Zhi LU Ph.D.
Associate Professor
2017-present Bioinformatics and Genomics Associate Professor Tsinghua University, Beijing, China
2011-2016 Bioinformatics and Genomics Assistant Professor Tsinghua University, Beijing, China
2008-2011 Bioinformatics Postdoc Yale University, New Haven, CT, US
2003-2008 Biophysics Ph.D. University of Rochester, Rochester, NY, US
1998-2003 Life Sciences B.S. University of Science and Technology of China
Research interest
Our group is interested in developing bioinformatics technologies, and practicing evidence-based precision medicine for diseases like cancer. We utilize machine learning and AI technologies, together with noncoding RNA (ncRNA) centered multi-omics data, to understand how genetic information is encoded in the structured DNA and RNA sequences, and how they interact and regulate each other in a biological system. Ultimately, this will help us understand and cure human diseases, know and improve ourselves.
We have two major research directions based on noncoding RNA (ncRNA):
I. Bioinformatics-driven Precision Medicine;
II. AI-driven RNA Target Prediction and Drug Design.
Selected publications
1. Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu* and Zhi John Lu* (2025) RNA–ligand interaction scoring via data perturbation and augmentation modeling. Nature Computational Science 10.1038/s43588-025-00820-x
2. Pengfei Bao1, Taiwei Wang1, Xiaofan Liu1, Shaozhen Xing, Hanjin Ruan, Hongli Ma, Yuhuan Tao, Qing Zhan, Efres Belmonte-Reche, Lizheng Qin, Zhengxue Han, Minghui Mao*, Mengtao Li* & Zhi John Lu* (2025) Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential. Genome Biology 26, 119
3. Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu (2024) OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics 40 (10), btae577
4. Xiaofan Liu1, Yuhuan Tao1, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li*, Yunping Zhu* & Zhi John Lu* (2024) Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data. Bioinformatics 40 (5), btae316 (1contributed equally, *co-corresponding authors)
5. Yuhuan Tao1, Shaozhen Xing1, Shuai Zuo1, Pengfei Bao, Yunfan Jin, Yu Li, Yingchao Wu, Shanwen Chen, Xiaojuan Wang, Yumin Zhu, Ying Feng, Xiaohua Zhang, Xianbo Wang, Qiaoran Xi, Qian Lu*, Pengyuan Wang*, Zhi John Lu* (2023) Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients’ blood. Cell Reports Medicine 4(11):101281
6. 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. eLife11:e75181 (1contributed equally, *co-corresponding authors)
7. 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 Research30(1):34-49 (1contributed equally, *co-corresponding authors)
8. 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)
Contact information
Tel. /FAX: +86-10-62789217
E-mail: lulab1 AT tsinghua.edu.cn
Lab page: https://www.ncRNAlab.org | http://lulab.life.tsinghua.edu.cn
MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
