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Photo of Yijun  Ruan, Ph.D.

Yijun Ruan, Ph.D.

Professor, Genetics and Genome Sciences
Academic Office Location:
The Jackson Laboratory for Genomic Medicine
263 Farmington Avenue
Farmington, CT 06030
Phone: 860-856-2484
Fax: 860-856-2398
Website(s):

Genetics and Developmental Biology Graduate Program

Ruan Lab Page

Education
DegreeInstitutionMajor
B.S.Huazhong Agricultural UniversityMicrobiology
M.S.Huazhong Agricultural UniversityMicrobiology
Ph.D.University of MarylandPlant Molecular Biology

Post-Graduate Training
TrainingInstitutionSpecialty
PostdoctoralMonsanto CompanyGene Discovery and Gene Expression

Awards
Name of Award/HonorAwarding Organization
Fellowship (1998-2001)Rockefeller Foundation
Carroll E. Cox Graduate Research Excellence Award University of Maryland

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.

Accepting students for Lab Rotations: Summer '17, Fall '17, Spring '18

Journal Articles

  • 3D-GNOME: an integrated web service for structural modeling of the 3D genome.
    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemyslaw; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz Nucleic acids research 2016 May;
  • Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
    Ricaño-Ponce, Isis; Zhernakova, Daria V; Deelen, Patrick; Luo, Oscar; Li, Xingwang; Isaacs, Aaron; Karjalainen, Juha; Di Tommaso, Jennifer; Borek, Zuzanna Agnieszka; Zorro, Maria M; Gutierrez-Achury, Javier; Uitterlinden, Andre G; Hofman, Albert; van Meurs, Joyce; BIOS consortium; Lifelines Cohort Study; Netea, Mihai G; Jonkers, Iris H; Withoff, Sebo; van Duijn, Cornelia M; Li, Yang; Ruan, Yijun; Franke, Lude; Wijmenga, Cisca; Kumar, Vinod Journal of autoimmunity 2016 Apr;6862-74
  • CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
    Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun Cell 2015 Dec;163(7):1611-27
  • Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.
    Yao, Fei; Kausalya, Jaya P; Sia, Yee Yen; Teo, Audrey S M; Lee, Wah Heng; Ong, Alicia G M; Zhang, Zhenshui; Tan, Joanna H J; Li, Guoliang; Bertrand, Denis; Liu, Xingliang; Poh, Huay Mei; Guan, Peiyong; Zhu, Feng; Pathiraja, Thushangi Nadeera; Ariyaratne, Pramila N; Rao, Jaideepraj; Woo, Xing Yi; Cai, Shaojiang; Mulawadi, Fabianus H; Poh, Wan Ting; Veeravalli, Lavanya; Chan, Chee Seng; Lim, Seong Soo; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D; Chew, Elaine G Y; Nagarajan, Niranjan; Jacques, Pierre-Étienne; So, Jimmy B Y; Ruan, Xiaoan; Yeoh, Khay Guan; Tan, Patrick; Sung, Wing-Kin; Hunziker, Walter; Ruan, Yijun; Hillmer, Axel M Cell reports 2015 Jul;12(2):272-85
  • Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.
    Bagamasbad, Pia D; Bonett, Ronald M; Sachs, Laurent; Buisine, Nicolas; Raj, Samhitha; Knoedler, Joseph R; Kyono, Yasuhiro; Ruan, Yijun; Ruan, Xiaoan; Denver, Robert J Molecular endocrinology (Baltimore, Md.) 2015 Jun;29(6):856-72
