Zhi John Lu

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 10

Top Topics

Transcriptional Regulation

Secondary Structure

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Letian Gao, Zhi John Lu
RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching. CoRR (2024)
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
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res. 50 (D1) (2022)
Jing Gong, Kui Xu, Ziyuan Ma, Zhi John Lu, Qiangfeng Cliff Zhang
A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. Nat. Mach. Intell. 3 (11) (2021)
Kequan Lin, Lu Li, Yifei Dai, Huili Wang, Shuaishuai Teng, Xilinqiqige Bao, Zhi John Lu, Dong Wang
A comprehensive evaluation of connectivity methods for L1000 data. Briefings Bioinform. 21 (6) (2020)
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, Dong Wang
Microarray is an efficient tool for circRNA profiling. Briefings Bioinform. 20 (4) (2019)
Yumin Zhu, Gang Xu, Yu-Cheng T. Yang, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu, Pengyuan Wang
POSTAR2: deciphering the post-transcriptional regulatory logics. Nucleic Acids Res. 47 (Database-Issue) (2019)
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yu-Cheng T. Yang, Qiangfeng Cliff Zhang
RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res. 46 (Database-Issue) (2018)
Boqin Hu, Yu-Cheng T. Yang, Yiming Huang, Yumin Zhu, Zhi John Lu
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res. 45 (Database-Issue) (2017)
Xihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip
Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations. Briefings Bioinform. 17 (6) (2016)
Yang Wu, Rihao Qu, Yiming Huang, Binbin Shi, Mengrong Liu, Yang Li, Zhi John Lu
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting-Fung Chan, Terrence Chi-Kong Lau, Siu-Ming Yiu, Kevin Y. Yip
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. Bioinform. 30 (8) (2014)
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, Mark Gerstein
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLoS Comput. Biol. 7 (11) (2011)
Zhi John Lu, David H. Mathews
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)