Aug. 2013 – Oct. 2019 Ph.D. Department of Automation, Tsinghua University

Aug. 2009 – July 2013 B.S. Department of Automation, Tsinghua University

Jan. 2022 – Present Assistant Research Professor, BNRIST, Tsinghua University

Dec. 2019 – Dec. 2021 Postdoc, Department of Automation, Tsinghua University

Served as a reviewer for journals including Nature Methods, Nature Communications, Cell Genomics, Genome Research, Cell Reports Methods, BMC Bioinformatics, Journal of Theoretical Biology, and Quantitative Biology.

（1）Single-cell bioinformatics

（2）Synthetic biology

Undertook projects funded by the National Natural Science Foundation of China (including General and Young Scientists’ projects). Published multiple research articles as (co-)first or corresponding author in journals such as Cell Reports, Nucleic Acids Research, Bioinformatics, Briefings in Bioinformatics, and Physical Review Research.

Google Scholar: https://scholar.google.com/citations?user=F1jKMakAAAAJ.

[1] Haiyang Bian, Yixin Chen, Lei Wei*, Xuegong Zhang*. uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization. Bioinformatics, 2025: btaf149.

[2] Haochen Li, Tianxing Ma, Zetong Zhao, Yixin Chen, Xi Xi, Xiaofei Zhao, Xiaoxiang Zhou, Yibo Gao, Lei Wei*, Xuegong Zhang. scTML: a pan-cancer single-cell landscape of multiple mutation types. Nucleic Acids Research, 2024: gkae898.

[3] Haoxiao Cai, Xiaoran Zhang, Rong Qiao, Xiaowo Wang*, Lei Wei*. Efficient computation by molecular competition networks. Physical Review Research, 2024, 6(3): 033208.

[4] Haoxiang Gao, Kui Hua, Xinze Wu, Lei Wei*, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang*. Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model. Communications Biology, 2024, 7(1): 977.

[5] Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei*, Xuegong Zhang*. scMulan: a multitask generative pre-trained language model for single-cell analysis. RECOMB, 2024: 479-482.

[6] Chuxi Xiao, Yixin Chen, Qiuchen Meng, Lei Wei*, Xuegong Zhang. Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data. Briefings in Bioinformatics, 2024, 25(2): bbae095.

[7] Qiuchen Meng,  Lei Wei*, Kun Ma, Ming Shi, Xinyi Lin, Joshua W K Ho, Yinqing Li*, Xuegong Zhang. scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. Briefings in Bioinformatics, 2024, 25(2): bbae011.

[8] Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei*, Xuegong Zhang*. STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning. Communications Biology, 2024, 7(1): 56.

[9] Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang*, Lei Wei*. Decoding functional cell–cell communication events by multi-view graph learning on spatial transcriptomics. Briefings in Bioinformatics, 2023, 24(6): bbad359.

[10] Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei*, Xiaowo Wang*. ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. Briefings in Bioinformatics. 2022, 23: bbab362.

[11] Lei Wei#, Shuailin Li#, Pengcheng Zhang, Tao Hu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang. Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits. Cell Reports, 2021, 36: 109573.

[12] Tao Hu#, Lei Wei#, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang. Single-cell transcriptomes reveal characteristics of micrornas in gene expression noise reduction. Genomics, Proteomics & Bioinformatics, 2021, 19: 394–407.

[13] Jiaqi Li#, Lei Wei#, Xianglin Zhang, Wei Zhang, Haochen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang, DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads. Briefings in Bioinformatics, 2021, 22(6): bbab250.

[14] Wei Zhang, Lei Wei*, Jiaqi Huang, Bixi Zhong, Jiaqi Li, Hanwen Xu, Shuying He, Yu Liu, Juhong Liu, Hairong Lv, Xiaowo Wang*, cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data. Bioinformatics, 2021, 37: 4251–4252.

[15] Xuehui Liu#, Lei Wei#, Qiongye Dong, Liyang Liu, Michael Q Zhang, Zhen Xie, Xiaowo Wang. A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass. Aging (Albany NY), 2019, 11: 4011.

[16] Lei Wei#, Ye Yuan#, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q Zhang, Xiaowo Wang, Regulation by competition: a hidden layer of gene regulatory network. Quantitative Biology, 2019, 7: 110–121.