Publications

Selected Publications

  1. 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 single-cell spatial expression data. Genome Biology. 2021 Mar 8. [ paper] [ Link to main website ][ Link to GitHub ]
  2. 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;36(12):1183. [ paper ] [ Research highlight from Nature Methods. ]
  3. 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 Mar 5;9(1):943. [ paper ].
  4. 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 ]
  5. Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 Jul 12;34(7):695-7. [ paper ].
  6. Dries R, Chen J, Del Rossi N, Khan MM, Sistig A, Yuan GC. Advances in spatial transcriptomic data analysis. Genome Res. 2021 Oct;31(10):1706-1718. [ paper ]
  7. 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 Aug 6;182(3):655-671.e22. [ Paper ]
  8. 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 Apr;568(7751):235-239. [ paper ]
  9. Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L. Integrated spatial genomics reveals global architecture of single nuclei.  Nature. 2021 Feb;590(7845):344-350.  [ paper ]
  10. 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 Feb 22;172(5):1091-1107. [ paper ].
  11. 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 ]

All Publications

Book

  1. Yuan, GC (Ed.). Computational methods for single-cell data analysis. Methods in Molecular Biology. Feb 2019. [ Product Flyer ] [ Publisher Website ].

Preprints

  1. Chen JG*, Chávez-Fuentes JC*, O’Brien M, Xu J, Ruiz E, Wang W, Amin I, Sarfraz I, Guckhool P, Sistig A, Yuan GC†, Dries R†. Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem. bioRxiv. 2023. [ paper ][ Link to main website ][ Link to GitHub ]
  2. Cao X, Ma T, Fan R, Yuan GC. Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development. bioRxiv. 2023. [ paper ]
  3. Choi J, Ehrlich ME, Roussos P, Wang P, Yuan GC, Song X. QuadST: A Powerful and Robust Approach for Identifying Cell–Cell Interaction-Changed Genes on Spatially Resolved Transcriptomics. bioRxiv. 2023. [ paper ]
  4. Polonsky M, Gerhardt LMS, Yun J, Koppitch K, Colón KL, Amrhein H, Zheng S, Yuan GC, Thomson M, Cai L, McMahon AP. Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease. bioRxiv. 2023. [ paper ]
  5. Liu T, Zhu Q, Yan K, Bingham T, Cha HJ, Mehta S, Schlaeger TM, Yuan GC, Orkin SH. Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions. bioRxiv. 2023. [ paper ]

