Searching journal content for Yijun Ruan in author.

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  1. Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
    • Zhizhuo Zhang,
    • Kern Rei Chng,
    • Shreyas Lingadahalli,
    • Zikai Chen,
    • Mei Hui Liu,
    • Huy Hoang Do,
    • Shaojiang Cai,
    • Nicola Rinaldi,
    • Huay Mei Poh,
    • Guoliang Li,
    • Ying Ying Sung,
    • Charlie L. Heng,
    • Leighton J. Core,
    • Si Kee Tan,
    • Xiaoan Ruan,
    • John T. Lis,
    • Manolis Kellis,
    • Yijun Ruan,
    • Wing-Kin Sung,
    • and Edwin Cheung
    Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
  2. Method: An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization
    • Przemysław Szałaj,
    • Zhonghui Tang,
    • Paul Michalski,
    • Michal J. Pietal,
    • Oscar J. Luo,
    • Michał Sadowski,
    • Xingwang Li,
    • Kamen Radew,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. December 2016 26: 1697-1709; Published in Advance October 27, 2016, doi:10.1101/gr.205062.116
  3. Research: Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Chao Cheng,
    • Roger Alexander,
    • Renqiang Min,
    • Jing Leng,
    • Kevin Y. Yip,
    • Joel Rozowsky,
    • Koon-Kiu Yan,
    • Xianjun Dong,
    • Sarah Djebali,
    • Yijun Ruan,
    • Carrie A. Davis,
    • Piero Carninci,
    • Timo Lassman,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Ewan Birney,
    • Zhiping Weng,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
    OPEN ACCESS ARTICLE
  4. Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Thomas Derrien,
    • Rory Johnson,
    • Giovanni Bussotti,
    • Andrea Tanzer,
    • Sarah Djebali,
    • Hagen Tilgner,
    • Gregory Guernec,
    • David Martin,
    • Angelika Merkel,
    • David G. Knowles,
    • Julien Lagarde,
    • Lavanya Veeravalli,
    • Xiaoan Ruan,
    • Yijun Ruan,
    • Timo Lassmann,
    • Piero Carninci,
    • James B. Brown,
    • Leonard Lipovich,
    • Jose M. Gonzalez,
    • Mark Thomas,
    • Carrie A. Davis,
    • Ramin Shiekhattar,
    • Thomas R. Gingeras,
    • Tim J. Hubbard,
    • Cedric Notredame,
    • Jennifer Harrow,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
    OPEN ACCESS ARTICLE
  5. Research: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
    • Axel M. Hillmer,
    • Fei Yao,
    • Koichiro Inaki,
    • Wah Heng Lee,
    • Pramila N. Ariyaratne,
    • Audrey S.M. Teo,
    • Xing Yi Woo,
    • Zhenshui Zhang,
    • Hao Zhao,
    • Leena Ukil,
    • Jieqi P. Chen,
    • Feng Zhu,
    • Jimmy B.Y. So,
    • Manuel Salto-Tellez,
    • Wan Ting Poh,
    • Kelson F.B. Zawack,
    • Niranjan Nagarajan,
    • Song Gao,
    • Guoliang Li,
    • Vikrant Kumar,
    • Hui Ping J. Lim,
    • Yee Yen Sia,
    • Chee Seng Chan,
    • See Ting Leong,
    • Say Chuan Neo,
    • Poh Sum D. Choi,
    • Hervé Thoreau,
    • Patrick B.O. Tan,
    • Atif Shahab,
    • Xiaoan Ruan,
    • Jonas Bergh,
    • Per Hall,
    • Valère Cacheux-Rataboul,
    • Chia-Lin Wei,
    • Khay Guan Yeoh,
    • Wing-Kin Sung,
    • Guillaume Bourque,
    • Edison T. Liu,
    • and Yijun Ruan
    Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
    OPEN ACCESS ARTICLE
  6. Research: Transcriptional consequences of genomic structural aberrations in breast cancer
    • Koichiro Inaki,
    • Axel M. Hillmer,
    • Leena Ukil,
    • Fei Yao,
    • Xing Yi Woo,
    • Leah A. Vardy,
    • Kelson Folkvard Braaten Zawack,
    • Charlie Wah Heng Lee,
    • Pramila Nuwantha Ariyaratne,
    • Yang Sun Chan,
    • Kartiki Vasant Desai,
    • Jonas Bergh,
    • Per Hall,
    • Thomas Choudary Putti,
    • Wai Loon Ong,
    • Atif Shahab,
    • Valere Cacheux-Rataboul,
    • Radha Krishna Murthy Karuturi,
    • Wing-Kin Sung,
    • Xiaoan Ruan,
    • Guillaume Bourque,
    • Yijun Ruan,
    • and Edison T. Liu
    Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
    OPEN ACCESS ARTICLE
  7. Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Melissa J. Fullwood,
    • Chia-Lin Wei,
    • Edison T. Liu,
    • and Yijun Ruan
    Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
    OPEN ACCESS ARTICLE
  8. LETTER: Evolution of the mammalian transcription factor binding repertoire via transposable elements
    • Guillaume Bourque,
    • Bernard Leong,
    • Vinsensius B. Vega,
    • Xi Chen,
    • Yen Ling Lee,
    • Kandhadayar G. Srinivasan,
    • Joon-Lin Chew,
    • Yijun Ruan,
    • Chia-Lin Wei,
    • Huck Hui Ng,
    • and Edison T. Liu
    Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
  9. Methods: Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    • Ghia M. Euskirchen,
    • Joel S. Rozowsky,
    • Chia-Lin Wei,
    • Wah Heng Lee,
    • Zhengdong D. Zhang,
    • Stephen Hartman,
    • Olof Emanuelsson,
    • Viktor Stolc,
    • Sherman Weissman,
    • Mark B. Gerstein,
    • Yijun Ruan,
    • and Michael Snyder
    Genome Res. June 2007 17: 898-909; doi:10.1101/gr.5583007
    OPEN ACCESS ARTICLE
  10. LETTER: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
    • Yijun Ruan,
    • Hong Sain Ooi,
    • Siew Woh Choo,
    • Kuo Ping Chiu,
    • Xiao Dong Zhao,
    • K.G. Srinivasan,
    • Fei Yao,
    • Chiou Yu Choo,
    • Jun Liu,
    • Pramila Ariyaratne,
    • Wilson G.W. Bin,
    • Vladimir A. Kuznetsov,
    • Atif Shahab,
    • Wing-Kin Sung,
    • Guillaume Bourque,
    • Nallasivam Palanisamy,
    • and Chia-Lin Wei
    Genome Res. June 2007 17: 828-838; doi:10.1101/gr.6018607
    OPEN ACCESS ARTICLE
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