In Association With

Journal of Biotechnology

Genomics

 

 

Yijun Ruan

Professional Positions

2003-present: Associate Director, Genome Technology, Genome Institute of Singapore
2002-present: 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

Education

1990-1994: PhD in Plant Molecular Biology, University of Maryland, College Park, Maryland, USA

Research Focus

My primary interest is in developing genomics technologies to address fundamental genome biology questions, and in using genomics approaches to elucidate the dynamic structures of genome functions and structural variations in complex genomes.

Publications (selected)

  1. Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E. Angly, Robert A. Edwards, Linlin Li, Rebecca Vega Thurber, R. Pamela Reid, Janet Siefert, Valeria Souza, David L. Valentine, Brandon K. Swan, Mya Breitbart, Forest Rohwer (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452: 340-343.
  2. Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. (2007) Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 17(6):828-38.
  3. 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
  4. 20.  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
  5. 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

Scientific Award

National Science Award 2006, Singapore

Research Grants

9/2007-10/2010 NIH/NHGRI ENCODE technology development (R01 HG004456-01)
Project Title: Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (ChIA-PET); Role: PI, Yijun Ruan; Total budget: $990,000

9/2007-10/2011 NIH/NHGRI ENCODE scale up grant (U54 HG004557)
Project Title: Comprehensive Characterization and Classification of the Human Transcriptome; Role: co-PI, Yijun Ruan; Total budget: $1,101,702 (total $11,934,472)

2006-2007 DARPA grant by US DOD (W911QY-06-C-0077)
Project Title: Viral metagenomics in human guts; Role: PI, Yijun Ruan; Total budget: $ US$325,000

9/2004-10/2007 NIH/NHGRI ENCODE technology development (R01HG003521-01)
Project Title: Ditag Technologies for Complete Transcriptome Annotation; Role: PI, Yijun Ruan
Total budget: $1,001,452

11/2003-5/2004 NIH/NIDDK MGC contract grant
Project Title: Zebrafish Gene Collection: Selection of Full-length cDNA Clones Using Colony Array Hybridization and EST sequencing; Role: PI, Yijun Ruan; Total budget: $613,036