Publications | Fan Research Lab

2022

1. Deng P, Yuan Q, Cheng Y, Li J, Liu Z, Liu Y, Li Y, Su T, Wang J, Salvo ME, Wang W, Fan G, Lyons K, Yu B, Wang CY. Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging. Cell Stem Cell. 2021 Jun 3;28(6):1057-1073.e7. doi: 10.1016/j.stem.2021.01.010. Epub 2021 Feb 10. PMID: 33571444

2. Wei Y, Zhang C, Fan G, Meng L. Organoids as Novel Models for Embryo Implantation Study. Reprod Sci. 2021 Jun;28(6):1637-1643. doi: 10.1007/s43032-021-00501-w. Epub 2021 Mar 1. PMID: 33650092 Review.

3. Jansova D, Aleshkina D, Jindrova A, Iyyappan R, An Q, Fan G, Susor A. Single Molecule RNA Localization and Translation in the Mammalian Oocyte and Embryo. J Mol Biol. 2021 Sep 17;433(19):167166. doi: 10.1016/j.jmb.2021.167166. Epub 2021 Jul 20. PMID: 34293340.

4. Ma L, Wang J, Ge J, Wang Y, Zhang W, Du Y, Luo J, Li Y, Wang F, Fan G, Chen R, Yao B, Zhao Z, Guo ML, Kim WK, Chai Y, Chen JF. Reversing neural circuit and behavior deficit in mice exposed to maternal inflammation by Zika virus. EMBO Rep. 2021 Aug 4;22(8):e51978. doi: 10.15252/embr.202051978. Epub 2021 Jul 7. PMID: 34232545

5. Song Y, Soto J, Wang P, An Q, Zhang X, Hong S, Lee LP, Fan G, Yang L, Li S. Asymmetric Cell Division of Fibroblasts is An Early Deterministic Step to Generate Elite Cells during Cell Reprogramming. Adv Sci (Weinh). 2021 Feb 25;8(7):2003516. doi: 10.1002/advs.202003516. eCollection 2021 Apr. PMID: 33854891

2021

1. Youjin Hu, Kevin Huang , Qiao Zeng , Yun Feng , Qiong Ke, Qin An, Lian-Ju Qin, YuGui Cui , Ying Guo , Dicheng Zhao , Yu Peng, Di Tian , Kun Xia , Yong Chen , Bin Ni , Jinmei Wang, Xianmin Zhu , Lai Wei, Yizhi Liu , Peng Xiang , Jia-Yin Liu , Zhigang Xue , Guoping Fan. Single-cell analysis of nonhuman primate preimplantation development in comparison to humans and mice. Developmental Dynamics. 2021 Jan 15. doi: 10.1002/dvdy.295

2. He D, Wang D, Lu P, Yang N, Xue Z, Zhu X, Zhang P, Fan G. Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations. Oncogene. 2021 Jan;40(2):355-368. doi: 10.1038/s41388-020-01528-0.

3. Pan B, Fan G. Stem cell-based treatment of kidney diseases Exp Biol Med (Maywood). 2020 May;245(10):902-910. doi: 10.1177/153537022091590.

4. Hu Y, Zhong J, Xiao Y, Xing Z, Sheu K, Fan S, An Q, Qiu Y, Zheng Y, Liu X, Fan G, Liu Y. Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation. Nat Commun. 2020 Oct 13;11(1):5148. doi: 10.1038/s41467-020-18976-7.

5. Lu P, Yang G, Jiang L, He W, Wu W, Qi L, Shen S, Rao J, Zhang P, Xue Z, Jiang C, Fan G, Zhu X. Characterizing disease progression of nonalcoholic steatohepatitis in Leptin-deficient rats by integrated transcriptome analysis. Exp Biol Med (Maywood). 2020 Dec 10:1535370220976530. doi: 10.1177/1535370220976530.

