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  谢丹

 

谢丹教授、博士生导师
教育经历:
1999-2003  中国科技大学,电子科学技术,学士
2003-2006  中国科技大学,生物医学工程,硕士
2006-2011  美国伊利诺伊大学,生物工程,博士
工作经历:
2011-2015  美国斯坦福大学,博士后
2015-至今 四川大学生物治疗国家重点实验室,教授、博士生导师
专业关键词
生物信息学、功能基因组学、基因调控、表观遗传学、遗传学、个性化医学
研究兴趣、领域:
长期从事基因组学以及生物信息学研究,主要结合近年来迅速发展的第二代测序技术和统计以及机器学习方法,系统深入地研究了多种基因调控机制和基因组间表观遗传谱的差异,揭示了基因调控导致性状差异的分子层面机理,研究成果在恶性肿瘤等重大疾病的基因调控和疾病进程,生物学行为以及恶性肿瘤个性化治疗方面具有很好应用价值。
代表性论文:
1.         Dynamic Trans-Acting Factor Co-localization in Human Cell; Cell; 155(3):713-724;Dan Xie,Alan Boyle,Linfeng Wu , Jie Zhai,Trupti Kwali,Michael Snyder*.
2.         Comparative epigenomic annotation of regulatory DNA; Cell; 149: 1381-1391. Shu Xiao, Dan Xie#, Xiaoyi Cao, Pengfei Yu, Xiaoyun Xing, Chieh-Chun Chen, Meagan Musselman, Mingchao Xie, Franklin D. West, Harris A. Lewin, Ting Wang, Sheng Zhong*.# Co-first author
3.         Whole-genome haplotyping using long reads and statistical method; Nature Biotechnology; 32 (3), 261-266; Volodymyr Kuleshov, Dan Xie#, Rui Chen, Dmitry Pushkarev, Zhihai Ma, Tim Blauwkamp, Michael Kertesz, Michael Snyder*.(# Co-first auhor)
4.         Rewirable gene regulatory networks in the preimplantation development of three mammalian species. Genome Research. 20:804-815. Dan Xie, Chieh-Chun Chen, Leon Ptaszek, Shu Xiao, Xiaoyi Cao, Yanen Li, Douglas A. Melton, Harris A Lewin, Chad Cowan, Sheng Zhong*.
5.         Towards an evolutionary model of transcription networks. PLoS Computational Biology. 7(6): e1002064. Dan Xie, Chieh-Chun Chen, Xin He, Sheng Zhong*.
6.         Variation and genetic control of protein abundance in humans; Nature; 499:79-82; Linfeng Wu, Sophie Candille, Yoonha Choi, Dan Xie, Lihua Jiang, Jennifer Li-Pook-Than, Hua Tang, Michael Snyder*.
7.         Extensive variation in chromatin states across humans; Science; 342(6159):750-2; Maya Kasowski, Sofia Kyriazopoulou-Panagiotopoulou, Fabian Grubert, Judith B Zaugg, Anshul Kundaje, Yuling Liu, Alan P Boyle, Qiangfeng Cliff Zhang, Fouad Zakharia, Damek V Spacek, Jingjing Li, Dan Xie, Lars M Steinmetz, John B. Hogenesch, Manolis Kellis, Serafim Batzoglou, Michael Snyder*.
8.         Regulatory analysis of the C. elegans genome with spatiotemporal resolution; Nature; 512:400-405; Carlos Araya, Trupti Kawli, Anshul Kundaje, Lixia Jiang, Beijing Wu, Dionne Vafreados, Robert Terrell, Peter Weissdepp, Louis Gevirtzman, Daniel Mace, Wei Niu, Alan Boyle, Dan Xie, Lijia Ma, John Murray, Valerie Reinke, Robert Waterston, Michael Snyder*.
9.         Comparative analysis of regulatory information and circuits across distant species; Nature; 512:453-456; Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White*, Manolis Kellis*, Michael Snyder*.
10.     Modeling Co-expression Across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells; PLoS Computational Biology; 6(3):e1000707; Jun Cai, Dan Xie, Zhewen Fan, John Marden, Wing H. Wong, Sheng Zhong*.
11.     Mapping personal functional data to personal genomes; Bioinformatics; 27(24):3427-3429; Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong*.
12.     Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions; PLoS Computational Biology; 9(12): e1003367; Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong*.
13.     Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells; PLoS Computational Biology; 5(12):e1000607; Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, NG Huck Hui, Wing H. Wong, Sheng Zhong*.

 

 
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