Research Scientist

Yijun RUAN, Ph.D.
Adjunct Senior Group Leader
Research Focus

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.


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
1982-1985 MS in Microbiology, Huazhong Agricultural University, Wuhan, China
1978-1982 BS in Microbiology, Huazhong Agricultural University, Wuhan, China

Professional Appointments

2006Adjunct Professor, National University of Singapore, Singapore
2003Associate Director, Genome Technology Genome Institute of Singapore
2002Senior Group Leader, Genome Technology and Biology Genome Institute of Singapore
1999-2002Director, Core Genomics and Applications Large Scale Biology Corporation, Vacaville, California, USA
1996-1999Senior Scientist, Genome Technology, Monsanto Company, St. Louis, Missouri, USA

Honors and Awards

2006 National Science Award 2006, Singapore
1998-2001Rockefeller 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

9/2007-8/2010Paired-end ditag technology for complete annotation of fusion genes by NIH/NCI, Cancer genome technology development (US$ 1,215,150)
9/2007-10/2011Comprehensive Characterization and Classification of the Human Transcriptome by NIH/NHGRI (U54 HG004557), an ENCODE scale up grant (US$1,101,702)
9/2007-10/2010Whole 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)
9/2004-10/2007Ditag Technologies for Complete Transcriptome Annotation by NIH/NHGRI (1R01HG003521-01), an ENCODE technology development grant (US$1,001,452)
4/2010-3/2013Identification of driver mutations in cancer progression and drug-resistance in primary human chronic myelogenous leukaemia cells by genome-wide massively parallel paired-end-tag sequencing by Singapore BMRC-NMRC Bedside-to-Bench grant (S$1,655,000)
11/2006-5/2008Viral Metagenome by DARPA, DOD USA (US$360,000)
11/2003-5/2004Zebrafish 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)
10/2010-9/2012Using ChIA-PET to unravel high order chromatin regulatory functions of MeCP2 by International Rett Syndrome Foundation (US$100,000)
1/2007-12/2007Large insert size PET technology development by ROCHE DIAGNOSTICS GMBH (US$75,000)


20094371967 : Method for gene identification signature (GIS) analysis (Granted)
2009155774 : Method to generate or determine nucleic acid tags corresponding to the terminal ends of DNA molecules using sequence analysis of gene expression (terminal SAGE) (Granted)
2006GB2409457 : Method to generate or determine nucleic acid tags corresponding to the terminal ends of DNA molecules using sequence analysis of gene expression 5 & 3 LongSAGE (Granted)

Selected Publications

  1. Edwin Cheung and Yijun Ruan (2011) Determination of transcription factor binding. Nature Genetics (in press; Vol. 43, Issue number 1, Jan. 2011)

  2. Hao Wu, Jifang Tao, Pauline J. Chen , Atif Shahab, Weihong Ge, Ronald P. Hart, Xiaoan Ruan, Yijun Ruan, Yi E. Sun (2010) Systematic screening identifies microRNAs dys-regulated in a mouse model of Rett syndrome. PNAS (ahead of print October 4, 2010, doi:10.1073/pnas.1005595107)

  3. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK "ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing." Genome Biol 2010 ; 11(2) : R22 Epub 2010 Feb 25 Abstract     

  4. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Moham ed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y "An oestrogen-receptor-alpha-bound human chromatin interactome." Nature 2009 Nov 5 ; 462(7269) : 58-64 Abstract     

  5. 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     

  6. ENCODE (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146):799-816.

  7. 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     

  8. 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     

  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 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     

Complete Publications List

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