; 13:946-986. PubMed
  • 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. PubMed
  • Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 2018; 172:1091-1107.e17. PubMed
  • Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics 2018. PubMed
  • Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma A, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu S, Wucherpfennig KW. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 2018. PubMed
  • 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; 359:1537-1542. PubMed
  • 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; 9:943. PubMed
  • Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 2018; 19:47. PubMed
  • Sun H, Wang J, Gong Z, Yao J, Wang Y, Xu J, Yuan GC, Zhang Y, Shao Z. Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters. Cell Discov 2018; 4:38. PubMed
  • Tsoucas D, Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biol 2018; 19:58. PubMed
  • 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; 21:65-77.e5. PubMed
  • 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; 27:842. PubMed
  • 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; 27:843. PubMed
  • 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; 18:84. PubMed
  • Adeegbe D, 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 JE, Quayle SN, Wong KK. Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-small Cell Lung Cancer. 2017. PubMed
  • 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; 8:15011. PubMed
  • 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; 49:625-634. PubMed
  • Min L, Zhang C, Qu L, Huang J, Jiang L, Liu J, Pinello L, Yuan GC, Shou C. Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. 2017; 8:21938-21953. PubMed
  • 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; 18:184-195. PubMed
  • 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; 7:41669. PubMed
  • 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. PubMed
  • Tsoucas D, Yuan GC. Recent progress in single-cell cancer genomics. Curr Opin Genet Dev 2017; 42:22-32. PubMed
  • 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. PubMed
  • 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; 1:e89014. PubMed
  • 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; 16:2053-60. PubMed
  • Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol 2016; 34:695-7. PubMed
  • 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; 22:723-6. PubMed
  • 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; 165:1389-400. PubMed
  • Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC. Robust lineage reconstruction from high-dimensional single-cell data. Nucleic Acids Res 2016. PubMed
  • 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; 531:53-8. PubMed
  • 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; 14:956-65. PubMed
  • 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; 22:163-74. PubMed
  • 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; 36:9-23. PubMed
  • 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. PubMed
  • 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; 17:144. PubMed
  • 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. PubMed
  • 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. PubMed
  • Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends Genet 2015; 31:576-86. PubMed
  • 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; 57:304-16. PubMed
  • Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. BMC Bioinformatics 2015; 16:115. PubMed
  • 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; 7:12. PubMed
  • 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; 8:53. PubMed
  • Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol 2015; 16:162. PubMed
  • 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; 111:E5643-50. PubMed
  • 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; 8:118. PubMed
  • 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; 159:1126-39. PubMed
  • 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; 130:1452-65. PubMed
  • Wu C, Wang Z, Song X, Feng XS, Abnet CC, He J, Hu N, Zuo XB, Tan W, Zhan Q, Hu Z, He Z, Jia W, Zhou Y, Yu K, Shu XO, Yuan JM, Zheng W, Zhao XK, Gao SG, Yuan ZQ, Zhou FY, Fan ZM, Cui JL, Lin HL, Han XN, Li B, Chen X, Dawsey SM, Liao L, Lee MP, Ding T, Qiao YL, Liu Z, Liu Y, Yu D, Chang J, Wei L, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Han JJ, Zhou SL, Zhang P, Zhang DY, Yuan Y, Huang Y, Liu C, Zhai K, Qiao Y, Jin G, Guo C, Fu J, Miao X, Lu C, Yang H, Wang C, Wheeler WA, Gail M, Yeager M, Yuenger J, Guo ET, Li AL, Zhang W, Li XM, Sun LD, Ma BG, Li Y, Tang S, Peng XQ, Liu J, Hutchinson A, Jacobs K, Giffen C, Burdette L, Fraumeni JF, Shen H, Ke Y, Zeng Y, Wu T, Kraft P, Chung CC, Tucker MA, Hou ZC, Liu YL, Hu YL, Liu Y, Wang L, Yuan G, Chen LS, Liu X, Ma T, Meng H, Sun L, Li XM, Li XM, Ku JW, Zhou YF, Yang LQ, Wang Z, Li Y, Qige Q, Yang WJ, Lei GY, Chen LQ, Li EM, Yuan L, Yue WB, Wang R, Wang LW, Fan XP, Zhu FH, Zhao WX, Mao YM, Zhang M, Xing GL, Li JL, Han M, Ren JL, Liu B, Ren SW, Kong QP, Li F, Sheyhidin I, Wei W, Zhang YR, Feng CW, Wang J, Yang YH, Hao HZ, Bao QD, Liu BC, Wu AQ, Xie D, Yang WC, Wang L, Zhao XH, Chen SQ, Hong JY, Zhang XJ, Freedman ND, Goldstein AM, Lin D, Taylor PR, Wang LD, Chanock SJ. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. Nat Genet 2014; 46:1001-6. PubMed
  • Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. 2014. PubMed
  • 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; 157:549-64. PubMed
  • 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; 111:E344-53. PubMed
  • 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; 53:32-48. PubMed
  • Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol 2014; 15:525. PubMed
  • 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; 8:1303-20. PubMed
  • 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; 342:253-7. PubMed
  • 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; 13:492-505. PubMed
  • 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; 33:2879-90. PubMed
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics 2013. PubMed
  • 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; 27:683-98. PubMed
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE 2013; 8:e64832. PubMed
  • Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA. Chromatin signature of widespread monoallelic expression. Elife 2013; 2:e01256. PubMed
  • Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E. Modeling the dynamics of bivalent histone modifications. PLoS ONE 2013; 8:e77944. PubMed
  • 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; 23:796-811. PubMed
  • Yuan GC. Linking genome to epigenome. 2012. PubMed
  • Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation stages. PLoS ONE 2012; 7:e31414. PubMed
  • 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; 13:R16. PubMed
  • 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; 286:30462-70. PubMed
  • Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics 2011; 12:408. PubMed
  • 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; 30:5364-80. PubMed
  • 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; 39:222-33. PubMed
  • Liu Y, Shao Z, Yuan GC. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010; 96:17-26. PubMed
  • 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; 107:8486-91. PubMed
  • Lantermann AB, Straub T, StrÃ¥lfors 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; 17:251-7. PubMed
  • Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics 2010; 11:557. PubMed
  • 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; 139:1303-14. PubMed
  • 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; 29:2960-81. PubMed
  • 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; 93:140-5. PubMed
  • Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol 2009; 16:341-55. PubMed
  • 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; 32:491-502. PubMed
  • Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol 2008; 4:e13. PubMed
  • 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; 17:928-39. PubMed
  • 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:R70. PubMed
  • 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; 309:626-30. PubMed
  • Yuan GC, Nam K, Antonsen TM, Ott E, Guzdar PN. Power spectrum of passive scalars in two dimensional chaotic flows. Chaos 2000; 10:39-49. PubMed
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DF/HCC members that share similar concepts* with Guo-Cheng Yuan, PhD but have yet to coauthor a publication with this researcher.

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