Yijun Ruan
Active 1995–2025
- 112
- Papers
- 45,464
- Citations
- 77
- h-index
- 106
- i10-index
Citations
Citation sources
Countries
Institutions
Fields
- Biochemistry, Genetics and Molecular Biology72.2%
- Medicine13.3%
- Agricultural and Biological Sciences5.5%
- Environmental Science3%
- Immunology and Microbiology3%
- Neuroscience0.8%
- Other2.2%
Topics
- Cancer-related molecular mechanisms research7.6%
- Genomics and Chromatin Dynamics7.6%
- RNA Research and Splicing6.4%
- RNA modifications and cancer6.1%
- Epigenetics and DNA Methylation3.5%
- Genomics and Phylogenetic Studies2.8%
- Other66%
Coauthors
- Chia‐Lin Wei35
- Guoliang Li22
- Xiaoan Ruan19
- Wing‐Kin Sung17
- Edison T. Liu16
- Zhonghui Tang16
- Ping Wang15
- Atif Shahab12
- Kuo Ping Chiu12
- Vinsensius B. Vega12
- Pramila Ariyaratne11
- Dariusz Plewczyński10
- Byoungkoo Lee9
- Guillaume Bourque9
- Fei Yao8
- Minji Kim8
- Chee‐Hong Wong7
- Haoxi Chai7
- Huay Mei Poh7
- Xingwang Li7
- Chew Yee Ngan6
- Fabianus Hendriyan Mulawadi6
- Huck‐Hui Ng6
- Jacqueline Jufen Zhu6
All papers
- Landscape of transcription in human cells
Authors: Sarah Djebali, Carrie Davis, Angelika Merkel, Alexander Dobin, Timo Lassmann, A Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K. Marinov, Jainab Khatun, Brian A. Williams, Chris Zaleski, Joel Rozowsky, Maik Röder, Felix Kokocinski, Rehab Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Nadav Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto K. Chakrabortty, Xian Chen, Jacqueline Chrast, João Curado, Thomas Derrien, Jörg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro G. Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David González, Assaf Gordon, Harsha P. Gunawardena, Cédric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar Junhong Luo, Eddie Park, Kimberly Persaud, Jonathan Preall, Paolo Ribeca, Brian A. Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jørgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John A. Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E. Antonarakis, Gregory J. Hannon, Morgan C. Giddings, Yijun Ruan, B Wold, Piero Carninci, Roderic Guigó, T Gingeras - Nature 2012 cited by 5,413
- The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Authors: Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Grégory Guernec, David Martı́n, Angelika Merkel, David G. Knowles, Julien Lagarde, Lavanya Veeravalli, Xiaoan Ruan, Yijun Ruan, Timo Lassmann, Piero Carninci, James Brown, Leonard Lipovich, José M. González, Mark Thomas, Carrie Davis, Ramin Shiekhattar, T Gingeras, Tim Hubbard, Cédric Notredame, Jennifer Harrow, Roderic Guigó - Genome Research 2012 cited by 5,217
- International network of cancer genome projects
Authors: Jennifer L. Jennings, Thomas J. Hudson, Arek Kasprzyk, John D. McPherson, Paul C. Boutros, Lakshmi Muthuswamy, B. F. Francis Ouellette, Lincoln D. Stein, Fabien Calvo, Iiro Eerola, Daniela S. Gerhard, Alan F. Guttmacher, Mark S. Guyer, Saravanamuttu Gnaneshan, Jennifer L. Jennings, David Kerr, Peter Klatt, Patrik Kolar, Michelle Sam, David P. Lane, Frank Laplace, Warwick Anderson, Gerd Nettekoven, Brad Ozenberger, Daniela S. Gerhard, T. S. Rao, Jacques Remacle, Carolyn C. Compton, Tatsuhiro Shibata, Karl W. Hasel, Joseph G. Vockley, Koichi Watanabe, Huanming Yang, M.M.F. Yuen, T. S. Rao, Martin Bobrow, Anne Cambon‐Thomsen, Lynn G. Dressler, Iris Pauporté, Yann Joly, Patrik