Medical Genetics, Genomics, and Bioinformatics

1996-1999, Doctor of Anatomy and Histology and Embryology

The First Military Medical University (present named as Southern Medical University), Guangzhou, China

1992-1995, Master of Immunology

The First Military Medical University, Guangzhou, China

1986-1992, Bachelor of Medicine

The First Military Medical University, Guangzhou, China

2009-Present, Professor

Beijing Institute of Genomics, Chinese Academy of Sciences

2000-2008, Post Doctor, Instructor and Research Assistant Professor

Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA

1999-2000, Assistant Professor

Gene Research Center, Shanghai Medical University, Shanghai, China

1995-1996, Assistant Professor

Institute of Molecular Immunology, The First Military Medical University

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1)      Li Y^#, Liu S^#, Ding N, Zhang Q, Yang Y, Qi H, Zhang Z, Xiong Q, Wang H, Zheng J, Zhang L, Ruan X, Yang Y, Deng Y, Du Z*, Fang X*. Hsa-miR-200a inhibits erythroid differentiation by targeting PDCD4 and THRB. Brit J Haematol 2016; [Epub ahead of print] PMID: 27734462

2)      Ding N^#, Xi J^#, Li Y^#, Xie X, Shi J, Zhang Z, Li Y, Fang F, Wang S, Yue W, Pei X^* , Fang X^*. Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. Front Med 2016; Jun 6. [Epub ahead of print]

3)      Wang D^#, Wang J^#, Ding N^#, Li Y, Yang Y, Fang X*, Zhao H*. MAGE-A1 promotes melanoma proliferation and migration through C-JUN activation. Biochem Biophys Res Commun 2016; 473: 959-965

4)      Wan Y^#, Zhang Q^#, Zhang Z, Song B, Wang X, Zhang Y, Jia Q, Cheng T, Zhu X, Leung A Y-H, Yuan W*, Jia H*, Fang X*. Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia. BMC Med Genomics 2016; 9: 13

5)      Li Y^#, Liu S^#, Sun H^#, Yang Y, Qi H, Ding N, Zheng J, Dong X, Qu H, Zhang Z, Fang X*. Regulation of ALAS2 by miR-218 during iron metabolism and erythroid differentiation. Int J Mol Sci 2015; 16: 28156-28168

6)      Zhang Q^#, Ding N^#, Xiong Q, Zheng J, Li Z, Li Y, Li Q, Fang X*, Zhang Z*. Regulatory roles of KLF3 in hematopoiesis of K562 leukemia cells. J Stem Cell Res Ther 2015; 5(9): 310

7)      Wang J^#, Ding N^#, Li Y^#, Cheng H^#, Wang D, Yang Q, Deng Y, Yang Y, Li Y, Ruan X, Xie F, Zhao H*, Fang X*. Insulin-like growth factor binding protein 5 (IGFBP5) functions as a tumor suppressor in human melanoma cells. Oncotarget 2015; 6(24): 20636-20649

8)      Ding N^#, Wang S^#, Yang Q^#, Li Y, Cheng H, Wang J, Wang D, Deng Y, Yang Y, Hu S, Zhao H*, Fang X*. Deep sequencing analysis of microRNA expression in human melanocyte and melanoma cell lines. Gene 2015; 572(1): 135-145

9)      Liang F^#, Qu H^#, Lin Q^#, Yang Y, Ruan X, Zhang B, Liu Y, Yu C, Zhang H*, Fang X*, Hao X*. Molecular biomarkers screened by next-generation RNA sequencing for non-sentinel lymph node status prediction in breast cancer patients with metastatic sentinel lymph nodes. World J Surg Oncol 2015; 13: 258

10)   Zhao M^#, Lei C^#, Yang Y^#, Bu X, Ma H, Gong H, Liu J, Fang X*, Hu Z*, Fang Q*. Abraxane, the nanoparticle formulation of paclitaxel can induce drug resistance by up-regulation of P-gp. PLoS One 2015; 10(7): e0131429

11)   Wang H^#, Li Y^#, Wang S^#, Zhang Q, Zheng J, Yang Y, Qi H, Qu H, Zhang Z, Liu F*, Fang X*. Knockdown of transcription factor forkhead box O3 (FOXO3) suppresses erythroid differentiation in human cells and zebrafish. Biochem Biophys Res Commun 2015; 460(4): 923-930