Papers

  1. Kai Y, Liu N, Orkin SH†, Yuan GC†. Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC. BMC Genomics. 2023 Oct 13;24(1):614. [ paper ]
  2. Zhu K, Bendl J, Rahman S, Vicari JM, Coleman C, Clarence T, Latouche O, Tsankova NM, Li A, Brennand KJ, Lee D, Yuan GC, Fullard JF, Roussos P. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Sci Adv. 2023 Oct 13;9(41):eadg3754. [ paper ][ Science News ]
  3. Zhou P, VanDusen NJ, Zhang Y, Cao Y, Sethi I, Hu R, Zhang S, Wang G, Ye L, Mazumdar N, Chen J, Zhang X, Guo Y, Li B, Ma Q, Lee JY, Gu W, Yuan GC, Ren B, Chen K, Pu WT. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation. Dev Cell. 2023 May 22;58(10):898-914.e7. [ paper ]
  4. Wang R, Zhang P, Wang J, Ma L, E W, Suo S, Jiang M, Li J, Chen H, Sun H, Fei L, Zhou Z, Zhou Y, Chen Y, Zhang W, Wang X, Mei Y, Sun Z, Yu C, Shao J, Fu Y, Xiao Y, Ye F, Fang X, Wu H, Guo Q, Fang X, Li X, Gao X, Wang D, Xu PF, Zeng R, Xu G, Zhu L, Wang L, Qu J, Zhang D, Ouyang H, Huang H, Chen M, Ng SC, Liu GH, Yuan GC, Guo G, Han X. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res. 2023 Jan 25;51(2):501-516. [ paper ]
  5. Qin G, Park ES, Chen X, Han S, Xiang D, Ren F, Liu G, Chen H, Yuan GC, Li Z. Distinct niche structures and intrinsic programs of fallopian tube and ovarian surface epithelial cells. iScience. 2022 Dec 22;26(1):105861. [ paper ]
  6. Badrinath S, Dellacherie MO, Li A, Zheng S, Zhang X, Sobral M, Pyrdol JW, Smith KL, Lu Y, Haag S, Ijaz H, Connor-Stroud F, Kaisho T, Dranoff G, Yuan GC, Mooney DJ, Wucherpfennig KW. Nature. 2022 May 25.  Online ahead of print. [ paper ]
  7. Olsen SN, Godfrey L, Healy JP, Choi YA, Kai Y, Hatton C, Perner F, Haarer EL, Nabet B, Yuan GC, Armstrong SA. MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. Mol Cell. 2022 Mar 17;82(6):1140-1155.e11. [ paper ]
  8. Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application. Mol Neurodegener. 2022 Mar 2;17(1):17. [ paper ]
  9. Del Rossi N*, Chen JG*, Yuan GC†, Dries R†. Analyzing Spatial Transcriptomics Data Using Giotto. Curr Protoc. 2022 Apr;2(4):e405. doi: 10.1002/cpz1.405. [ paper ][ website ]
  10. Gao X, Wang Y, Ribeiro CF, Manokaran C, Chang H, Von T, Rodrigues S, Cizmecioglu O, Jia S, Korpal M, Korn JM, Wang Z, Schmit F, Jiang L, Pagliarini R, Yang Y, Sethi I, Signoretti S, Yuan GC, Loda M, Zhao JJ, Roberts TM. Blocking PI3K p110β Attenuates Development of PTEN-Deficient Castration-Resistant Prostate Cancer. Mol Cancer Res. 2022 May 4;20(5):673-685. [ paper ]
  11. Xu P, Wang M, Song WM, Wang Q, Yuan GC, Sudmant PH, Zare H, Tu Z, Orr ME, Zhang B. The landscape of human tissue and cell type specific expression and co-regulation of senescence genes. Mol Neurodegener. 2022 Jan 9;17(1):5. [ paper ]
  12. 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 Oct 29;12(1):6241. [ paper ]
  13. Takei Y, Zheng S, Yun J, Shah S, Pierson N, White J, Schindler S, Tischbirek CH, Yuan GC, Cai L. Single-cell nuclear architecture across cell types in the mouse brain. Science. 2021 Sep 30:eabj1966. [ paper ]
  14. 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 Sep 15;22(1):269. [ paper ]
  15. Dries R, Chen J, Del Rossi N, Khan MM, Sistig A, Yuan GC. Advances in spatial transcriptomic data analysis. Genome Res. 2021 Oct;31(10):1706-1718. [ paper ]
  16. Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O’Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol. 2021 Aug 5;22(1):220. [ paper ]
  17. VanDusen NJ, Lee JY, Gu W, Butler CE, Sethi I, Zheng Y, King JS, Zhou P, Suo S, Guo Y, Ma Q, Yuan GC, Pu WW. Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation. Nat Commun. 2021 Jul 21;12(1):4442. [ paper ]
  18. Fullard JF, Lee HC, Voloudakis G, Suo S, Javidfar B, Shao Z, Peter C, Zhang W, Jiang S, Corvelo A, Wargnier H, Woodoff-Leith E, Purohit DP, Ahuja S, Tsankova NM, Jette N, Hoffman GE, Akbarian S, Fowkes M, Crary JF, Yuan GC, Roussos P. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19.  Genome Med. 2021 Jul 19;13(1):118. [ paper ].
  19. Dong R, Yuan, GC. SpatialDWLS: accurate deconvolution of spatial transcriptomic data.  Genome Biology. 2021 May 10. [ paper ][ GitHub ][ implementation in Giotto ]
  20. 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. Cancer Discov. 2021 May 3 [ paper ].
  21. 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 Apr;53(4):511-520. [paper].
  22. 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 single-cell spatial expression data. Genome Biology. 2021 Mar 8. [ paper][ Link to main website ][ Link to GitHub ].
  23. Wang J, Sun H, Jiang M, Li J, Zhang P, Chen H, Mei Y, Fei L, Lai S, Han X, Song X, Xu S, Chen M, Ouyang H, Zhang D†, Yuan GC†, Guo G†. Tracing cell-type evolution by cross-species comparison of cell atlases. Cell Rep. 2021 Mar 2;34(9):108803 [ paper ]
  24. Cartwright ANR, Suo S, Badrinath S, Kumar S, Melms JC, 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 Jan 29. [paper]
  25. Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L. Integrated spatial genomics reveals global architecture of single nuclei.  Nature. 2021 Feb;590(7845):344-350.  [ paper ]
  26. 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. Jul 9:btab507. [ paper ][ Link to GitHub ]
  27. Kai Y, Tsoucas S, Suo S, Yuan GC. Multi-scale annotations of chromatin states in 127 human cell-types [ bioRxiv ][ Link to GitHub ].
  28. Guo Y, Cao Y, Jardin BD, Sethi I, Ma Q, Moghadaszadeh B, Troiano EC, Mazumdar N, Trembley MA, Small EM, Yuan GC, Beggs AH, Pu WT. Sarcomeres regulate murine cardiomyocyte maturation through MRTF-SRF signaling. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2008861118. [ paper ]