  • Super-enhancers delineate disease-associated regulatory nodes in T cells.
    Vahedi, Golnaz; Kanno, Yuka; Furumoto, Yasuko; Jiang, Kan; Parker, Stephen C J; Erdos, Michael R; Davis, Sean R; Roychoudhuri, Rahul; Restifo, Nicholas P; Gadina, Massimo; Tang, Zhonghui; Ruan, Yijun; Collins, Francis S; Sartorelli, Vittorio; O'Shea, John J Nature 2015 Feb;520(7548):558-62
  • Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization.
    Kuznetsova, Tatyana; Wang, Shuang-Yin; Rao, Nagesha A; Mandoli, Amit; Martens, Joost H A; Rother, Nils; Aartse, Aafke; Groh, Laszlo; Janssen-Megens, Eva M; Li, Guoliang; Ruan, Yijun; Logie, Colin; Stunnenberg, Hendrik G Genome biology 2015 Jan;16264
  • The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres.
    Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong Scientific reports 2015 Jan;517662
  • Dissecting the chromatin interactome of microRNA genes.
    Chen, Dijun; Fu, Liang-Yu; Zhang, Zhao; Li, Guoliang; Zhang, Hang; Jiang, Li; Harrison, Andrew P; Shanahan, Hugh P; Klukas, Christian; Zhang, Hong-Yu; Ruan, Yijun; Chen, Ling-Ling; Chen, Ming Nucleic acids research 2014 Mar;42(5):3028-43
  • Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells.
    Maejima, Takashi; Inoue, Tsuyoshi; Kanki, Yasuharu; Kohro, Takahide; Li, Guoliang; Ohta, Yoshihiro; Kimura, Hiroshi; Kobayashi, Mika; Taguchi, Akashi; Tsutsumi, Shuichi; Iwanari, Hiroko; Yamamoto, Shogo; Aruga, Hirofumi; Dong, Shoulian; Stevens, Junko F; Poh, Huay Mei; Yamamoto, Kazuki; Kawamura, Takeshi; Mimura, Imari; Suehiro, Jun-ichi; Sugiyama, Akira; Kaneki, Kiyomi; Shibata, Haruki; Yoshinaka, Yasunobu; Doi, Takeshi; Asanuma, Akimune; Tanabe, Sohei; Tanaka, Toshiya; Minami, Takashi; Hamakubo, Takao; Sakai, Juro; Nozaki, Naohito; Aburatani, Hiroyuki; Nangaku, Masaomi; Ruan, Xiaoan; Tanabe, Hideyuki; Ruan, Yijun; Ihara, Sigeo; Endo, Akira; Kodama, Tatsuhiko; Wada, Youichiro PloS one 2014 Jan;9(5):e96005
  • Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.
    Kieffer-Kwon, Kyong-Rim; Tang, Zhonghui; Mathe, Ewy; Qian, Jason; Sung, Myong-Hee; Li, Guoliang; Resch, Wolfgang; Baek, Songjoon; Pruett, Nathanael; Grøntved, Lars; Vian, Laura; Nelson, Steevenson; Zare, Hossein; Hakim, Ofir; Reyon, Deepak; Yamane, Arito; Nakahashi, Hirotaka; Kovalchuk, Alexander L; Zou, Jizhong; Joung, J Keith; Sartorelli, Vittorio; Wei, Chia-Lin; Ruan, Xiaoan; Hager, Gordon L; Ruan, Yijun; Casellas, Rafael Cell 2013 Dec;155(7):1507-20
  • Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.
    Zhang, Yubo; Wong, Chee-Hong; Birnbaum, Ramon Y; Li, Guoliang; Favaro, Rebecca; Ngan, Chew Yee; Lim, Joanne; Tai, Eunice; Poh, Huay Mei; Wong, Eleanor; Mulawadi, Fabianus Hendriyan; Sung, Wing-Kin; Nicolis, Silvia; Ahituv, Nadav; Ruan, Yijun; Wei, Chia-Lin Nature 2013 Dec;504(7479):306-10
  • The draft genome of sweet orange (Citrus sinensis).