2020

1. Kevin Huang, Qiao Zeng, Yun Feng, Youjin Hu, Qin An, Taibo Li, Lian-Ju Qin, Jia-yin Liu, Zhigang Xue, Guoping Fan X-chromosome dosage compensation dynamics in human early embryos. bioRxiv 2020.03.08.982694; doi: https://doi.org/10.1101/2020.03.08.982694

3. Youjin Hu, Jiawei Zhong, Yuhua Xiao, Zheng Xing, Katherine Sheu, Shuxin Fan, Qin An, Yuanhui Qiu, Yingfeng Zheng, Xialin Liu, Guoping Fan, Yizhi Liu scCAT-seq:single-cell identification and quantification of mRNA isoforms by cost-effective short-read sequencing of cap and tail. bioRxiv 2019.12.11.873505; doi: https://doi.org/10.1101/2019.12.11.873505

4. Ping Lu, Guang Yang, Wen He, Wanwan Wu, Lingbin Qi, Shijun Shen, Junhua Rao, Guoping Fan, Zhigang Xue, Peng Zhang, Cizhong Jiang, Xianmin Zhu Leptin deficient rats develop nonalcoholic steatohepatitis with unique disease progression. bioRxiv 594978; doi: https://doi.org/10.1101/594978

2019

1. Fan S, Ding X, Rao P, Zheng Y, Mao F, Hu Y, Liu X, Fan G. Multimodal imaging of the retina and choroid in healthy Macaca fascicularis at different ages. Graefes Arch Clin Exp Ophthalmol. 2019 Mar;257(3):455-463.

2. An Q, Hu Y, Li Q, Chen X, Huang J, Pellegrini M, Zhou X, Rettig M, Fan G. The size of cell free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients. Precision Clinical Medicine. September 2019, Pages 131-139.

3. Mao X*, An Q*, Xi H, Yuan S, Yang X, Wang J, Hu Y, Liu Q, Fan G, Single cell RNA sequencing of hESC-derived 3D retinal organoids reveals novel genes regulating RPC commitment in early human retinogenesis. Stem Cell Reports. 2019 Sep 11. pii: S2213-6711(19)30306-6. doi: 10.1016/j.stemcr.2019.08.012.

4. Lv B, An Q, Zeng Q, Zhang X, Lu P, Wang Y, Zhu X, Ji Y, Fan G, Xue Z, Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses. PLoS Biol. 2019 Oct 9;17(10):e3000187. doi: 10.1371/journal.pbio.3000187. [Epub ahead of print]

5. Hu Y, An Q, Guo Y, Zhong J, Fan S, Rao P, Liu X, Liu Y, Fan G, Simultaneous Profiling of mRNA Transcriptome and DNA Methylome from a Single Cell. Methods Mol Biol. 2019;1979:363-377. doi: 10.1007/978-1-4939-9240-9_21.

2018

1. Yang J, Yi N, Zhang J, He W, He D, Wu W, Xu S, Li F, Fan G, Zhu X, Xue Z, Zhou W. Generation and characterization of a hypothyroidism rat model with truncated thyroid stimulating hormone receptor. Sci Rep. 2018 Mar 5;8(1):4004.

2. He D, Zhang J, Wu W, Yi N, He W, Lu P, Li B, Yang N, Wang D, Xue Z, Zhang P, Fan G, Zhu X. A novel immunodeficient rat model supports human lung cancer xenografts. FASEB J. 2018 Jun 26:fj201800102RR. doi: 10.1096/fj.201800102RR.

3. Li Y, Zhang Z, Chen J, Liu W, Lai W, Liu B, Li X, Liu L, Xu S, Dong Q, Wang M, Duan X, Tan J, Zheng Y, Zhang P, Fan G, Wong J, Xu GL1, Wang Z, Wang H, Gao S, Zhu B. Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1. Nature. 2018 Dec;564(7734):136-140. doi: 10.1038/s41586-018-0751-5. Epub 2018 Nov 28.

2017

1. 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.

2. Chunyuan Guo, Lirong Pei, Xiao Xiao, Qingqing Wei, Han-Fei Ding, Shuang Huang, Guoping Fan, Huidong Shi, Zheng Dong. DNA methylation protects against cisplatin-induced kidney injury by regulating specific genes including Irf8. Kidney International (in press)

2016

1. Xia Li, Qian Zhang, Yuanyuan Ding, Yiqi Liu, Dezhi Zhao, Kai Zhao, Qicong Shen, Xingguang Liu, Xuhui Zhu, Nan Li, Zhongyi Cheng, Guoping Fan, Qingqing Wang, Xuetao Cao. Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat Immunol. 2016 Jul;17(7):806-15.

2. Youjin Hu, Kevin Huang, Qin An, Guizhen Du, Ganlu Hu, Jinfeng Xue, Xianmin Zhu, Cun-Yu Wang, Zhigang Xue, and Guoping Fan Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 2016 May 5;17(1):88.

3. Moyon S, Huynh JL, Dutta D, Zhang F, Ma D, Yoo S, Lawrence R, Wegner M, John GR, Emery B, Lubetzki C, Franklin RJ, Fan G, Zhu J, Dupree JL, Casaccia P. Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage. Cell Rep. 2016 Apr 13. pii: S2211-1247(16)30331-X.

