MarkUs: a server to navigate sequence-structure-function space. - Markus Fischer; Qiangfeng Cliff Zhang; Fabian Dey; Brian Y. Chen; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

PredUs: a web server for predicting protein interfaces using structural neighbors. - Qiangfeng Cliff Zhang; Lei Deng 002; Markus Fisher; Jihong Guan; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. - Lei Deng 002; Jihong Guan; Xiaoming Wei; Yuan Yi; Qiangfeng Cliff Zhang; Shuigeng Zhou (J. Comput. Biol., 2013)

PrePPI: a structure-informed database of protein-protein interactions. - Qiangfeng Cliff Zhang; Donald Petrey; José Ignacio Garzón; Lei Deng 002; Barry Honig (Nucleic Acids Res., 2013)

PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. - Lei Deng 002; Qiangfeng Cliff Zhang; Zhigang Chen 001; Yang Meng; Jihong Guan; Shuigeng Zhou (Nucleic Acids Res., 2014)

Harnessing Big Data for Precision Medicine: Infrastructures and Applications. - Kun-Hsing Yu; Steven N. Hart; Rachel L. Goldfeder; Qiangfeng Cliff Zhang; Stephen C. J. Parker; Michael Snyder 001 (PSB, 2017)

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. - Meiling Piao; Lei Sun; Qiangfeng Cliff Zhang (Genom. Proteom. Bioinform., 2017)

RISE: a database of RNA interactome from sequencing experiments. - Jing Gong; Di Shao; Kui Xu 004; Zhipeng Lu 002; Zhi John Lu; Yu-Cheng T. Yang; Qiangfeng Cliff Zhang (Nucleic Acids Res., 2018)

Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale. - Jing Gong; Yanyan Ju; Di Shao; Qiangfeng Cliff Zhang (Quant. Biol., 2018)

A2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes. - Kui Xu 004; Zhe Wang 006; Jianping Shi; Hongsheng Li 001; Qiangfeng Cliff Zhang (AAAI, 2019)

A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes. - Kui Xu 004; Zhe Wang 006; Jianping Shi; Hongsheng Li 001; Qiangfeng Cliff Zhang (CoRR, 2019)

Prediction and differential analysis of RNA secondary structure. - Bo Yuan 004; Yao Lu; Qiangfeng Cliff Zhang; Lin Hou (Quant. Biol., 2020)

IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. - Jianyu Zhou; Pan Li; Wanwen Zeng; Wenxiu Ma; Zhipeng Lu 002; Rui Jiang 001; Qiangfeng Cliff Zhang; Tao Jiang 001 (Quant. Biol., 2020)

VRmol: an integrative web-based virtual reality system to explore macromolecular structure. - Kui Xu 004; Nan Liu; Jingle Xu; Chunlong Guo; Lingyun Zhao; Hongwei Wang; Qiangfeng Cliff Zhang (Bioinform., 2021)

RASP: an atlas of transcriptome-wide RNA secondary structure probing data. - Pan Li; Xiaolin Zhou; Kui Xu 004; Qiangfeng Cliff Zhang (Nucleic Acids Res., 2021)

A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. - Jing Gong; Kui Xu 004; Ziyuan Ma; Zhi John Lu; Qiangfeng Cliff Zhang (Nat. Mach. Intell., 2021)

PrismNet: predicting protein-RNA interaction using in vivo RNA structural information. - Yiran Xu; Jianghui Zhu; Wenze Huang; Kui Xu 004; Rui Yang; Qiangfeng Cliff Zhang; Lei Sun (Nucleic Acids Res., 2023)

RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells. - Boyang Shi; Ke An; Yueqin Wang; Yuhan Fei; Caixia Guo; Qiangfeng Cliff Zhang; Yun-Gui Yang; Xin Tian; Quancheng Kan (Genom. Proteom. Bioinform., 2023)

CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps. - Muzhi Dai; Zhuoer Dong; Weining Fu; Kui Xu; Qiangfeng Cliff Zhang (AAAI, 2025)