Lei Wei

According to our database, Lei Wei authored at least 25 papers between 2019 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Computational methods and data resources for predicting tumor neoantigens.

Xiaofei Zhao, Lei Wei, Xuegong Zhang

Briefings Bioinform., July, 2025

DrVD-Bench: Do Vision-Language Models Reason Like Human Doctors in Medical Image Diagnosis?

Tianhong Zhou, Yin Xu, Yingtao Zhu, Chuxi Xiao, Haiyang Bian, Lei Wei, Xuegong Zhang

CoRR, May, 2025

Benchmarking AI scientists in omics data-driven biological research.

Erpai Luo, Jinmeng Jia, Yifan Xiong, Xiangyu Li, Xiaobo Guo, Baoqi Yu, Lei Wei, Xuegong Zhang

CoRR, May, 2025

Quantifying Early-Stage Lung Adenocarcinoma Progression with a Radiomic Trajectory.

Zhen-Bin Qiu, Jiaqi Li, Shihua Dou, Qiuchen Meng, Meng-Min Wang, Hong-Ji Li, Chao Zhang, Hongsheng Xie, Ben-Yuan Jiang, Jun-Tao Lin, Jia-Tao Zhang, Fang-Ping Xu, Jin-Hai Yan, Lei Wei, Yi-Long Wu, Haibo Wang, Lin Yang, Xuegong Zhang, Wen-Zhao Zhong

npj Digit. Medicine, 2025

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data.

Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei, Xu Qiao, Rui Gao, Zhiping Liu, Xiaowo Wang

Genom. Proteom. Bioinform., 2025

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization.

Haiyang Bian, Yinxin Chen, Lei Wei, Xuegong Zhang

Bioinform., 2025

GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context.

Minsheng Hao, Nan Yan, Haiyang Bian, Yixin Chen, Jin Gu, Lei Wei, Xuegong Zhang

Proceedings of the 20th Machine Learning in Computational Biology (MLCB), 2025

2024

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data.

Chuxi Xiao, Yixin Chen, Qiuchen Meng, Lei Wei, Xuegong Zhang

Briefings Bioinform., March, 2024

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq.

Qiuchen Meng, Lei Wei, Kun Ma, Ming Shi, Xinyi Lin, Joshua W. K. Ho, Yinqing Li, Xuegong Zhang

Briefings Bioinform., March, 2024

NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data.

Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang

Quant. Biol., 2024

Current opinions on large cellular models.

Minsheng Hao, Lei Wei, Fan Yang, Jianhua Yao, Christina V. Theodoris, Bo Wang, Xin Li, Ge Yang, Xuegong Zhang

Quant. Biol., 2024

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding.

Mo Chen, Minsheng Hao, Xuegong Zhang, Lei Wei

CoRR, 2024

scDiffusion: conditional generation of high-quality single-cell data using diffusion model.

Erpai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang

Bioinform., 2024

Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models.

Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang

Proceedings of the Research in Computational Molecular Biology, 2024

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis.

Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Machine Learning in Lung Cancer Radiomics.

Jiaqi Li, Zhuofeng Li, Lei Wei, Xuegong Zhang

Mach. Intell. Res., December, 2023

Building digital life systems for future biology and medicine.

Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv

Quant. Biol., September, 2023

Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics.

Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang, Lei Wei

Briefings Bioinform., September, 2023

2022

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data.

Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang

Briefings Bioinform., 2022

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA.

Xianglin Zhang, Xiaodong Jia, Bixi Zhong, Lei Wei, Jiaqi Li, Wei Zhang, Huan Fang, Yanda Li, Yinying Lu, Xiaowo Wang

Briefings Bioinform., 2022

2021

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data.

Wei Zhang, Lei Wei, Jiaqi Huang, Bixi Zhong, Jiaqi Li, Hanwen Xu, Shuying He, Yu Liu, Juhong Liu, Hairong Lv, Xiaowo Wang

Bioinform., November, 2021

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction.

Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang

Genom. Proteom. Bioinform., 2021

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images.

Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang

Bioinform., 2021

DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads.

Jiaqi Li, Lei Wei, Xianglin Zhang, Wei Zhang, Haochen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang

Briefings Bioinform., 2021

2019

Regulation by competition: a hidden layer of gene regulatory network.

Lei Wei, Ye Yuan, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang

Quant. Biol., 2019