    Xu, Qiang; Chen, Ling-Ling; Ruan, Xiaoan; Chen, Dijun; Zhu, Andan; Chen, Chunli; Bertrand, Denis; Jiao, Wen-Biao; Hao, Bao-Hai; Lyon, Matthew P; Chen, Jiongjiong; Gao, Song; Xing, Feng; Lan, Hong; Chang, Ji-Wei; Ge, Xianhong; Lei, Yang; Hu, Qun; Miao, Yin; Wang, Lun; Xiao, Shixin; Biswas, Manosh Kumar; Zeng, Wenfang; Guo, Fei; Cao, Hongbo; Yang, Xiaoming; Xu, Xi-Wen; Cheng, Yun-Jiang; Xu, Juan; Liu, Ji-Hong; Luo, Oscar Junhong; Tang, Zhonghui; Guo, Wen-Wu; Kuang, Hanhui; Zhang, Hong-Yu; Roose, Mikeal L; Nagarajan, Niranjan; Deng, Xiu-Xin; Ruan, Yijun Nature genetics 2013 Jan;45(1):59-66
  • Large-scale functional organization of long-range chromatin interaction networks.
    Sandhu, Kuljeet Singh; Li, Guoliang; Poh, Huay Mei; Quek, Yu Ling Kelly; Sia, Yee Yen; Peh, Su Qin; Mulawadi, Fabianus Hendriyan; Lim, Joanne; Sikic, Mile; Menghi, Francesca; Thalamuthu, Anbupalam; Sung, Wing Kin; Ruan, Xiaoan; Fullwood, Melissa Jane; Liu, Edison; Csermely, Peter; Ruan, Yijun Cell reports 2012 Nov;2(5):1207-19
  • A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer.
    Ng, King Pan; Hillmer, Axel M; Chuah, Charles T H; Juan, Wen Chun; Ko, Tun Kiat; Teo, Audrey S M; Ariyaratne, Pramila N; Takahashi, Naoto; Sawada, Kenichi; Fei, Yao; Soh, Sheila; Lee, Wah Heng; Huang, John W J; Allen, John C; Woo, Xing Yi; Nagarajan, Niranjan; Kumar, Vikrant; Thalamuthu, Anbupalam; Poh, Wan Ting; Ang, Ai Leen; Mya, Hae Tha; How, Gee Fung; Yang, Li Yi; Koh, Liang Piu; Chowbay, Balram; Chang, Chia-Tien; Nadarajan, Veera S; Chng, Wee Joo; Than, Hein; Lim, Lay Cheng; Goh, Yeow Tee; Zhang, Shenli; Poh, Dianne; Tan, Patrick; Seet, Ju-Ee; Ang, Mei-Kim; Chau, Noan-Minh; Ng, Quan-Sing; Tan, Daniel S W; Soda, Manabu; Isobe, Kazutoshi; Nöthen, Markus M; Wong, Tien Y; Shahab, Atif; Ruan, Xiaoan; Cacheux-Rataboul, Valère; Sung, Wing-Kin; Tan, Eng Huat; Yatabe, Yasushi; Mano, Hiroyuki; Soo, Ross A; Chin, Tan Min; Lim, Wan-Teck; Ruan, Yijun; Ong, S Tiong Nature medicine 2012 Apr;18(4):521-8
  • CTCF-mediated functional chromatin interactome in pluripotent cells.
    Handoko, Lusy; Xu, Han; Li, Guoliang; Ngan, Chew Yee; Chew, Elaine; Schnapp, Marie; Lee, Charlie Wah Heng; Ye, Chaopeng; Ping, Joanne Lim Hui; Mulawadi, Fabianus; Wong, Eleanor; Sheng, Jianpeng; Zhang, Yubo; Poh, Thompson; Chan, Chee Seng; Kunarso, Galih; Shahab, Atif; Bourque, Guillaume; Cacheux-Rataboul, Valere; Sung, Wing-Kin; Ruan, Yijun; Wei, Chia-Lin Nature genetics 2011 Jul;43(7):630-8
  • Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.
    Hillmer, Axel M; Yao, Fei; Inaki, Koichiro; Lee, Wah Heng; Ariyaratne, Pramila N; Teo, Audrey S M; Woo, Xing Yi; Zhang, Zhenshui; Zhao, Hao; Ukil, Leena; Chen, Jieqi P; Zhu, Feng; So, Jimmy B Y; Salto-Tellez, Manuel; Poh, Wan Ting; Zawack, Kelson F B; Nagarajan, Niranjan; Gao, Song; Li, Guoliang; Kumar, Vikrant; Lim, Hui Ping J; Sia, Yee Yen; Chan, Chee Seng; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D; Thoreau, Hervé; Tan, Patrick B O; Shahab, Atif; Ruan, Xiaoan; Bergh, Jonas; Hall, Per; Cacheux-Rataboul, Valère; Wei, Chia-Lin; Yeoh, Khay Guan; Sung, Wing-Kin; Bourque, Guillaume; Liu, Edison T; Ruan, Yijun Genome research 2011 May;21(5):665-75