4. Lina Lu, Bo Lv, Kevin Huang, Zhigang Xue, Xianmin Zhu, Guoping Fan (2016) Recent advances in preimplantation genetic diagnosis and screening (Mini-review) J Assist Reprod Genet. 2016 Jun 7. [Epub ahead of print]

5. Xu S, Zhu X, Li H, Hu Y, Zhou J, He D, Feng Y, Lu L, Du G, Hu Y, Liu T, Wang Z, Ding G, Chen J, Gao S, Wu F, Xue Z, Li Y, Fan G. The 14th Ile residue is essential for Leptin function in regulating energy homeostasis in rat. Sci Rep. 2016 Jul 5;6:28508.

6. Huang B, Ning S, Zhang Q, Chen A, Jiang C, Cui Y, Hu J, Li H, Fan G, Qin L, Liu J. Bisphenol A Represses Dopaminergic Neuron Differentiation from Human Embryonic Stem Cells through Downregulating the Expression of Insulin-like Growth Factor 1. Mol Neurobiol. 2016 Jun 7. [Epub ahead of print]

7. King AD, Huang K., Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, and Fan G. Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2016 Sep 27;17(1):289-302.

8. Hu G, Huang K, Hu Y, Du G, Xue Z, Zhu X and Fan G. Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons. Sci Rep. 2016 Aug 25;6:31851.

9. Song Q, Yuan S, An Q, Chen Y, Mao FF, Liu Y, Liu Q, Fan G. Directed differentiation of human embryonic stem cells to corneal endothelial cell-like cells: A transcriptomic analysis. Exp Eye Res. 2016 Aug 11.

10. Lu P, Chen X, Feng Y, Zeng Q, Jiang C, Zhu X, Fan G, Xue Z. Integrated transcriptome analysis of human iPS cells derived from a fragile X syndrome patient during neuronal differentiation. Sci China Life Sci. 2016 Oct 11.

11. Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X, White S, Dahdouli M, Rio Deiros D, Below JE, Salerno W, Cox L, Fan G, Ferguson B, Horvath J, Johnson Z, Kanthaswamy S, Kubisch HM, Liu D, Platt M, Smith DG, Sun B, Vallender EJ, Wang F, Wiseman RW, Chen R, Muzny DM, Gibbs RA, Yu F, Rogers J. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res. 2016 Dec;26(12):1651-1662. Epub 2016 Oct 17.

2015

1. Huang B, Ning S, Zhuang L, Jiang C, Cui Y, Fan G, Qin L, Liu J. Ethanol Inactivated Mouse Embryonic Fibroblasts Maintain the Self-Renew and Proliferation of Human Embryonic Stem Cells. PLoS One. 2015 Jun 19;10(6):e0130332.

2. Yuan S, Fan G. 2015. Stem cell-based therapy of corneal epithelial and endothelial diseases. Regen Med. 2015 May;10(4):495-504. PDF

3. Feng J, Shao N, Szulwach KE, Vialou V, Huynh J, Zhong C, Le T, Ferguson D, Cahill ME, Li Y, Koo JW, Ribeiro E, Labonte B, Laitman BM, Estey D, Stockman V, Kennedy P, Courousse T, Mensah I, Turecki G, Faull KF, Ming GL, Song H, Fan G, Casaccia P, Shen L, Jin P, Nestler EJ.. 2015. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nat Neurosci. 2015 Apr;18(4):536-44.

4. Hou S, Choi JS, Chen KJ, Zhang Y, Peng J, Garcia MA, Yu JH, Thakore-Shah K, Ro T, Chen JF, Peyda P, Fan G, Pyle AD, Wang H, Tseng HR. 2015. Supramolecular Nanosubstrate-Mediated Delivery for Reprogramming and Transdifferentiation of Mammalian Cells. Small. 2015 Jun 3;11(21):2499-504.

5. Huang B, Jiang C, Chen A, Cui Y, Xie J, Shen J, Chen J, Cai L, Liao T, Ning S, Jiang SW, Fan G, Qin L, Liu J. Establishment of human-embryonic-stem-cell line from mosaic trisomy 9 embryo. Taiwan J Obstet Gynecol. 2015 Oct;54(5):505-11.

2014

1. Kohno D, Lee S, Harper MJ, Kim KW, Sone H, Sasaki T, Kitamura T, Fan G, Elmquist JK. 2014. Dnmt3a in Sim1 neurons is necessary for normal energy homeostasis.
J Neurosci. 2014 Nov 12;34(46):15288-96.