Kolar, Jacques Remacle, Pilar Nicolás, Michael Parker, Emmanuelle Rial‐Sebbag, Carlos M. Romeo-Casabona, Laura Lyman Rodriguez, Susan Wallace, Georgia L. Wiesner, Nikolajs Zeps, Jun Kusuda, Tohru Masui, Christian Chabannon, Youyong Lu, Bruno Clément, Feng Chen, Françoise Degos, Xiaofang Xing, Peter Geary, D. Neil Hayes, Thomas J. Hudson, Amber L. Johns, Yasushi Totoki, Hidewaki Nakagawa, Michael R. Stratton, Miguel Á. Piris, Rajiv Sarin, Aldo Scarpa, Zemin Ning, Marc J. van de Vijver, P. Andrew Futreal, Hiroyuki Aburatani, Mónica Bayés, Sancha Martin, Koichi Watanabe, Xavier Estivill, Guangwu Guo, Sean M. Grimmond, Qibin Li, Martin Hirst, Honglong Wu, Shancen Zhao, Marco A. Marra, John D. McPherson, Hidewaki Nakagawa, Zemin Ning, Geng Tian, Yijun Ruan, Yann Joly, Susan Wallace, Bartha M. Knoppers, Harold Swerdlow, Victor E. Velculescu, Emmanuelle Rial-Sebbag, Lynn G. Dressler, Liu Yang, Pilar Nicolás, Gary D. Bader, Paul C. Boutros, Georgia L. Wiesner and 156 more - Nature 2010 cited by 2,428
- An oestrogen-receptor-α-bound human chromatin interactome
Authors: Melissa J. Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Xu Han, Yusoff Bin Mohamed, Yuriy L. Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine Guo Yan Chew, Phillips Huang, Willem-Jan Welboren, Yuyuan Han, Hong Ooi, Pramila Ariyaratne, Vinsensius B. Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D. Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V. Desai, Jane S. Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Hervé Thoreau, Guillaume Bourque, Hendrik G. Stunnenberg, Xiaoan Ruan, Valère Cacheux-Rataboul, Wing‐Kin Sung, Edison T. Liu, Chia‐Lin Wei, Edwin Cheung, Yijun Ruan - Nature 2009 cited by 1,838
- The Energetics and Physiological Impact of Cohesin Extrusion
Authors: Laura Vian, Aleksandra Pękowska, Suhas S.P. Rao, Kyong-Rim Kieffer-Kwon, Seolkyoung Jung, Laura Baranello, Su‐Chen Huang, Laïla El Khattabi, Marei Dose, Nathanael Pruett, Adrian L. Sanborn, Andrés Canela, Yaakov Maman, Anna Oksanen, Wolfgang Resch, Xingwang Li, Byoungkoo Lee, Alexander L. Kovalchuk, Zhonghui Tang, Steevenson Nelson, Michele Di Pierro, Ryan R. Cheng, Ido Machol, Brian Glenn St Hilaire, Neva C. Durand, Muhammad S. Shamim, Elena K. Stamenova, José N. Onuchic, Yijun Ruan, André Nussenzweig, David Levens, Erez Lieberman Aiden, Rafael Casellas - Cell 2018 cited by 642
- CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Authors: Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, Meizhen Zheng, Jacqueline Jufen Zhu, Przemysław Szałaj, Paweł Trzaskoma, Adriana Magalska, Jakub Włodarczyk, Błażej Ruszczycki, Paul J. Michalski, Emaly Piecuch, Ping Wang, Danjuan Wang, Simon Zhongyuan Tian, May Penrad‐Mobayed, Laurent M. Sachs, Xiaoan Ruan, Chia‐Lin Wei, Edison T. Liu, Grzegorz M. Wilczyński, Dariusz Plewczyński, Guoliang Li, Yijun Ruan - Cell 2015 cited by 1,137
- Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription
Authors: Yanfen Zhu, Amit D. Gujar, Chee‐Hong Wong, Harianto Tjong, Chew Yee Ngan, Liang Gong, Yi‐An Chen, Hoon Kim, Jihe Liu, Meihong Li, Adam Mil-Homens, Rahul Maurya, Chris Kuhlberg, Fanyue Sun, Eunhee Yi, Ana C. deCarvalho, Yijun Ruan, Roel G.W. Verhaak, Chia‐Lin Wei - Cancer Cell 2021 cited by 289
- The draft genome of sweet orange (Citrus sinensis)