  • Transcriptional consequences of genomic structural aberrations in breast cancer.
    Inaki, Koichiro; Hillmer, Axel M; Ukil, Leena; Yao, Fei; Woo, Xing Yi; Vardy, Leah A; Zawack, Kelson Folkvard Braaten; Lee, Charlie Wah Heng; Ariyaratne, Pramila Nuwantha; Chan, Yang Sun; Desai, Kartiki Vasant; Bergh, Jonas; Hall, Per; Putti, Thomas Choudary; Ong, Wai Loon; Shahab, Atif; Cacheux-Rataboul, Valere; Karuturi, Radha Krishna Murthy; Sung, Wing-Kin; Ruan, Xiaoan; Bourque, Guillaume; Ruan, Yijun; Liu, Edison T Genome research 2011 May;21(5):676-87
  • Genome-sequencing anniversary. Presenting the human genome: now in 3D!
    Ruan, Yijun Science (New York, N.Y.) 2011 Feb;331(6020):1025-6
  • Determination of transcription factor binding.
    Cheung, Edwin; Ruan, Yijun Nature genetics 2011 Jan;43(1):11-2
  • Protocol: Sonication-based Circular Chromosome Conformation Capture with nextgeneration sequencing analysis for the detection of chromatin interactions
    Phillips Yao Hui Huang, Yuyuan Han, Lusy Handoko, Stoyan Velkov, Eleanor Wong, Edwin Cheung, Xiaoan Ruan, Chia-Lin Wei, Melissa Jane Fullwood, Yijun Ruan Nature Protocol 2011 Jan;
  • Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome.
    Wu, Hao; Tao, Jifang; Chen, Pauline J; Shahab, Atif; Ge, Weihong; Hart, Ronald P; Ruan, Xiaoan; Ruan, Yijun; Sun, Yi E Proceedings of the National Academy of Sciences of the United States of America 2010 Oct;107(42):18161-6
  • A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.
    Nandi, Tannistha; Ong, Catherine; Singh, Arvind Pratap; Boddey, Justin; Atkins, Timothy; Sarkar-Tyson, Mitali; Essex-Lopresti, Angela E; Chua, Hui Hoon; Pearson, Talima; Kreisberg, Jason F; Nilsson, Christina; Ariyaratne, Pramila; Ronning, Catherine; Losada, Liliana; Ruan, Yijun; Sung, Wing-Kin; Woods, Donald; Titball, Richard W; Beacham, Ifor; Peak, Ian; Keim, Paul; Nierman, William C; Tan, Patrick PLoS pathogens 2010 Apr;6(4):e1000845
  • ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.
    Li, Guoliang; Fullwood, Melissa J; Xu, Han; Mulawadi, Fabianus Hendriyan; Velkov, Stoyan; Vega, Vinsensius; Ariyaratne, Pramila Nuwantha; Mohamed, Yusoff Bin; Ooi, Hong-Sain; Tennakoon, Chandana; Wei, Chia-Lin; Ruan, Yijun; Sung, Wing-Kin Genome biology 2010 Jan;11(2):R22
  • Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.
    Schoenfelder, Stefan; Sexton, Tom; Chakalova, Lyubomira; Cope, Nathan F; Horton, Alice; Andrews, Simon; Kurukuti, Sreenivasulu; Mitchell, Jennifer A; Umlauf, David; Dimitrova, Daniela S; Eskiw, Christopher H; Luo, Yanquan; Wei, Chia-Lin; Ruan, Yijun; Bieker, James J; Fraser, Peter Nature genetics 2010 Jan;42(1):53-61
  • An oestrogen-receptor-alpha-bound human chromatin interactome.