12)   Hu Y^#, Xiong Q^#, Yang Y, Wang H, Shu C, Xu W, Fang X*, Hu S*. Integrated analysis of gene expression and microRNA regulation in three leukemia-related lymphoblastic cell lines. Gene 2015; 564: 39-52

13)   Yang Y, Dong X, Xie B, Ding N, Chen J, Li Y, Zhang Q, Qu H, Fang X*. Databases and web tools for cancer genomics study. Genomics Proteomics Bioinformatics 2015; 13(1): 46-50

14)   Song B^#, Zhang Q^#, Zhang Z, Wan Y, Jia Q, Wang X, Zhu X, Leung AY, Cheng T, Fang X*, Yuan W*, Jia H*. Systematic transcriptome analysis of the zebrafish model of Diamond-Blackfan anemia induced by RPS24 deficiency. BMC Genomics 2014; 15: 759

15)   Zhang Z^#, Jia H^#, Zhang Q, Wan Y, Song B, Jia Q, Liu H, Zhu X*, Fang X*. Transcriptome analysis of Rpl11-deficient zebrafish model of Diamond-Blackfan anemia. Genomics Data 2014; 2: 173-175

16)   Zhao H^#, Li Y^#, Wang S^#, Yang Y, Wang J, Ruan X, Yang Y, Cai K, Zhang B, Cui P, Yan J, Zhao Y, Wakeland EK, Li Q, Hu S*, Fang X*. Whole transcriptome RNA-seq analysis: the tumorigenesis and metastasis of melanoma. Gene 2014; 548(2): 234-243

17)   Xiong Q^#, Yang Y^#, Wang H, Li J, Wang S, Li Y, Yang Y, Cai K, Ruan X, Yan J, Hu S*, Fang X*. Characterization of miRNomes in acute and chronic myeloid leukemia cell lines. Genomics Proteomics Bioinformatics 2014; 12(2): 79-91

18)   Zhang Z^#, Jia H^#, Zhang Q, Wan Y, Zhou Y, Jia Q, Zhang W, Yuan W, Cheng T, Zhu X*, Fang X*. Assessment of hematopoietic failure due to RPL11 deficiency in a zebrafish model of Diamond-Blackfan anemia by deep sequencing. BMC Genomics 2013; 14: 896

19)   Yang Y^#, Wang H^#, Chang KH^#, Qu H, Zhang Z, Xiong Q, Qi H, Cui P, Lin Q, Ruan X, Yang Y, Li Y, Shu C, Li Q, Wakeland EK, Yan J, Hu S*, Fang X*. Transcriptome dynamics during human erythroid differentiation and development. Genomics 2013; 102(5-6): 431-441

20)   Wang Y^#, Zhang Z^#, Chi Y, Zhang Q, Xu F, Yang Z, Meng L, Yang S, Yan S, Mao A, Zhang J, Yang Y, Wang S, Cui J, Liang L, Ji Y, Han ZB*, Fang X*, Han Z*. Long-term cultured mesenchymal stem cells frequently develop genomic mutations but do not undergo malignant transformation. Cell Death Dis 2013; 4: e950

21)   Chang KH^#, Fang X^#, Wang H, Huang A, Cao H, Yang Y, Bonig H, Stamatoyannopoulos JA, Papayannopoulou T*. Epigenetic modifications and chromosome conformations of the beta-globin locus throughout development. Stem Cell Rev 2013; 9(4): 397-407

22)   Xiong Q^#, Zhang Z^#, Chang KH^#, Qu H, Wang H, Qi H, Li Y, Ruan X, Yang Y, Yang Y, Li Y, Sandstrom R, Sabo PJ, Li Q, Stamatoyannopoulos G, Stamatoyannopoulos JA*, Fang X*. Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors. BMC Genomics 2013; 14: 587

23)   Jia Q^#, Zhang Q^#, Zhang Z, Wang Y, Zhang W, Zhou Y, Wan Y, Cheng T, Zhu X, Fang X, Yuan W*, Jia H*. Transcriptome analysis of the zebrafish model of Diamond-Blackfan anemia from RPS19 deficiency via p53-dependent and -independent pathways. PLoS One 2013; 8(8): e71782

