My 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 we have developed paired-end-ditag (PET) based high throughput and high precision DNA sequencing and mapping methodologies. We are applying these sequencing-based measurements to address complex biological questions such as how cancer cells progress and how stem cells maintain their unique properties. Another major interest of mine is to discover previously uncharacterized microbial genes and genomes that are relevant to human health. To this end, we have established a metagenome analysis capability that includes a filtration system for isolating uncultured microbes, shotgun and PET sequencing of metagenomes to uncover viral and bacterial genome sequences from a variety of environment settings and cavities of the human body.
EDUCATION
1995-1996 Post-doctoral Fellow, Program of Gene Discovery and Gene Expression, Monsanto Company, St Louis, Missouri, USA
1990-1994 Doctor of philosophy in Plant Molecular Biology, University of Maryland, College Park, Maryland, USA
PROFESSIONAL APPOINTMENTS
2003 Associate Director, Genome Technology Genome Institute of Singapore
2002 Senior Group Leader, Genome Technology and Biology Genome Institute of Singapore
1999-2002 Director, Core Genomics and Applications Large Scale Biology Corporation, Vacaville, California, USA
1996-1999 Senior Scientist, Genome Technology, Monsanto Company, St. Louis, Missouri, USA
HONORS AND AWARDS
2006 National Science Award 2006, Singapore
1998-2001 Rockefeller Foundation Fellow Helped China to initiate rice functional genomics research sponsored by Rockefeller Foundation under a rice biotech fellowship program.
1995 Carroll E. Cox Graduate Research Excellence Award, University of Maryland, 1995. For the best Ph.D dissertation in biology submitted in 1994
EXTERNAL GRANT
9/2007-8/2010 Paired-end ditag technology for complete annotation of fusion genes by NIH/NCI, Cancer genome technology development (US$ 1,215,150)
9/2007-10/2011 Comprehensive Characterization and Classification of the Human Transcriptome by NIH/NHGRI (U54 HG004557), an ENCODE scale up grant (US$1,101,702)
9/2007-10/2010 Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (ChIA-PET) by NIH/NHGRI (1 R01 HG004456-01), an ENCODE technology development grant (US$990,000)
9/2004-10/2007 Ditag Technologies for Complete Transcriptome Annotation by NIH/NHGRI (1R01HG003521-01), an ENCODE technology development grant (US$1,001,452)
11/2006-5/2008 Viral Metagenome by DARPA, DOD USA (US$360,000)
11/2003-5/2004 Zebrafish Gene Collection: Selection of Full-length cDNA Clones Using Colony Array Hybridization and EST sequencing by NIH/NIDDK, an MGC contract grant (US$613,036)
1/2007-12/2007 Large insert size PET technology development by ROCHE DIAGNOSTICS GMBH (US$75,000)
SELECTED PUBLICATIONS
1. Fullwood Melissa J, Wei Chia-Lin, Liu Edison T, Ruan Yijun "Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses." Genome Res. 2009 Apr ; 19(4) : 521-32
Abstract
2. Desnues Christelle, Rodriguez-Brito Beltran, Rayhawk Steve, Kelley Scott, Tran Tuong, Haynes Matthew, Liu Hong, Furlan Mike, Wegley Linda, Chau Betty, Ruan Yijun, Hall Dana, Angly Florent E, Edwards Robert A, Li Linlin, Thurber Rebecca Vega, Reid R Pamela, Siefert Janet, Souza Valeria, Valentine David L, Swan Brandon K, Breitbart Mya, Rohwer Forest "Biodiversity and biogeography of phages in modern stromatolites and thrombolites." Nature 2008 Mar 20 ; 452(7185) : 340-3 Epub 2008 Mar 2
Abstract
3. Chen Xi, Xu Han, Yuan Ping, Fang Fang, Huss Mikael, Vega Vinsensius B, Wong Eleanor, Orlov Yuriy L, Zhang Weiwei, Jiang Jianming, Loh Yuin-Han, Yeo Hock Chuan, Yeo Zhen Xuan, Narang Vipin, Govindarajan Kunde Ramamoorthy, Leong Bernard, Shahab Atif, Ruan Yijun, Bourque Guillaume, Sung Wing-Kin, Clarke Neil D, Wei Chia-Lin, Ng Huck-Hui "Integration of external signaling pathways with the core transcriptional network in embryonic stem cells." Cell 2008 Jun 13 ; 133(6) : 1106-17
Abstract
4. ENCODE (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146):799-816.
5. Ruan Yijun, Ooi Hong Sain, Choo Siew Woh, Chiu Kuo Ping, Zhao Xiao Dong, Srinivasan K G, Yao Fei, Choo Chiou Yu, Liu Jun, Ariyaratne Pramila, Bin Wilson G W, Kuznetsov Vladimir A, Shahab Atif, Sung Wing-Kin, Bourque Guillaume, Palanisamy Nallasivam, Wei Chia-Lin "Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)." Genome Res. 2007 Jun ; 17(6) : 828-38
Abstract
6. Wei Chia-Lin, Wu Qiang, Vega Vinsensius B, Chiu Kuo Ping, Ng Patrick, Zhang Tao, Shahab Atif, Yong How Choong, Fu YuTao, Weng Zhiping, Liu JianJun, Zhao Xiao Dong, Chew Joon-Lin, Lee Yen Ling, Kuznetsov Vladimir A, Sung Wing-Kin, Miller Lance D, Lim Bing, Liu Edison T, Yu Qiang, Ng Huck-Hui, Ruan Yijun "A global map of p53 transcription-factor binding sites in the human genome." Cell 2006 Jan 13 ; 124(1) : 207-19
Abstract
7. 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
8. The FANTOM Consortium, … Yijun Ruan, …, etc (2005) “The Transcriptional Landscape of the Mammalian Genome” Science 309: 1559-1563
9. Patrick Wei Pern NG, Chia Lin WEI, Ken Wing Kin SUNG, Kuo Ping CHIU, Leonard LIPOVICH, Ang Chin Chin, Sanjay GUPTA, Shahab Atif, Wong Chee Hong, Ridwan Azmi, Edison Tak-Bun LIU, Yijun RUAN (2005) "Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation" Nature Method 2 105-111
Supplemental Link Supplemental Data File
10. Ruan Yi Jun, Wei Chia Lin, Ee Ai Ling, Vega Vinsensius B, Thoreau Herve, Su Se Thoe Yun, Chia Jer-Ming, Ng Patrick, Chiu Kuo Ping, Lim Landri, Zhang Tao, Peng Chan Kwai, Lin Ean Oon Lynette, Lee Ng Mah, Yee Sin Leo, Ng Lisa F P, Chee Ren Ee, Stanton Lawrence W, Long Philip M, Liu Edison T "Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection." Lancet 2003 May 24 ; 361(9371) : 1779-85
Abstract
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