Systematic Discovery of Xist RNA Binding Proteins von Chu, Ci, Zhang, Qiangfeng Cliff, da Rocha, Simão Teixeira, Flynn, Ryan A., Bharadwaj, Maheetha, Calabrese, J. Mauro, Magnuson, Terry, Heard, Edith, Chang, Howard Y.

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Structure-based prediction of protein–protein interactions on a genome-wide scale von Zhang, Qiangfeng Cliff, Petrey, Donald, Deng, Lei, Qiang, Li, Shi, Yu, Thu, Chan Aye, Bisikirska, Brygida, Lefebvre, Celine, Accili, Domenico, Hunter, Tony, Maniatis, Tom, Califano, Andrea, Honig, Barry

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RNA structure probing uncovers RNA structure-dependent biological functions von Wang, Xi-Wen, Liu, Chu-Xiao, Chen, Ling-Ling, Zhang, Qiangfeng Cliff

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Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures von Sun, Lei, Xu, Kui, Huang, Wenze, Yang, Yucheng T., Li, Pan, Tang, Lei, Xiong, Tuanlin, Zhang, Qiangfeng Cliff

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RNA structure probing reveals the structural basis of Dicer binding and cleavage von Luo, Qing-Jun, Zhang, Jinsong, Li, Pan, Wang, Qing, Zhang, Yue, Roy-Chaudhuri, Biswajoy, Xu, Jianpeng, Kay, Mark A., Zhang, Qiangfeng Cliff

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A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice von Kim, Hak Kyun, Xu, Jianpeng, Chu, Kirk, Park, Hyesuk, Jang, Hagoon, Li, Pan, Valdmanis, Paul N., Zhang, Qiangfeng Cliff, Kay, Mark A.

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The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling von Ding, Yanyan, Li, Yuzhe, Zhao, Ziqian, Cliff Zhang, Qiangfeng, Liu, Feng

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Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches von Qian, Xingyang, Zhao, Jieyu, Yeung, Pui Yan, Zhang, Qiangfeng Cliff, Kwok, Chun Kit

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RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells von Shi, Boyang, An, Ke, Wang, Yueqin, Fei, Yuhan, Guo, Caixia, Cliff Zhang, Qiangfeng, Yang, Yun-Gui, Tian, Xin, Kan, Quancheng

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PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution von Lu, Zhipeng, Gong, Jing, Zhang, Qiangfeng Cliff

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U1 snRNP regulates chromatin retention of noncoding RNAs von Yin, Yafei, Lu, J. Yuyang, Zhang, Xuechun, Shao, Wen, Xu, Yanhui, Li, Pan, Hong, Yantao, Cui, Li, Shan, Ge, Tian, Bin, Zhang, Qiangfeng Cliff, Shen, Xiaohua

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SCALE method for single-cell ATAC-seq analysis via latent feature extraction von Xiong, Lei, Xu, Kui, Tian, Kang, Shao, Yanqiu, Tang, Lei, Gao, Ge, Zhang, Michael, Jiang, Tao, Zhang, Qiangfeng Cliff

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In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs von Sun, Lei, Li, Pan, Ju, Xiaohui, Rao, Jian, Huang, Wenze, Ren, Lili, Zhang, Shaojun, Xiong, Tuanlin, Xu, Kui, Zhou, Xiaolin, Gong, Mingli, Miska, Eric, Ding, Qiang, Wang, Jianwei, Zhang, Qiangfeng Cliff

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Targeting RNA structures in diseases with small molecules von Shao, Yanqiu, Zhang, Qiangfeng Cliff

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A novel cell culture system modeling the SARS-CoV-2 life cycle von Ju, Xiaohui, Zhu, Yunkai, Wang, Yuyan, Li, Jingrui, Zhang, Jiaxing, Gong, Mingli, Ren, Wenlin, Li, Sai, Zhong, Jin, Zhang, Linqi, Zhang, Qiangfeng Cliff, Zhang, Rong, Ding, Qiang

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Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space von Xiong, Lei, Tian, Kang, Li, Yuzhe, Ning, Weixi, Gao, Xin, Zhang, Qiangfeng Cliff

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RASP: an atlas of transcriptome-wide RNA secondary structure probing data von Li, Pan, Zhou, Xiaolin, Xu, Kui, Zhang, Qiangfeng Cliff

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Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2 von Zhang, Shaojun, Huang, Wenze, Ren, Lili, Ju, Xiaohui, Gong, Mingli, Rao, Jian, Sun, Lei, Li, Pan, Ding, Qiang, Wang, Jianwei, Zhang, Qiangfeng Cliff

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IRIS: A method for predicting in vivo RNA secondary structures using PARIS data von Zhou, Jianyu, Li, Pan, Zeng, Wanwen, Ma, Wenxiu, Lu, Zhipeng, Jiang, Rui, Cliff Zhang, Qiangfeng, Jiang, Tao

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RNA structure maps across mammalian cellular compartments von Sun, Lei, Fazal, Furqan M., Li, Pan, Broughton, James P., Lee, Byron, Tang, Lei, Huang, Wenze, Kool, Eric T., Chang, Howard Y., Zhang, Qiangfeng Cliff

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