24)   Wang H^#, Hu H^#, Zhang Q, Yang Y, Li Y, Hu Y, Ruan X, Yang Y, Zhang Z, Shu C, Yan J, Wakeland EK, Li Q, Hu S*, Fang X*. Dynamic transcriptomes of human myeloid leukemia cells. Genomics 2013; 102(4): 250-256

25)   Qu H, Fang X*. A brief review on the human encyclopedia of DNA elements (ENCODE) project. Genomics Proteomics Bioinformatics 2013; 11(3): 135-141

26)   Su RJ^#, Yang Y^#, Neises A, Payne KJ, Wang J, Viswanathan K, Wakeland EK, Fang X*, Zhang XB*. Few de novo single nucleotide variations in exomes of human cord blood induced pluripotent stem cells. PLoS One 2013; 8(4): e59908

27)   Li Y^#, Wang H^#, Yang B^#, Yang J, Ruan X, Yang Y, Wakeland EK, Li Q*, Fang X*. Influence of carbon monoxide on growth and apoptosis of human umbilical artery smooth muscle cells and vein endothelial cells. Int J Biol Sci 2012; 8(10): 1431-1446

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Invention Patent of China, ZL201610015109.1

M5 Acute Myeloid Leukemia Related miRNA and Its Application

Invention Patent of China, ZL201510958796.6

A siRNA Specifically Inhibit MAGEA1 Gene Expression in Malignant Melanoma

Invention Patent of China, ZL201510958362.6

A siRNA Specifically Inhibit CTGF Gene Expression in Malignant Melanoma

Invention Patent of China, ZL201310551809.9

Primers, Oligos and Diagnosis Kit for Hepatocellular Carcinoma Screening.

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(1) Identification of Disease Targets for Precision Medicine by Systematically Integrative Analysis of Multi-Omics Data.

We will keep focus on erythroid differentiation and melanoma metastasis. Currently, most of our researches focus on function of genes and miRNAs in erythroid differentiation and melanoma metastasis. However, the genesis and development of disease are controlled by diverse factors at multiple distinct and interactional levels. Current studies focusing only on the function of genes and miRNAs could not interpret all puzzles, leaving many questions open. Considering that genes and miRNAs do not cover all the genetic information, we plan to broaden our research to non-coding area. On one hand, the huge number of long non-coding RNAs, at least four times more than coding RNA sequences, has been recognized to be involved in a variety of disease states especially in oncogenesis by functioning in regulation of gene transcription and post-transcriptional regulation. On the other hand, the structure plasticity and chromatin dynamic play dominant roles in genome organization and gene expression. Therefore, we intend to reveal function of these non-coding areas in erythroid differentiation and melanoma metastasis by studying chromatin conformation and long non-coding RNA. We plan to analyze chromatin conformation capture data and lncRNA expression data globally during erythroid differentiation (among normal and melanoma patient samples) and screen out appropriate candidates for further functional study. We hope to form a relative comprehensive understanding on erythroid differentiation and melanoma initiation and development.

(2) Construction of the System of Big Data Processing and Standardization for Precision Medicine.

The Omics-data and medical information are diverse, heteroid, scattered stored, and nonstandard. Fast and accurate to utilize the omics data and medical information is absolutely crucial to capitalize on the opportunities presented by big data in precision medicine. Standardizing, integrating, and processing biomedical data is challenging both within and across data types, and needs large amount of data as the training basis. Currently, we are still at the data collecting stage including the public data at present mainly and data that yield in China and will be submitted to our system in the future. We will continue to establish criterions of storage, management, processing, and utilization of multiple omics data and medical information, and establish disease related population database. At present, integrated models are not yet sufficiently developed to where they can accommodate both the diversity of data sources, but also their dimension and speed. Therefore, to produce a set of integrated models which update on a weekly-to-monthly time scale, and are likely fast enough for most diseases is the core of our system. We expect to use computational biology methods to obtain comprehensive understanding on clinical phenotypes and molecular variants by developing and utilizing a series of tools to integrative analyze omics and medical data sets to find biomarkers of cancer and other diseases, explore the mechanisms of cell differentiation, tumor progression, and provide clues for precision medicine.

