OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. - Zhi John Lu; David H. Mathews (Nucleic Acids Res., 2008)

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. - Chao Cheng; Koon-Kiu Yan; Woochang Hwang; Jiang Qian; Nitin Bhardwaj; Joel S. Rozowsky; Zhi John Lu; Wei Niu; Pedro Alves; Masaomi Kato; Michael Snyder 001; Mark Gerstein (PLoS Comput. Biol., 2011)

Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. - Xihao Hu; Thomas K. F. Wong; Zhi John Lu; Ting-Fung Chan; Terrence Chi-Kong Lau; Siu-Ming Yiu; Kevin Y. Yip (Bioinform., 2014)

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations. - Xihao Hu; Yang Wu; Zhi John Lu; Kevin Y. Yip (Briefings Bioinform., 2016)

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. - Yang Wu; Rihao Qu; Yiming Huang; Binbin Shi; Mengrong Liu; Yang Li; Zhi John Lu (Nucleic Acids Res., 2016)

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. - Boqin Hu; Yu-Cheng T. Yang; Yiming Huang; Yumin Zhu; Zhi John Lu (Nucleic Acids Res., 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)

Microarray is an efficient tool for circRNA profiling. - Shasha Li; Shuaishuai Teng; Junquan Xu; Guannan Su; Yu Zhang; Jianqing Zhao; Suwei Zhang; Haiyan Wang; Wenyan Qin; Zhi John Lu; Yong Guo; Qianyong Zhu; et al. (Briefings Bioinform., 2019)

POSTAR2: deciphering the post-transcriptional regulatory logics. - Yumin Zhu; Gang Xu; Yu-Cheng T. Yang; Zhiyu Xu; Xinduo Chen; Binbin Shi; Daoxin Xie; Zhi John Lu; Pengyuan Wang 004 (Nucleic Acids Res., 2019)

A comprehensive evaluation of connectivity methods for L1000 data. - Kequan Lin; Lu Li; Yifei Dai; Huili Wang; Shuaishuai Teng; Xilinqiqige Bao; Zhi John Lu; Dong Wang 055 (Briefings Bioinform., 2020)

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)

POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. - Weihao Zhao; Shang Zhang; Yumin Zhu; Xiaochen Xi; Pengfei Bao; Ziyuan Ma; Thomas H. Kapral; Shuyuan Chen; Bojan Zagrovic; Yu-Cheng T. Yang; Zhi John Lu (Nucleic Acids Res., 2022)

RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching. - Letian Gao; Zhi John Lu (CoRR, 2024)