个人简历

2017-至今 清华大学 生命科学学院 副教授,博士生导师\r
2011-2016 清华大学 生命科学学院 助理教授，博士生导师\r
2008-2011 耶鲁大学 生物信息学 博士后\r
2003-2008 罗切斯特大学 生物物理学 博士\r
1998-2003 中国科学技术大学 生命科学学院 学士

研究领域

"我们实验室致力于发展生物信息学技术，并探索能够广泛应用于动植物基因组学和癌症生物学的具体实践。我们利用高通量测序，结合机器学习和人工智能技术，来研究遗传信息是如何被编码在结构化的DNA和RNA分子之中，以及它们是如何在一个生命体系中相互作用、彼此调控。\r
“上工治未病”，我们的使命，是帮助人们更早期的发现癌症。我们相信，这种使命感以及为此付出的实践和努力，将帮助我们理解和治疗人类疾病，并最终认识和提高我们自己。\r
我们希望把生物信息技术运用到重要的生物和医学问题中，实验室的科研项目主要包括三个方向: \r
1. [RNA调控]：动植物中编码和非编码RNA的转录后调控研究 \r
2. [精准医疗]：癌症等疾病中新型RNA分子标识物的发现和机理研究\r
3. [人工智能]：机器学习等数据挖掘技术的研究及其在基因组学大数据上的应用"

近期论文

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)\r
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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\r
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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\r
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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)\r
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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\r
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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)\r
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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\r
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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 \r
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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)\r
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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)\r
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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)\r
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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)\r
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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)\r
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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\r
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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)\r
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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)\r
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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)\r
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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)\r
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[spotlight]: Binbin Shi and Zhi John Lu* (2018) Decoding Plant RNA Structurome. Molecular Plant 11:3\r
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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)\r
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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