2. Huang K, Maruyama T, Fan G. 2014. The naive state of human pluripotent stem cells: a synthesis of stem cell and preimplantation embryo transcriptome analyses.
Cell Stem Cell. 2014 Oct 2;15(4):410-5. Data

3. Huang K, Wu Z, Liu Z, Hu G, Yu J, Chang K, Kim KP, Le T, Faull K, Rao N, Xue Z, Wang CY, Pellegrini M, Fan G. 2014. Selective demethylation and altered gene expression are associated with ICF Syndrome in human induced pluripotent stem cells and mesenchymal stem cells. Hum Mol Genet. 2014 Dec 15;23(24):6448-57 [Epub 2014 Jul 15].

4. Zhang, X, Li B, Li W, Ma L, Li L, Zheng D, Yang W, Chu M, Mailman R, Zhu J, Fan G, Archer T, Wang Y. 2014. Transcriptional repression by BRG1-SWI/SNF components affects pluripotency of human embryonic stem cells. Stem Cell Reports. 2014 Sep 9;3(3):460-74.

5. Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T, Suver C, Molony C, Melquist S, Johnson AD, Fan G, Stone DJ, Schadt EE, Casaccia P, Emilsson V, Zhu J. 2014. Common dysregulation Network in the Human Prefrontal Cortex underlies Two Neurodegenerative Diseases. Molecular Systems Biology. 2014 Jul 30;10(7):743.

6. Liu Z, Jiang RF, Yuan S, Wang N, Feng Y, Hu G, Zhu X, Huang K, Xu G, Liu Q, Xue Z, Fan G. 2014. Integrated analysis of DNA methylation and RNA transcriptome during the differentiation of human pluripotent stem cells into retinal pigment epithelial cells. PLoS One. 2014 Mar 17;9(3):e91416.

7. Liu B, Tahk S, Yee KM, Yang R, Yang Y, Mackie R, Hsu C, Chernishof V, O'Brien N, Jin Y, Fan G, Lane TF, Rao J, Slamon D, Shuai K. 2014. PIAS1 regulates breast tumorigenesis through selective epigenetic gene silencing. PLoS One. 2014 Feb 24;9(2):e89464.

8. Guo JU, Su Y, Shin JH, Shin J, Li H, Xie B, Zhong C, Hu S, Le T, Fan G, Zhu H, Chang Q, Gao Y, Ming GL, Song H. 2014. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci. 2014 Feb;17(2):215-22.Epub 2013 Dec 22.

9. Huang K and Fan G. 2014. "Epigenomics: An Overview", in The OMICs: Applications in Neuroscience. Coppola G, Ed. New York: Oxford University Press, 2014, pp. 27-41.

10. Yuan Songtao, Xue Zhigang, LIN Qing, Liu Qinghuai, Fan Guoping (2014). Characterization of human fetal retinal pigment epithelial cells in culture: proliferation rate and marker expression. Chinese Journal of Cell Stem Cell Vol 4 No. 1. Pp16-20.

2013

1. Huang K*, Shen Y*, Bibikova M, April C, Wang AY, Cheng LZ, Nagy A, Pellegrini M, Fan JB, Fan G. 2013. A panel of CG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells.
Stem Cell Reports. 2013 Dec 26;2(1):36-43.

2. Wang QC, Zhu X, Feng Y, Xue, Z, and Fan G. 2013. Single-Cell Genomics: An Overview (Review). Frontier in Biology Vol 8, Issue 6, pp 569-576.

3. Xue Z*, Huang K* (*co-first authors), Cai C, Huang Q, Cai L, Jiang C, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu J, Horvath S, Fan G. 2013. Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing.
Nature. Aug 29;500(7464):593-7

4. Vincent JJ, Huang Y, Chen PY, Feng S, Calvopina JH, Nee K, Lee SA, Le T, Yoon AJ, Faull K, Fan G, Rao A, Jacobsen SE, Pellegrini M, Clark AT. 2013. Stage-specific Roles for Tet1 and Tet2 in DNA demethylation in primordial germ cells.
Cell Stem Cell. 2013 Apr 4;12(4):470-8.