    Fullwood, Melissa J; Liu, Mei Hui; Pan, You Fu; Liu, Jun; Xu, Han; Mohamed, Yusoff Bin; Orlov, Yuriy L; Velkov, Stoyan; Ho, Andrea; Mei, Poh Huay; Chew, Elaine G Y; Huang, Phillips Yao Hui; Welboren, Willem-Jan; Han, Yuyuan; Ooi, Hong Sain; Ariyaratne, Pramila N; Vega, Vinsensius B; Luo, Yanquan; Tan, Peck Yean; Choy, Pei Ye; Wansa, K D Senali Abayratna; Zhao, Bing; Lim, Kar Sian; Leow, Shi Chi; Yow, Jit Sin; Joseph, Roy; Li, Haixia; Desai, Kartiki V; Thomsen, Jane S; Lee, Yew Kok; Karuturi, R Krishna Murthy; Herve, Thoreau; Bourque, Guillaume; Stunnenberg, Hendrik G; Ruan, Xiaoan; Cacheux-Rataboul, Valere; Sung, Wing-Kin; Liu, Edison T; Wei, Chia-Lin; Cheung, Edwin; Ruan, Yijun Nature 2009 Nov;462(7269):58-64
  • Metagenomic analysis of viruses in reclaimed water.
    Rosario, Karyna; Nilsson, Christina; Lim, Yan Wei; Ruan, Yijun; Breitbart, Mya Environmental microbiology 2009 Nov;11(11):2806-20
Title or AbstractTypeSponsor/EventDate/YearLocation
3D Chromatin Architecture and Transcription RegulationLectureCSH-Asia conference High Throughput Biology2011Suzhou, China
3D Chromatin Architecture and Transcription RegulationLecture2011 HUGO meeting2011Dubai
Comprehensive Paired-End-Tag Mapping Reveals Characteristic Structural Variations with Mechanistic Implications in Cancer GenomesLecturePersonalized Cancer Medicine, Towards Individualized Cancer Treatments2011Singapore
Chromatin Interaction and Transcription RegulationLectureThe 9th Asia-Pacific Conference on Human Genetics2010Hong Kong, China
Chromatin Looping Architecture and Models of Transcription Regulation in Human Cancer CellsLectureBGI International Genome Conference 2010
Chromatin Looping Architecture and Models of Transcription Regulation in Human Cancer Cells LectureFrontier Cancer Science CSI-NUS2010
Chromatin Looping Architecture and Models of Transcription Regulation in Human Cancer CellsLectureUC Irvin, Department of Biological Chemistry and Bioinformatics Program 2010Irvine, CA
Chromatin Looping Architecture and Models of Transcription Regulation in Human Cancer CellsLectureGenomics and Bioinformatics program seminar2010McGill University
Comprehensive Paired-End-Tag Mapping Reveals Characteristic Structural Variations with Mechanistic Implications in Cancer Genomes LectureHUGO-IABCR Congress2010Biopolis, Singapore
Spatial genomics, Chromatin Architecture and Functional Implementation LectureDUKE-NUS medical school seminar 2010DUKE-NUS medical school
3D Chromatin Conformation and Transcription RegulationLecture2010 Shanghai Summer Stem Cell Symposium2010Tongji University, Shanghai, China
Long-Range Chromatin Interaction and Transcription Regulation Plenary LectureThe 3rd Berlin Summer Meeting2010Berlin, Germany
Genome-Wide Mapping Chromatin Interaction and Transcription RegulationPlenary LectureHUGO 14th Human Genome Meeting2010Montpellier, France
Genome-Wide Mapping of Long-Range Chromatin Interactions and Transcription Regulatory Networks in Human CellsPlenary LectureThe Biology of Genomes2010Cold Spring Harbor Laboratory NY