Elucidates the structures and dynamics of DNA elements in complex genomes, including physical three-dimensional structures.Visit The Ruan Lab
My primary interest is to elucidate the structures and dynamics of all functional DNA elements in complex genomes through DNA sequencing analysis of genetic variations in genomes and transcriptomes. To facilitate such understanding, my lab and I contribute to the technology development for high-throughput DNA sequencing and mapping methodologies, including the paired-end-tag (PET) sequencing strategy for RNA-PET/Seq, ChIP-PET/Seq, DNA-PET and ChIA-PET analysis. We are applying these sequencing-based methodologies to address complex genetic questions between normal versus disease states. A specific interest is to apply ChIA-PET and related methodologies to understand the three-dimensional (3-D) higher-order structures of chromosomal folding conformation and their impact on nuclear processes, such as gene transcription regulation and DNA replication.
2006 - National Science Award, Singapore
1998-2001 - Rockefeller Foundation Fellowship
1995 - Carroll E. Cox Graduate Research Excellence Award
University of Maryland
Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SC, Erdos MR, et al. Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature. 2015 Apr 23;520(7548):558-62.
Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, et al. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell. 2014 Dec 18;159(7):1524-37.
Jiang Z, Sun J, Dong H, Luo O, Zheng X, Obergfell C, Tang Y, Bi J, O'Neill R, Ruan Y, Chen J1, Tian XC. Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics. 2014 Sep 4;15:756.
Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL8, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 2015 Dec 17;163(7):1611-27.
Protein factors are responsible for organizing chromosomes inside the nucleus in three dimensions (3D), forming a shape like a gift bow, with proteins aggregating as the central “knot” holding the ribbon-like loops of DNA when genes are organized for proper expression, or a tangled mess in the presence of certain mutations.
Yijun Ruan, Ph.D., received a three-year, $150,000 grant from the National Human Genome Research Institute (NHGRI) to present workshops on a technique for analyzing genomes known as ChIA-PET (for Chromatin Interaction Analysis Using Paired-End Tag Sequencing).
Studying the gastric cancers of 15 Southeast Asian patients, researchers at The Jackson Laboratory, the Genome Institute of Singapore and other institutions identified five recurrent fusion genes, one of which appears to lead to cellular changes involved in acute gastritis and cancer.
National Cancer Institute awards $2.2 M grant to Professor Yijun Ruan for his research into the role of noncoding RNAs in cancer and other diseases.
New sequencing tools are uncovering how the unpacked sections of DNA can interact with each other in three-dimensional space, leading to new insights in the relationships between distant sections of DNA.
A $3.7 million grant has been awarded to Professor Yijun Ruan, Ph.D., to fund research into how the human genome is organized in the nucleus of the cell.
Six senior officials and scientists from The Jackson Laboratory (JAX) will visit Ewha Womans University in Seoul for an International Joint Symposium on Genomic Medicine on Oct. 2.
NIH, Jackson Laboratory researchers reveal link between powerful gene regulatory elements and autoimmune diseases