5. Chen Y, Huang K, Xue Z, Nakatsu, MN, Deng SX, Fan G. Identification of Novel Molecular Markers through Transcriptomic Analysis in Human Fetal and Adult Corneal Endothelial Cells. Human Molecular Genetics 22(7):1271-9

2012

1. Kun-Do Rhee, Juehua Yu, Carrie Yue Zhao, Guoping Fan, and Xian-Jie Yang. 2012. Dnmt1-dependent DNA methylation is essential for photoreceptor terminal differentiation and retinal neuron survival. Cell Death Dis. 2012 Nov 22;3:e427.

2. Cushman JD, Maldonado J, Kwon EE, Garcia AD, Fan G, Imura T, Sofronlew MV, Fanselow MS. 2012. Juvenile neurogenesis makes essential contributions to adult brain structure and plays a sex-dependent role in fear memories. Front Behav Neurosci. 2012;6:3. Epub 2012 Feb 2.

3. Hu G*, Huang K*, Yu J, Gopalakrishna-Pillai S, Kong J, Xu H, Liu Z, Zhang K, Xu J, Luo Y, Li S, Sun YE, Iverson LE, Xue Z, Fan G. 2012. Identification of miRNA Signatures during the Differentiation of hESCs into Retinal Pigment Epithelial Cells.
PLoS One. 2012;7(7):e37224. Epub 2012 Jul 27.

4. Moore LD, Le T, Fan G. 2012. DNA Methylation and Its Basic Function. Neuropsychopharmacology. 2012 Jul 11. doi: 10.1038/npp.2012.112.

5. Li J, Jiang TX, Hughes MW, Wu P, Widelitz RB, Fan G, Chuong CM. 2012. Progressive Alopecia Reveals Decreasing Stem Cell Activation Probability during Aging of Mice with Epidermal Deletion of DNA Methyltransferase 1. J Invest Dermatol. 2012 Jul 5. doi: 10.1038/jid.2012.206. [Epub ahead of print] PDF

6. Wu Z, Huang K, Yu J, Le T, Namihira M, Liu Y, Zhang J, Xue Z, Cheng L, Fan G. 2012. Dnmt3a regulates both proliferation and differentiation of mouse neural stem cells. J Neurosci Res. 2012 Oct;90(10):1883-91. doi: 10.1002/jnr.23077. Epub 2012 Jun 20.

7. Biswas A, Liu Y, Liu T, Fan G, Tang Y. 2012. Polyethylene glycol-based protein nanocapsules for functional delivery of a differentiation transcription factor. Biomaterials. 2012 Jul;33(21):5459-67. Epub 2012 Apr 21.

2011

1. F. Gomez-Pinilla, Y. Zhuang, J. Feng, Z. Ying and G. Fan. 2011. Exercise impacts brain-derived neurotrophic factor plasticity by engaging mechanisms of epigenetic regulation. European Journal of Neuroscience Volume 33, Issue 3,383:390

2. Biswas, Anuradha; Joo, Kye-Il; Liu, Jing; Zhao, Muxun; Fan, Guoping; Wang, Pin; Gu, Zhen; Tang, Yi. 2011. Endoprotease-Mediated Intracellular Protein Delivery Using Nanocapsules. ACS Nano. 2011 Feb 22;5(2):1385-94. Epub 2011 Jan 26.

3. Le T, Kim KP, Fan G* (*corresponding author), Faull KF. 2011. A sensitive mass-spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem. 2011 May 15;412(2):203-9. Epub 2011 Jan 24.PMID: 21272560

4. Dhawa S, Georgia S, Tschen S, Fan G and Bhushan A. Pancreatic beta cell identity is maintained by DNA methylation-mediated repression of Arx. Developmental Cell. 2011 Apr 19;20(4):419-29.

5. Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. 2011. Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells. Stem Cells Dev. 2011 Nov;20(11):1937-50.

6. Huang K, Fan G. 2011. Epigenetic Modifications in Distinction: Histone versus DNA Methylation in ESCs. Cell Stem Cell. 2011 Jun 3;8(6):604-5.

7. Fan G, Tran J. 2011. X chromosome inactivation in human and mouse pluripotent stem cells. Hum Genet. 2011 Aug;130(2):217-22.

2010

1. Jin Zhong, Albert Chan, Leeron Morad, Harley I. Kornblum, Guoping Fan, and S. Thomas Carmichael. 2010. Hydrogel Matrix to Support Stem Cell Survival After Brain Transplantation in Stroke. Neurorehabil Neural Repair. 2010 Sep;24(7):636-44. Epub 2010 Apr 27.