Authors: Qiang Xu, Ling-Ling Chen, Xiaoan Ruan, Dijun Chen, Andan Zhu, Chunli Chen, Denis Bertrand, Wen‐Biao Jiao, Bao-Hai Hao, Matthew P Lyon, Jiongjiong Chen, Song Gao, Xing Feng, Hong Lan, Ji-Wei Chang, Xianhong Ge, Lei Yang, Qun Hu, Yin Miao, Lun Wang, Shixin Xiao, Manosh Kumar Biswas, Wenfang Zeng, Fei Guo, Hongbo Cao, Xiaoming Yang, Xi-Wen Xu, Yun-Jiang Cheng, Juan Xu, Jihong Liu, Oscar Junhong Luo, Zhonghui Tang, Wen-Wu Guo, Hanhui Kuang, Hong Yu Zhang, Mikeal L. Roose, Niranjan Nagarajan, Xiuxin Deng, Yijun Ruan - Nature Genetics 2012 cited by 1,052
- RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses
Authors: Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin‐Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin L. Hibberd, Edison T. Liu, Forest Rohwer, Yijun Ruan - PLoS Biology 2005 cited by 828
- Evolutionarily Conserved Principles Predict 3D Chromatin Organization
Authors: M. Jordan Rowley, Michael H. Nichols, Xiaowen Lyu, Masami Ando‐Kuri, S. Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G. Corces - Molecular Cell 2017 cited by 598
- Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
Authors: Xi Chen, Xu Han, Ping Yuan, Fang Fang, Mikael Huss, Vinsensius B. Vega, Eleanor Wong, Yuriy L. Orlov, Weiwei Zhang, Jianming Jiang, Yuin‐Han Loh, Hock Chuan Yeo, Zhen Xuan Yeo, Vipin Narang, Kunde Ramamoorthy Govindarajan, Bernard Leong, Atif Shahab, Yijun Ruan, Guillaume Bourque, Wing‐Kin Sung, Neil D. Clarke, Chia‐Lin Wei, Huck‐Hui Ng - Cell 2008 cited by 2,577
- Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
Authors: Xia Wang, Yuantao Xu, Siqi Zhang, Li Cao, Yue Huang, Jun-Feng Cheng, Guizhi Wu, Shilin Tian, Chunli Chen, Yan Liu, Huiwen Yu, Xiaoming Yang, Hong Lan, Nan Wang, Lun Wang, Jidi Xu, Xiaolin Jiang, Zongzhou Xie, Meilian Tan, Robert M. Larkin, Ling‐Ling Chen, Bin‐Guang Ma, Yijun Ruan, Xiuxin Deng, Qiang Xu - Nature Genetics 2017 cited by 488
- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
Authors: Guoliang Li, Xiaoan Ruan, Raymond K. Auerbach, Kuljeet Singh Sandhu, Meizhen Zheng, Ping Wang, Huay Mei Poh, Yufen Goh, Joanne Lim, Jingyao Zhang, Hui Shan Sim, Su Qin Peh, Fabianus Hendriyan Mulawadi, Chin Thing Ong, Yuriy L. Orlov, Shuzhen Hong, Zhizhuo Zhang, Steve Landt, Debasish Raha, Ghia Euskirchen, Chia‐Lin Wei, Weihong Ge, Huaien Wang, Carrie Davis, Katherine Fisher-Aylor, A Mortazavi, Mark Gerstein, T Gingeras, B Wold, Yi Sun, Melissa J. Fullwood, Edwin Cheung, Edison Liu, Wing‐Kin Sung, M Snyder, Yijun Ruan - Cell 2012 cited by 1,345
- Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty
Authors: Oscar Junhong Luo, Wen Lei, Guodong Zhu, Zhiyao Ren, Yudai Xu, Chanchan Xiao, Hongyi Zhang, Junxiang Cai, Zhiping Luo, Lijuan Gao, Jun Su, Lei Tang, Wei Guo, Huanxing Su, Zhang‐Jin Zhang, Evandro Fei Fang, Yijun Ruan, Sean X. Leng, Zhenyu Ju, Huiling Lou, Junling Gao, Nan Peng, Jie Chen, Zhijun Bao, Feng Liu, Guobing Chen - Nature Aging 2022 cited by 144
- A supervised learning framework for chromatin loop detection in genome-wide contact maps
Authors: T. Salameh, Xiaotao Wang, Fan Song, Bo Zhang, Sage M. Wright, Chachrit Khunsriraksakul, Yijun Ruan, Feng Yue - Nature Communications 2020 cited by 172
- Evolution of the mammalian transcription factor binding repertoire via transposable elements
Authors: 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, Edison T. Liu - Genome Research 2008 cited by 630
