报告题目： The Third Waves of Genomics
报告人： Yijun Ruan, Ph.D.
Sr. Group Leader, Genome Technology & Biology Group
Associate Director, Genome Technology
Genome Institute of Singapore
主持人： 冯新华 教授
时 间： 2011年9月7日（星期三）下午四点
地 点： 医学院综合楼205报告厅
Brief Introduction of Speaker:
Pro. Yijun Ruan received his B.S. and M.S. from Huazhong Agricultural University in 1985 and Ph.D. from University of Maryland ,USA, in 1994. He got the National Science Award 2006, Singapore. Now his primary interest is to elucidate the structures and dynamics of all functional DNA elements in complex genomes through transcriptome characterizations and genome interrogation. To facilitate such understanding he has developed Paired-End-diTag (PET) based high throughput and high precision DNA sequencing and mapping methodologies. He has been applying these sequencing-based measurements to address complex biological questions such as how cancer cells progress and how stem cells maintain their unique properties.
Selected Papers:
1. Lusy Handoko, Han Xu, Guoliang Li, Chew Yee Ngan, Elaine Chew, Charlie Wah Heng Lee, Chaopeng Ye, Eleanor Wong, Yubo Zhang, Fabianus Mulawadi, Jianpeng Sheng, Thompson Poh, Chee Seng Chan, Galih Kunarso, Atif Shahab, Guillaume Bourque, Valere Cacheux-Rataboul, Wing-Kin Sung, Yijun Ruan*, Chia-Lin Wei* (2011) Functional Genome Architecture Revealed by CTCF-Associated Chromatin Interactome in Pluripotent Cells. Nature Genetics 43: 630–638
2. Axel M. Hillmer, Yao Fei1, Koichiro Inaki, Wah Heng Lee, Pramila N. Ariyaratne, Audrey S.M. Teo, Xing Yi Woo, Zhenshui Zhang, Zhao Hao, Leena Ukil, Jieqi P. Chen, Zhu Feng, Jimmy B.Y. So, Manuel Salto-Tellez, Wan Ting Poh, Kelson F.B. Zawack, Hui Ping J. Lim, Yee Yen Sia, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Choi, Hervé Thoreau, Patrick B.O. Tan, Atif Shahab, Xiaoan Ruan, Jonas Bergh, Per Hall, Valère Cacheux-Rataboul, Chia-Lin Wei, Khay Guan Yeoh, Wing-Kin Sung, Guillaume Bourque, Edison T. Liu, Yijun Ruan* (2011) Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. Genome Research 21 (5): 665-675
3. Yijun Ruan (2011) Presenting the Human Genome: NOW IN 3D. Science 331: 1025-1026
4. Edwin Cheung and Yijun Ruan* (2011) Determination of transcription factor binding. Nature Genetics 43: 11-12
5. Guoliang Li, Melissa J. Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B Vega S N, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei1, Yijun Ruan*, Wing-Kin Sung* (2010). ChIA-PET Tool: A comprehensive software for chromatin interaction analysis with paired-end-tag sequencing. Genome Biology 11:R22
6. Melissa J. Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Xu Han, Yusoff Bin Mohamed, Yuriy L. Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine G. Y. Chew, Phillips Yao Hui Huang, Willem-Jan Welboren, Yuyuan Han, Hong-Sain Ooi, Pramila N. Ariyaratne, Vinsensius B. Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D. Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V. Desai, Jane S. Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Thoreau Herve, Guillaume Bourque, Hendrik G. Stunnenberg, Xiaoan Ruan, Valere Cacheux-Rataboul, Wing-Kin Sung, Edison T. Liu, Chia-Lin Wei, Edwin Cheung, and Yijun Ruan* (2009). An oestrogen-receptor-α-bound human chromatin interactome. Nature 462: 58-64.
7. Melissa J. Fullwood, Chia Lin Wei, Edison T. Liu, and Yijun Ruan* (2009) Next-Generation DNA Sequencing of Paired End diTags for Transcriptome and Genome Analysis (Review) Genome Research 19: 521-532.
8. Chia-Lin Wei, Qiang Wu, Vinsensius Vega, Kuo Ping Chiu, Patrick Ng, Tao Zhang, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Jian Jun Liu, XiaoDong Zhao, Yen Ling Lee, Vladimir A. Kuznetsov, Ken Sung, Bing Lim, Edison T. Liu, Qiang Yu, Huck Hui Ng, and Yijun Ruan* (2006) A Global Map of p53 Transcription Factor Binding Sites in the Human Genome. Cell 124: 207-219.
9. Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin L. Hibberd1, Edison T. Liu, Forest Rohwer, and Yijun Ruan* (2006) RNA Viral Community in the Human Gut: Prevalence of plant pathogenic viruses. PLoS Biology 4: Issue 1, e3.
10. Patrick Ng, Chia-Lin Wei, Wing-Kin Sung, Kuo Ping Chiu, Leonard Lipovich, Chin Chin Ang, Sanjay Gupta, Atif Shahab, Azmi Ridwan, Chee Hong Wong, Edison T. Liu, and Yijun Ruan* (2005) Gene Identification Signature (GIS) Analysis for Transcriptome Characterization and Genome Annotation. Nature Methods 2: 105-111.