2. Feng, J., Zhou, Y., Campbell, SL., Le, T., Li, E., Sweatt, JD., Silva, AJ., and Fan, G. 2010. Dnmt1 and Dnmt3a are required for the maintenance of DNA methylation and synaptic function in adult forebrain neurons. Nature Neuroscience.13:423-432

3. Leah K Hutnick, Xinhua Huang, Tao-Chuan Loo, Zhicheng Ma and Guoping Fan. 2010. Repression of Retrotransposal elements in mouse embryonic stem cells is primarily mediated by DNA methylation-independent mechanism. The Journal of Biological Chemistry. 285(27):21082-91

4. Huang K, Fan G. 2010. DNA methylation in cell differentiation and reprogramming: an emerging systematic view. Regenerative Medicine 5(4):531-44

5. Tamar Dvash, Neta Lavon and Guoping Fan. 2010. Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells. PLOS ONE. Jun 25;5(6):e11330

6. Liao JL, Yu J, Huang K, Hu J, Diemer T, Ma Z, Dvash T, Yang XJ, Travis GH, Williams DS, Bok D, Fan G. 2010. Molecular Signature of Primary Retinal Pigment Epithelium and Stem-Cell derived RPE cells. Aug 13. Hum Mol Genet. 2010 Nov 1;19(21):4229-38. Epub 2010 Aug 13.

7. Laplant Q, Vialou V, Covington HE 3rd, Dumitriu D, Feng J, Warren BL, Maze I, Dietz DM, Watts EL, Iñiguez SD, Koo JW, Mouzon E, Renthal W, Hollis F, Wang H, Noonan MA, Ren Y, Eisch AJ, Bolaños CA, Kabbaj M, Xiao G, Neve RL, Hurd YL, Oosting RS, Fan G, Morrison JH, Nestler EJ. 2010. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci. V. 13: 1137-1143.

8. Liu B, Tahk S, Yee K., Fan G, Shuai K. 2010. The Ligase PIAS1 Restricts Natural Regulatory T-cell Differentiation by Epigenetic Repression. Science. 2010 Oct 22;330(6003):521-5.

9. Zhi-Gang Xue, Zhan-Ping Shi, Juan Dong, Ting-Ting Liao, Yan-Peng Wang,Xue-Ping Sun, Zheng-Jie Yan, Xiao-Qiao Qian, Yu-Gui Cui, Juan Chen,Jia-Yin Liu, and Guoping Fan. (2010) Evaluation of X-Inactivation Status and Cytogenetic Stability of Human Dermal Fibroblasts after Long-Term Culture. International Journal of Cell Biology. 289653. Epub 2010 Dec 27.

2009

1. Dvash, T., Fan, G., 2009. Epigenetic regulation of X-chromosome inactivation in human embryonic stem cells. Epigenetics 4:19-22

2 Hutnick, L. and Fan, G. 2009. DNMT1. Targeted Proteins Database 1, [22563], 10.2970/tpdb.2009.221

3. Hutnick, L., Golshi, P., Namihira, M., Xue, Z., Matynia, A., Yang, W., Silva, A. Schweizer, F., Fan, G. (2009). DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation Human Molecular Genetics 8(15):2875-2888 doi: 10.1093/hmg/ddp222. Published online May 10th, 2009

4. Mason MJ, Fan G, Plath K, Zhou Q, Horvath S..2009. Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells BMC Genomics Jul 20;10(1):327 .PMID: 19619308

5. Shen Y, Fouse SD, Fan G. 2009. Genome-Wide DNA Methylation Profiling: The mDIP-Chip Technology. Methods Mol Biol 2009;568:203-16.PMID: 19582429

6. Fan Z, Yamaza T, Lee JS, Yu J, Wang S, Fan G, Shi S, Wang CY. 2009. BCOR regulates mesenchymal stem cell function by epigenetic mechanisms. Nat Cell Biol Jul 5. PMID: 19578371

7. Feng, J., Fan, G. 2009. The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int Rev Neurobiol V.89:67-84. (review) PMID: 19900616

2008

1. Coskun, V., Wu, H., Blanchi, B., Tsao, S., Kim, K., Zhao, J., Biancotti, J-C., Hutnick, L., Krueger, RC., Fan, G., de Vellis, J., Sun, YE. (2008). Multipotent CD133+ neural stem cells in the ependyma of mammalian postnatal forebrain. PNAS 2008 105(3):1026-31.