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1. Identification of Disease Targets for Precision Medicine. The 18th Shanghai International Forum on Biotechnology & Pharmaceutical Industry (Bio-Forum 2016), Jun. 20-22, 2016, Shanghai, China

2. Integration and Sharing of Precision Medicine-based Big Data. The International Symposium on the Frontiers of Precision Medicine and Future Healthcare, Dec. 9-12, 2015, Shanghai, China

3. Identification of Disease Targets for Precision Medicine by Systematically Integrative Analysis of Multi-Omics Data. Taishan Academic Forum-Translational Medicine, May 15-17, 2015, Jinan, China

4. Delineate the Molecular Mechanism of Erythroid Differentiation by Omics Data Mining. 2014 International Symposium on Erythrocyte Biology: From Basic, Clinical Research to Translational Medicine, Apr. 24-25, 2014, Zhengzhou, China

5. Comprehensive Investigation of the Molecular Mechanism of Primitive Hematopoiesis Regulating by KLF3. The 54th Annual Meeting of the American Society of Hematology, Dec. 8-11, 2012, Atlanta, GA, USA

6. Systematic Investigation on Regulation of Hematopoiesis by KLF3. World Congress on Medical Physics and Biomedical Engineering, May 26-31, 2012, Beijing, China

7. Trancriptome Analysis of Undifferentiated Human ES Cells and Primary Erythroid Cells At Different Developmental Stages. International Forum on Stem Cells, Nov. 11-14, 2010, Tianjin, China

8. Chromatin Profiling of the Globins and KLFs Genomic Regions of Human ES Cells and ES-Derived Erythroid Cells. NSFC-FRSQ Joint Workshop on Genomics, Oct. 12-15, 2009, Beijing, China

9. Chromatin Profiling of the Globin Loci of Human ES Cells and ES-Derived Erythroid Cells. ISEH 38th Annual Scientific Meeting, Sep. 9-12, 2009, Athens, Greece

10. Genetic and Epigenetic Platforms Based on the Next-Generation Sequencing Technology. Westlake International Conference on Personalized Medicine, May 29-31, 2009, Hangzhou, China

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已指导学生

张倩  硕士研究生  071022-基因组学  

孙红英  硕士研究生  071022-基因组学  

王海  博士研究生  071007-遗传学  

熊倩  博士研究生  071022-基因组学  

李杰  硕士研究生  085238-生物工程  

亓合媛  博士研究生  071022-基因组学  

王均云  博士研究生  071022-基因组学  

刘淑阁  硕士研究生  071007-遗传学  

邓友辉  硕士研究生  071022-基因组学  

李艳明  博士研究生  071007-遗传学  

郑佳文  硕士研究生  071007-遗传学  

杨琼  博士研究生  071007-遗传学  

丁楠  博士研究生  0710Z1-基因组学  

任岚  硕士研究生  071007-遗传学  

施剑  硕士研究生  071007-遗传学  

梁明珠  博士研究生  071010-生物化学与分子生物学  

董绪浓  硕士研究生  0710Z1-基因组学  

刘彦霞  博士研究生  071010-生物化学与分子生物学  

张璐  硕士研究生  071007-遗传学  

李品  硕士研究生  071007-遗传学  

徐洪凯  硕士研究生  071010-生物化学与分子生物学  

杨玲玲  硕士研究生  071010-生物化学与分子生物学  

贺宁  硕士研究生  071007-遗传学  

杨亚东  博士研究生  0710Z1-基因组学  

谢兵兵  博士研究生  0710J3-生物信息学  

龚春丽  硕士研究生  071010-生物化学与分子生物学  

任云晓  硕士研究生  071007-遗传学  

祝俊伟  硕士研究生  071007-遗传学  

吴森  硕士研究生  085238-生物工程  

钱颖  博士研究生  0710J3-生物信息学  

龚尚瑾  硕士研究生  071007-遗传学  

现指导学生

张苇  博士研究生  071007-遗传学  

张宇星  博士研究生  071010-生物化学与分子生物学  

王晨  博士研究生  0710Z1-基因组学  

张立娟  硕士研究生  071007-遗传学  

彭勇飞  硕士研究生  071007-遗传学  

赵学彤  博士研究生  0710Z1-基因组学  

辛子娟  博士研究生  0710Z1-基因组学  

吴静  硕士研究生  071007-遗传学  

谭肖喻  硕士研究生  071007-遗传学  

陈永森  硕士研究生  071007-遗传学  

赵思琪  博士研究生  0710J3-生物信息学  

隋阳  博士研究生  1001Z1-精准医学