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Ashoor, Haitham, Chen, Xiaowen, Rosikiewicz, Wojciech, Wang, Jiahui, Cheng, Albert, Wang, Ping, Ruan, Yijun, Li, Sheng
Published in Nature communications (03.03.2020)
Published in Nature communications (03.03.2020)
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A supervised learning framework for chromatin loop detection in genome-wide contact maps
Salameh, Tarik J., Wang, Xiaotao, Song, Fan, Zhang, Bo, Wright, Sage M., Khunsriraksakul, Chachrit, Ruan, Yijun, Yue, Feng
Published in Nature communications (09.07.2020)
Published in Nature communications (09.07.2020)
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CTCF-mediated functional chromatin interactome in pluripotent cells
Ruan, Yijun, Wei, Chia-Lin, 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
Published in Nature genetics (01.07.2011)
Published in Nature genetics (01.07.2011)
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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
Published in Cell (17.12.2015)
Published in Cell (17.12.2015)
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Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions
Li, Xingwang, Luo, Oscar Junhong, Wang, Ping, Zheng, Meizhen, Wang, Danjuan, Piecuch, Emaly, Zhu, Jacqueline Jufen, Tian, Simon Zhongyuan, Tang, Zhonghui, Li, Guoliang, Ruan, Yijun
Published in Nature protocols (01.05.2017)
Published in Nature protocols (01.05.2017)
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Spatial chromatin architecture alteration by structural variations in human genomes at the population scale
Sadowski, Michal, Kraft, Agnieszka, Szalaj, Przemyslaw, Wlasnowolski, Michal, Tang, Zhonghui, Ruan, Yijun, Plewczynski, Dariusz
Published in Genome Biology (30.07.2019)
Published in Genome Biology (30.07.2019)
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The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations
Menghi, Francesca, Barthel, Floris P., Yadav, Vinod, Tang, Ming, Ji, Bo, Tang, Zhonghui, Carter, Gregory W., Ruan, Yijun, Scully, Ralph, Verhaak, Roel G.W., Jonkers, Jos, Liu, Edison T.
Published in Cancer cell (13.08.2018)
Published in Cancer cell (13.08.2018)
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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
Published in Nature (London) (12.12.2013)
Published in Nature (London) (12.12.2013)
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Metagenomic analysis of viruses in reclaimed water
Rosario, Karyna, Nilsson, Christina, Lim, Yan Wei, Ruan, Yijun, Breitbart, Mya
Published in Environmental microbiology (01.11.2009)
Published in Environmental microbiology (01.11.2009)
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Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response
Amin, Ruhul, Shukla, Anjali, Zhu, Jacqueline Jufen, Kim, Sohyoung, Wang, Ping, Tian, Simon Zhongyuan, Tran, Andy D., Paul, Debasish, Cappell, Steven D., Burkett, Sandra, Liu, Huaitian, Lee, Maxwell P., Kruhlak, Michael J., Dwyer, Jennifer E., Simpson, R. Mark, Hager, Gordon L., Ruan, Yijun, Hunter, Kent W.
Published in Nature communications (13.12.2021)
Published in Nature communications (13.12.2021)
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Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture
Lin, Da, Hong, Ping, Zhang, Siheng, Xu, Weize, Jamal, Muhammad, Yan, Keji, Lei, Yingying, Li, Liang, Ruan, Yijun, Fu, Zhen F., Li, Guoliang, Cao, Gang
Published in Nature genetics (01.05.2018)
Published in Nature genetics (01.05.2018)
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Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization
Trzaskoma, Paweł, Ruszczycki, Błażej, Lee, Byoungkoo, Pels, Katarzyna K., Krawczyk, Katarzyna, Bokota, Grzegorz, Szczepankiewicz, Andrzej A., Aaron, Jesse, Walczak, Agnieszka, Śliwińska, Małgorzata A., Magalska, Adriana, Kadlof, Michal, Wolny, Artur, Parteka, Zofia, Arabasz, Sebastian, Kiss-Arabasz, Magdalena, Plewczyński, Dariusz, Ruan, Yijun, Wilczyński, Grzegorz M.
Published in Nature communications (01.05.2020)
Published in Nature communications (01.05.2020)
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Transcriptional profiles of bovine in vivo pre-implantation development
Jiang, Zongliang, Sun, Jiangwen, Dong, Hong, Luo, Oscar, Zheng, Xinbao, Obergfell, Craig, Tang, Yong, Bi, Jinbo, O'Neill, Rachel, Ruan, Yijun, Chen, Jingbo, Tian, Xiuchun Cindy
Published in BMC genomics (04.09.2014)
Published in BMC genomics (04.09.2014)
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Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
Li, Guoliang, Ruan, Xiaoan, Auerbach, Raymond K., Sandhu, Kuljeet Singh, Zheng, Meizhen, Wang, Ping, Poh, Huay Mei, Goh, Yufen, Lim, Joanne, Zhang, Jingyao, Sim, Hui Shan, Peh, Su Qin, Mulawadi, Fabianus Hendriyan, Ong, Chin Thing, Orlov, Yuriy L., Hong, Shuzhen, Zhang, Zhizhuo, Landt, Steve, Raha, Debasish, Euskirchen, Ghia, Wei, Chia-Lin, Ge, Weihong, Wang, Huaien, Davis, Carrie, Fisher-Aylor, Katherine I., Mortazavi, Ali, Gerstein, Mark, Gingeras, Thomas, Wold, Barbara, Sun, Yi, Fullwood, Melissa J., Cheung, Edwin, Liu, Edison, Sung, Wing-Kin, Snyder, Michael, Ruan, Yijun
Published in Cell (20.01.2012)
Published in Cell (20.01.2012)
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Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
Fraser, Peter, 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
Published in Nature genetics (01.01.2010)
Published in Nature genetics (01.01.2010)
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Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes
Ng, Terry Fei Fan, Willner, Dana L, Lim, Yan Wei, Schmieder, Robert, Chau, Betty, Nilsson, Christina, Anthony, Simon, Ruan, Yijun, Rohwer, Forest, Breitbart, Mya
Published in PloS one (06.06.2011)
Published in PloS one (06.06.2011)
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Evolution of the mammalian transcription factor binding repertoire via transposable elements
Bourque, Guillaume, Leong, Bernard, Vega, Vinsensius B, Chen, Xi, Lee, Yen Ling, Srinivasan, Kandhadayar G, Chew, Joon-Lin, Ruan, Yijun, Wei, Chia-Lin, Ng, Huck Hui, Liu, Edison T
Published in Genome Research (01.11.2008)
Published in Genome Research (01.11.2008)
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Functional metagenomic profiling of nine biomes
Nilsson, Christina, Furlan, Mike, Thurber, Rebecca Vega, McDaniel, Lauren, Stevens, Rick, Li, Linlin, Brito, Beltran Rodriguez, Ruan, Yijun, Wegley, Linda, Paul, John, Brulc, Jennifer M, Breitbart, Mya, Nelson, Karen E, Desnues, Christelle, Dinsdale, Elizabeth A, Valentine, David L, White, Bryan A, Angly, Florent, Olson, Robert, Edwards, Robert A, Haynes, Matthew, Swan, Brandon K, Moran, Mary Ann, Hall, Dana, Rohwer, Forest
Published in Nature (03.04.2008)
Published in Nature (03.04.2008)
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