  29. 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 Sep 1;117(35):21450-21458.  [ paper ]
  30. 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 Aug 6;182(3):655-671.e22.  [ paper ]
  31. Dong R. Yuan GC. GiniClust3: a fast and memory-efficient tool for rare cell type identification. BMC Bioinformatics.2020 Apr 25;21(1):158 [ paper ][ Link to Github ].
  32. 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 5;26(3):391-402.e5 [ paper ]
  33. 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 Jan 30;11(1):75. [ paper ].
  34. 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 Jr, 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. 2020 Jan 13;37(1):37-54.e9. [ paper ]
  35. 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 Dec 5;4(23). [ paper ]
  36. 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 Oct 28;10(1):4907. [ paper ].
  37. HuBMAP Consortium^. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019 Oct;574(7777):187-192. (^ including Dries R, Zhu Q, and Yuan GC). [ paper ].
  38. Zhu Q, Liu N, Orkin SH†, Yuan GC†. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol. 2019 Sep 9;20(1):192. [ paper ][ website ].
  39. 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 Aug;572(7771):676-680. [ paper ].
  40. 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 Oct;38(44):7017-7034 [ paper ].
  41. Tracy S, Yuan GC, Dries R. RESCUE: imputing dropout events in single-cell RNA-sequencing data. BMC Bioinformatics. 2019 Jul 12;20(1):388 [ paper ][ GitHub ].
  42. 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 Jul 10. [ paper ].
  43. 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 Jul 5;10(1):2975. [ paper ][ GitHub ][ latest version in CRAN R ].
  44. 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 Jun 18;130 [ paper ].
  45. 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 Apr 23;10(1):1903 [ paper ][ [ website ]
  46. 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 Apr 15;10(1):1757. [ paper ].
  47. 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 Apr;568(7751):235-239. [ paper ]
  48. Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. iScience. 2019 Apr 26;14:226-240. [ paper ] [ website ].
  49. 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. Science. 2019 Mar 1;363(6430):993-998. [ paper ].
  50. 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 Feb;29(2):193-207. [ paper ].
  51. 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 Dec 18;25(12):3504-3518.e6. [ paper ].
  52. 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 Nov 6;25(6):1436-1445.e3 [ paper ][ Website ].
  53. 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. [ paper ][ Research highlight from Nature Methods. ][ CRAN R ][ implemetnation in Giottto ]
  54. 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 Sep 21;9(1):3837. [ paper ].
  55. 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 Aug 24;8(1):12750. [ paper ].
  56. 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 Jul 10;4:38. [ paper ].
  57. Tsoucas D, Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biology. 2018 May 10;19(1):58. [ paper ] [ see latest version in GutHub].
  58. 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 May;13(5):946-986. [ paper ].
  59. 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 via high throughput single-cell RNA-sequencing. Genome Biol. 2018 Apr 5;19(1):47. [ paper ].
  60. 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 Apr 5;173(2):430-442.e17. [ paper ].
  61. Ferrari de Andrade L, Tay RE, Pan D, Luoma AM, Ito Y, Badrinath S, Tsoucas D, Franz B, May KF Jr., 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. [ paper ].
  62. 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 Mar 5;9(1):943. [ paper ].
  63. Jiang L, Tsoucas D, Yuan GC. Assessing Inequality in Transcriptomic Data. Cell Syst. 2018 Feb 28;6(2):149-150 [ paper ] (Preview)
  64. 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 Feb 22;172(5):1091-1107. [ paper ].
  65. Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics. 2018 Jun 1;34(11):1930-1933 [ paper ] [ GitHub ].
  66. 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 Feb 16;359(6377):770-775. [ paper ].
  67. 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 Apr;141(4):1250-1258. [ paper ].
  68. Huang D, Guo G, Yuan P, Ralston A, Sun L, Huss M, Mistri T, Pinello L, Ng HH, Yuan G, Ji J, Rossant J, Robson P, Han X. The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation. Sci Rep. 2017 Dec 7;7(1):17156. [ paper ].
  69. 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 Jul 6;21(1):65-77.e5. [ paper ].
  70. 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 May 8;18(1):84. [ paper ].
  71. 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. Cancer Discov. 2017 Aug;7(8):852-867. [ paper ]
  72. 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. Oncotarget. 2017 Mar 28;8(13):21938-21953. [ paper ].
  73. 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. Nature Communications. 2017 Apr 7;8:15011. [ paper ]. [ Chromatin state annotations in 3 human cell lines ] [ the latest version in GitHub ].
  74. 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 9;120(12):1874-1888. [ paper ].
  75. 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. [ paper ]
  76. 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 Jan 31;7:41669. [ paper ]
  77. 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 Mar;27(3):386-401. [ paper ]
  78. Tsoucas D, Yuan GC. Recent Progress in Single-Cell Cancer Genomics. Current Opinion in Genetics & Development. 2017 42:22–32. Review. [ paper ]
