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Xing, S.1, Zhu, Y.1, You, Y., Wang, S., Wang, H., Ning, M., Jin, H., Liu, Z., Zhang, X., Yu, C. * & Lu, Z. J. * (2023). Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WIREs RNA, e1791 (1contributed equally, *co-corresponding authors)
Shanwen Chen1, Yunfan Jin1, Siqi Wang1, Shaozhen Xing1, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu*, Zhi John Lu*, Pengyuan Wang* (2022) Cancer Type Classification Using Plasma Cell Free RNAs Derived from Human and Microbes. eLife 11:e75181 (1contributed equally, *co-corresponding authors)
Haipeng Fu, Tingyu Wang, Xiaohui Kong, Kun Yan, Yang Yang, Jingyi Cao, Yafei Yuan, Nan Wang, Kehkooi Kee, Zhi John Lu & Qiaoran Xi (2022) A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nature Communications 13(1):3984
Liuqing Yang, Kequan Lin, Lin Zhu, Huili Wang, Shuaishuai Teng, Lijun Huang, Shiyi Zhou, Guanbin Zhang, Zhi John Lu & Dong Wang (2022) Long non-coding RNA DARS-AS1 promotes tumor progression by directly suppressing PACT-mediated cellular stress. Communications Biology 5, 822
Weihao Zhao1, Shang Zhang1, Yumin Zhu, Xiaochen Xi, Pengfei Bao, Ziyuan Ma, Thomas H Kapral, Shuyuan Chen, Bojan Zagrovic, Yucheng T Yang*, Zhi John Lu* (2022) POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Research 50(D1):D287-D294 (1contributed equally, *co-corresponding authors)
Thomas H Kapral, Fiona Farnhammer, Weihao Zhao, Zhi J Lu and Bojan Zagrovic (2022) Widespread autogenous mRNA–protein interactions detected by CLIP-seq. Nucleic Acids Research, 50(17):9984-9999
Yumin Zhu1, Siqi Wang1, Xiaochen Xi1, Minfeng Zhang1, Xiaofan Liu, Weina Tang, Peng Cai, Shaozhen Xing, Pengfei Bao, Yunfan Jin, Weihao Zhao, Yinghui Chen, Huanan Zhao, Xiaodong Jia, Shanshan Lu, Yinying Lu, Lei Chen*, Jianhua Yin*, Zhi John Lu* (2021) Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 11(1):181-193 (1contributed equally, *co-corresponding authors)
Jing Gong1, Kui Xu1, Ziyuan Ma, Zhi John Lu & Qiangfeng Cliff Zhang (2021) A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. Nature Machine Intelligence 3:995–1006
Jia Li, Lei Sun, Xue-Liang Peng, Xiao-Ming Yu, Shao-Jun Qi, Zhi John Lu, Jing-Dong J Han, Qin Shen (2021) Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons. PLoS Genetics 17(3):e1009355
Shuaishuai Teng1, Yang Eric Li1, Ming Yang, Rui Qi, Yiming Huang, Qianyu Wang, Yanmei Zhang, Shanwen Chen, Shasha Li, Kequan Lin, Yang Cao, Qunsheng Ji, Qingyang Gu, Yujing Cheng, Zai Chang, Wei Guo, Pengyuan Wang, Ivan Garcia-Bassets, Zhi John Lu* and Dong Wang* (2020) Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer. Cell Research 30(1):34-49 (1contributed equally, *co-corresponding authors)
Yu-Xiang Chen1, Zhi-yu Xu1, Xueliang Ge, Suparna Sanyal, Zhi John Lu* and Babak Javid* (2020) Selective translation by alternative bacterial ribosomes. PNAS 117(32):19487-19496 (1contributed equally, *co-corresponding authors)
Yu Ma1, Shang Zhang1, Chao Bi1, Chao Mei, Shang-Chuan Jiang, Xiao-Fang Wang, Zhi John Lu* and Da-Peng Zhang* (2020) Arabidopsis exoribonuclease USB1 interacts with the PPR-domain protein SOAR1 to negatively regulate abscisic acid signaling. Journal of Experimental Botany 71(19): 5837-5851 (1contributed equally, *co-corresponding authors)
Kequan Lin1, Lu Li1, Yifei Dai, Huili Wang, Shuaishuai Teng, Xilinqiqige Bao, Zhi John Lu* and Dong Wang* (2019) A comprehensive evaluation of connectivity methods for L1000 data Briefings in Bioinformatics bbz129 (1contributed equally, *co-corresponding authors)
Rui Xiao1,*, Jia-Yu Chen1, Zhengyu Liang1, Daji Luo, Geng Chen, Zhi John Lu, Yang Chen, Bing Zhou, Hairi Li, Xian Du, Yang Yang, Mingkui San, Xintao Wei, Wen Liu, Eric Lecuyer, Brenton R. Graveley, Gene W. Yeo, Christopher B. Burge, Michael Q. Zhang, Yu Zhou and Xiang-Dong Fu* (2019) Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription Cell 178, 107–121 (1contributed equally, *co-corresponding authors)
Maoguo Luo, Jianbo Bai, Bofeng Liu, Peiqiang Yan, Feifei Zuo, Hongyao Sun, Ye Sun, Xuanhao Xu, Zhihong Song, Yang Yang, Joan Massagué, Xun Lan, Zhi Lu, Ye-Guang Chen, Haiteng Deng, Wei Xie, Qiaoran Xi (2019) H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling Stem Cell Reports 13(4):642-656
Chang Tan1, Jingyi Cao1, Lu Chen1, Xiaochen Xi, Siqi Wang, Yumin Zhu, Liuqing Yang, Longteng Ma, Dong Wang, Jianhua Yin*, Ti Zhang* and Zhi John Lu* (2019) Noncoding RNAs serve as diagnosis and prognosis biomarkers for hepatocellular carcinoma Clinical Chemistry 65(7):905-915 (1contributed equally, *co-corresponding authors)
Yumin Zhu1, Gang Xu1, Yucheng T Yang1, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu*, Pengyuan Wang* (2019) POSTAR2: deciphering the post-transcriptional regulatory logics Nucleic Acids Research (D1):D203-D211 (1contributed equally, *co-corresponding authors)
Zhiyu Xu1, Long Hu1, Binbin Shi, SiSi Geng, Longchen Xu, Dong Wang* and Zhi John Lu* (2018) Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Research 46 (18), e109-e109 (1contributed equally, *co-corresponding authors)
Shasha Li1, Shuaishuai Teng1, Junquan Xu, Guannan Su, Yu Zhang, Jianqing Zhao, Suwei Zhang, Haiyan Wang, Wenyan Qin, Zhi John Lu, Yong Guo, Qianyong Zhu and Dong Wang (2018) Microarray is an efficient tool for circRNA profiling. Briefings in Bioinformatics doi: 10.1093/bib/bby006 (1contributed equally)
[spotlight]: Binbin Shi and Zhi John Lu* (2018) Decoding Plant RNA Structurome. Molecular Plant 11:3
J Yuan1, J Li1, Y Yang, C Tan, Y Zhu, L Hu, Y Qi*, ZJ Lu* (2018) Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa. The Plant Journal 93:5, 814-827 (1contributed equally, *co-corresponding authors)
J Gong, D Shao, K Xu, Z Lu, ZJ Lu, YT Yang, QC Zhang (2018) RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Research 46 (D1), D194-D201
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