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Authors: Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont, Lacramioara Bintu, Alistair N. Boettiger, Riccardo Calandrelli, Christine M. Distèche, David M. Gilbert, Thomas Gregor, Anders S. Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina S. Leslie, Wenbo Li, Yun Li, Jian Ma, William Stafford Noble, Peter J. Park, Jennifer E. Phillips‐Cremins, Katherine S. Pollard, Susanne M. Rafelski, Bing Ren, Yijun Ruan, Yaron Shav‐Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio‐De‐Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong - Molecular Cell 2023 cited by 97
- The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
Authors: Yuin‐Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W Sung, Charlie W. H. Lee, Xiao-Dong Zhao, Kuo‐Ping Chiu, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia‐Lin Wei, Yijun Ruan, Bing Lim, Huck‐Hui Ng - Nature Genetics 2006 cited by 2,456
- Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations
Authors: Yubo Zhang, Chee‐Hong Wong, Ramon Y. Birnbaum, Guoliang Li, Rebecca Favaro, Chew Yee Ngan, Joanne Lim, Eunice Tai, Huay Mei Poh, Eleanor Wong, Fabianus Hendriyan Mulawadi, Wing‐Kin Sung, Silvia K. Nicolis, Nadav Ahituv, Yijun Ruan, Chia‐Lin Wei - Nature 2013 cited by 505
- Super-enhancers delineate disease-associated regulatory nodes in T cells
Authors: Golnaz Vahedi, Yuka Kanno, Yasuko Furumoto, Kan Jiang, Stephen C.J. Parker, Michael R. Erdos, Sean Davis, Rahul Roychoudhuri, Nicholas P. Restifo, Massimo Gadina, Zhonghui Tang, Yijun Ruan, Francis S. Collins, Vittorio Sartorelli, John J. O’Shea - Nature 2015 cited by 404
- Multiplex chromatin interactions with single-molecule precision
Authors: Meizhen Zheng, Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Rahul Maurya, Byoungkoo Lee, Emaly Piecuch, Liang Gong, Jacqueline Jufen Zhu, Zhihui Li, Chee‐Hong Wong, Chew Yee Ngan, Ping Wang, Xiaoan Ruan, Chia‐Lin Wei, Yijun Ruan - Nature 2019 cited by 262
- Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application
Authors: Guoliang Li, Liuyang Cai, Huidan Chang, Ping Hong, Qiangwei Zhou, E.V. Kulakova, Н. А. Колчанов, Yijun Ruan - BMC Genomics 2014 cited by 127
- Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma
Authors: Yige Wu, Nadezhda V. Terekhanova, Wagma Caravan, Nataly Naser Al Deen, Preet Lal, Siqi Chen, Chia-Kuei Mo, Song Cao, Yize Li, Alla Y. Karpova, Ruiyang Liu, Yanyan Zhao, Andrew Shinkle, Ilya Strunilin, Cody Weimholt, Kazuhito Sato, Lijun Yao, Mamatha Serasanambati, Xiaolu Yang, Matthew A. Wyczalkowski, Houxiang Zhu, Daniel Cui Zhou, Reyka G. Jayasinghe, Daniel Mendez, Michael C. Wendl, David Clark, Chelsea J. Newton, Yijun Ruan, Melissa A. Reimers, Russell K. Pachynski, Chris Kinsinger, Scott D. Jewell, Daniel W. Chan, Hui Zhang, Aadel A. Chaudhuri, Milan G. Chheda, Benjamin D. Humphreys, Mehdi Mesri, Henry Rodriguez, James J. Hsieh, Li Ding, Feng Chen - Nature Communications 2023 cited by 49
- Functional metagenomic profiling of nine biomes
Authors: Elizabeth A. Dinsdale, Robert A. Edwards, Dana Hall, Florent Angly, Mya Breitbart, Jennifer M. Brulc, Mike Furlan, Christelle Desnues, Matthew Haynes, Linlin Li, Lauren D. McDaniel, Mary Ann Moran, Karen E. Nelson, Christína Nilsson, Robert Olson, John H. Paul, Beltran Rodriguez Brito, Yijun Ruan, Brandon K. Swan, Rick Stevens, David L. Valentine, Rebecca Vega Thurber, Linda Wegley, Bryan A. White, Forest Rohwer - Nature 2008 cited by 982