  79. 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 Feb;18(2):184-195. [ paper ].
  80. 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 ].
  81. 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 ].
  82. 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 ].
  83. 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 ] [ see latest version in GitHub ].
  84. 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 ] [see latest version in GitHub ].
  85. 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 ].
  86. 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 ].
  87. 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 ] [ GitHub ].
  88. 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 ].
  89. 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 3;531(7592):53-8. [ paper ].
  90. 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 ].
  91. 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 ].
  92. 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 ]
  93. 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 ].
  94. Saadatpour A, Lai S, Guo G†, Yuan GC†. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015 Oct;31(10):576-86. Review. [ paper ]
  95. 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 ]
  96. Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol. 2015 Aug 14;16(1):162. [ paper ] [ GitHub ]
  97. 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 ]
  98. 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 ]
  99. 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 ]
  100. 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 ]
  101. 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 ] [ GitHub ]
  102. 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 ]
  103. 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 ]
  104. 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 ]
  105. 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 ]
  106. Pinello L, Lo Bosco G†, Yuan GC†. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May;15(3):419-30. Review. [ paper ] [ GitHub ].
  107. 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 ]
  108. 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 ].
  109. 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) ] [ see latest version in GitHub ]
  110. 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. [ Paper ]
  111. 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. [ paper ].
  112. 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 ]
  113. 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. (Cover Article) [ paper ] [ Commentary Article ]
  114. 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 ]
  115. 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)
  116. 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]
  117. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE. 2013 8(5): e64832. [paper] [ website ].
  118. 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] [ superceded by diHMM ].
  119. 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]
  120. 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]
  121. 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). [paper] [ website ]
  122. Yuan GC. Linking genome to epigenome. Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):297-309. Review. [paper]
  123. Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation status. PLoS ONE. 2012. 7(2): e31414. [paper]
  124. 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].
  125. 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]
  126. 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]
  127. Larson JL, Yuan GC. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12;11:557. [paper] [ superceded by diHMM ].
  128. 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. [paper]
  129. 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]
  130. 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]
  131. 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]
  132. 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]
  133. 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]
  134. 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]
  135. Yuan GC. Targeted recruitment of histone modifications in humans predicted by genomic sequences. J Comput Biol 2009 Feb;16(2):341-355.[paper]
  136. 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]
  137. 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]
  138. Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol 2008 Jan;4(1):e13. [paper] [MATLAB code]
  139. 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]
  140. 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]
  141. 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

  142. 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 ].
  143. 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 ].
  144. 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 ].
  145. 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 ].
  146. 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 ].
  147. Haller, G, Yuan G. Lagrangian coherent structures and mixing in two-dimensional turbulence. Physica D 2000;147(3-4):352-370. [ paper ].
  148. 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 ]
  149. Yuan GC, Yorke JA. Collapsing of chaos in one dimensional maps. Physica D 2000;36(1-2):18-30. [ paper ]
  150. 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 ]
  151. Yuan G, Hunt BR. Optimal orbits of hyperbolic systems. Nonlinearity 1999;12(4):1207-1224. [ paper ]