Zhi John Lu

16 papers Journal 16
YearRankTypeTitle / Venue / Authors
2025 J jnl
RNA-ligand interaction scoring via data perturbation and augmentation modeling.
Nat. Comput. Sci.
Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu, Zhi John Lu
2024 J jnl
OligoFormer: an accurate and robust prediction method for siRNA design.
Bioinform.
Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu
2024 J jnl
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data.
Bioinform.
Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li, Yunping Zhu, Zhi John Lu
2024 J jnl
RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching.
CoRR
Letian Gao, Zhi John Lu
2022 J jnl
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.
Nucleic Acids Res.
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
2021 J jnl
A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments.
Nat. Mach. Intell.
Jing Gong, Kui Xu, Ziyuan Ma, Zhi John Lu, Qiangfeng Cliff Zhang
2020 J jnl
A comprehensive evaluation of connectivity methods for L1000 data.
Briefings Bioinform.
Kequan Lin, Lu Li, Yifei Dai, Huili Wang, Shuaishuai Teng, Xilinqiqige Bao, Zhi John Lu, Dong Wang
2019 J jnl
Microarray is an efficient tool for circRNA profiling.
Briefings Bioinform.
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
2019 J jnl
POSTAR2: deciphering the post-transcriptional regulatory logics.
Nucleic Acids Res.
Yumin Zhu, Gang Xu, Yu-Cheng T. Yang, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu, Pengyuan Wang
2018 J jnl
RISE: a database of RNA interactome from sequencing experiments.
Nucleic Acids Res.
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yu-Cheng T. Yang, Qiangfeng Cliff Zhang
2017 J jnl
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.
Nucleic Acids Res.
Boqin Hu, Yu-Cheng T. Yang, Yiming Huang, Yumin Zhu, Zhi John Lu
2016 J jnl
Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations.
Briefings Bioinform.
Xihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip
2016 J jnl
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.
Nucleic Acids Res.
Yang Wu, Rihao Qu, Yiming Huang, Binbin Shi, Mengrong Liu, Yang Li, Zhi John Lu
2014 J jnl
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
Bioinform.
Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting-Fung Chan, Terrence Chi-Kong Lau, Siu-Ming Yiu, Kevin Y. Yip
2011 J jnl
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data.
PLoS Comput. Biol.
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
2008 J jnl
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.
Nucleic Acids Res.
Zhi John Lu, David H. Mathews