2. Fouse, S., Shen, Y., Pellegrini, M., Cole, S., Meissner, A., Van Neste, L., Jaenisch, R., Fan, G. (2008). Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, Polycomb binding and histone H3 lys4/lys27 trimethylation. Cell Stem Cell 2008 2(2):160-9 Data

3. Shen, Y., Matsuno, Y., Fouse, S., Rao, N., Root, S., Xu, R.H., Pellegrini, Riggs, A., Fan, G. (2008). X-inactivation in female human embryonic stem cells is in a non-random pattern and prone to epigenetic alterations. PNAS 2008 published online March 13, 2008, 10.1073/pnas.0712018105.

4. Wu, H., Kim, K.J., Mehta, K., Paxia, S., Sundstrom, A., Anantharaman, T., Kuraishy, A., Tri Doan, T., Ghosh, J., Pyle, A., Clark, A., Lowry, W., Fan, G., Baxter, T., Mishra, B., Sun, Y.E., Teitell, M.A. (2008). Copy Number Variant Analysis of Human Embryonic Stem Cells. Stem Cells Jun;26(6):1484-9. Epub 2008 Mar 27 PMID: 18369100

5. Zeng, Q. An, S., Pan, Q., Xia, K., Xia, J., Zhang, Z., Sun, YE., ang Fan G. (2008). Efficient derivation of mesenchymal stem cells and neural precusor cells from human embryonic stem cells through teratoma formation. Progress in Biochemistry and Biophysics 35(12):1417-1424

2007

1. Golshani, P., Hutnick, L., Schweizer, F., Fan, G. (2007). Conditional Dnmt1 deletion in dorsal forebrain disrupts development of somatosensory barrel cortex and thalamocortical long-term potentiation. Thalamus and Related System doi: 10.1017/S1472928807000222, Published online by Cambridge University Press 05 Mar 2007

2. Feng, J., Fouse, S., Fan, G. (2007). Epigenetic regulation of neural gene expression and neuronal function. Pediatric Research 2007 May;61(5 Pt 2):58R-63R

2006

1. Shen, Y., Chow, J., Wang, Z., Fan, G. (2006). Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Human Molecular Genetics 2006 15(17):2623-35.

2. Lu Y-C., Song J., Cho H-Y, Fan G., Yokoyama K.K., and Chiu R. (2006). Cyclophilin A protects Peg3 from hypermethylation and inactive histone modification J. Biol. Chem. 2006 281:39081-7. Epub 2006 Oct 26.

2005

1. Feng, J., Chang, H., Li, E., and Fan. G. (2005) Dynamic expression of De novo DNA methyltransferases Dnmt3a and 3b in the central nervous system. Journal of Neuroscience Research. 79, 734-746.

2. Lyckman, AW., Fan, G., Rios, M., Jaenisch, R., Sur, M. (2005) Normal eye-specific patterning of retinal inputs to murine subcortical visual nuclei in the absence of brain-derived neurotrophic factor. Visual Science 22, 27-36.

3. He, F., Ge, W., Zhu, W., Becker-Catania, S., Martinowich, K., Wu, H., Coskun, V., Fan, G., deVellis, J., Sun, Y. (2005) A positive autoregulation loop of JAK-STAT signaling is part of the clock mechanism regulating astrogliogenesis. Nature Neuroscience. 8, 616-625.

4. Fan, G. and Hutnick, L. (2005) Methyl-CpG binding proteins in the nervous system (review paper). Cell Research 4, 255-61.

5. Fan, G., Martinowich, K., Chin, M., He, F., Fouse, S., Hutnick, L., Hattori, D., Ge, W., Shen, Y., Wu, H., ten Hoeve, T., Shuai, K., and Sun, Y. (2005) DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development 2005 Aug;132(15):3345-56.

2004

1. Chi, M.M., Fan, G., Fox, E.A. (2004) Increased short-term food satiation and sensitivity to cholecystokinin in neurotrophin-4 knock-in mice. Am J Physiol Regul Integr Comp Physiol. 2004 Nov;287(5):R1044-53.

2003

1. Endres, M., Fan, G., Hirt, L. and Jaenisch, R. (2003) Stroke damage in mice after knocking the NT4 gene into the BDNF locus. J. Cereb.Blood Flow. Metab. 23: 150-153.

2. Martinowich, K., Hatorri, D., Wu, H., Fouse, S., He, F., Hu, Y., Fan, G*., Sun, Y*. (*Corresponding authors) (2003) DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302: 890-893.

2002

1. Ge, W., Martinowich, K., Wu, X., He, F., Miyamoto, A., Fan, G., Weinmaster, G., and Sun, YE. (2002) Notch signaling promotes astrogliogenesis via direct CSL mediated glial gene activation. Journal of Neuroscience Research 69: 848-860.

2001

1. Endres, M., Fan, G., Meisel, A., Dirnagl, U.and Jaenisch, R. 2001. (2001) Effects of cerebral ischemia in mice lacking DNA methyltransferase 1 in postmitotic neurons. Neuroreport 12: 3763-66.

2. Fan, G., Beard, C., Chen, R., Csankovszki, G., Sun, Y., Siniaia, M., Bates, B., Lee, P., Trumpp, A., Poon, C., Wilson, C., and Jaenisch, R. (2001) DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals. Journal of Neuroscience 21: 788-797.

3. Sun, Y., Nadal-Vicens, M., Misono, S., Lin, MZ., Zubiaga, A., Hua, X., Fan, G., Greenberg, ME. (2001) Neurogenin promotes neurogenesis and inhibits glial differentiation by independent mechanisms. Cell 104: 365-376.

4. Fan, G., Siniaia, M., Poon, C., and Jaenisch, R. (2001) Effect of DNA hypomethylation on neural control of respiration: a genetic model. Adv. Exp. Med. Biol. 499: 195-200.

5. Akbarian, S., Bates, B., Liu, RJ., Skirball, SL., Pejchal, T., Coppola, V., Sun, LD., Fan, G., Kucera, J., Wilson, MA., Tessarollo, L., Kosofsky, BE., Taylor, JR., Bothwell, M., Nestler, EJ., Aghajania, GK., and Jaenisch, R. (2001) Neurotrophin-3 modulates noradrenergic neuron function and opiate withdrawl. Molecular Psychiatry 6: 593-604.

6. Rio, M., Fan, G., Fekete, C., Kelly, J., Bates, B., Lechan, RM., Jaenisch, J. (2001) Conditional deletion of brain-drived neurotrophic factor in the postnatal brain causes hyperactivity and obesity. Molecular Endocrinology. 15: 1748-1757.

Before 2001

1. Fan, G., Copray, S., Wong, E., Yan, Q., Jones, K., Walro, J., Jaenisch, R., and Kucera, J. (2000) Formation of the cranial proprioceptive system requires multiple neurotrophins. Developmental Dynamics 218: 359-370.

2. Endres, M, Fan, G (equal contribution), Hirt, L., Fujji, M., Liu, X., Jaenisch, R., and Moskowitz, M.A. (2000) Ischemic brain damage after selectively modifying BDNF or NT-4 expression in vivo. J. Cereb.Blood Flow. Metab. 20: 139-144.

3. Fan, G., Lei, X. , Cheng, H., Wang, X., Sun, B., and Hu, G. (2000) Targeted disruption of NDST-1 gene leads to pulmonary hypoplasia and neonatal respiratory distress in mice. FEBS. Letter 467: 7-11.

4. Fan, G., Egles, C., Sun, Y., Minichiello, L., Renger, J., Klein, R., Liu, G., and Jaenisch, R. (2000) Knocking the NT4 gene into the BDNF locus rescues BDNF deficient mice and reveals distinct NT4 and BDNF activities. Nature Neuroscience 3: 350-357.

5. Fan, G., Jaenisch, R., and Kucera, J. (1999) A role for p75 receptor in NT3 functioning during the development of limb proprioception. Neuroscience 90: 259-268.

6. Bates, B., Rios, M., Trumpp, A., Chen, C., Fan, G., Bishop, J.M., and Jaenisch, R. (1999) Neurotrophin-3 is required for proper cerebellar development. Nature Neurosci. 2: 115-7 .

7. Kucera, J., Fan, G., Walro, J., Copray, S., Tessarollo, L., and Jaenisch, R. (1998) Neurotrophin-3 and trkC in muscle are non-essential for the development of mouse muscle spindles. Neuroreport9: 905-909.

8. Kucera, J., Fan, G., Jaenisch, R., Linnarsson, S., and Ernfors, P. (1995) Dependence of developing group Ia afferents on neurotrophin-3. J. Comp. Neurol. 363: 307-320. PDF

9. Hertzberg, T., Fan, G., Finley, J.C.W., Erickson, J.T., and Katz, D.M. (1994) BDNF supports mammalian chemoafferent neurons in vitro and following peripheral target removal in vivo. Dev. Biol. 166: 801-11.

10. Fan, G., and Katz, D.M. (1993) Non-neuronal cells inhibit the catecholaminergic differentiation of primary sensory neurons: role of leukemia inhibitory factor. Development 118: 83-93.