DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. - Tiansheng Zhu; Yi Zhu; Yue Xuan; Huanhuan Gao; Xue Cai; Sander R. Piersma; Thang Viet Pham; Tim Schelfhorst; Richard R. G. D. Haas; Irene V. Bijnsdorp; Rui Sun; Liang Yue; et al. (Genom. Proteom. Bioinform., 2020)

On the feasibility of deep learning applications using raw mass spectrometry data. - Joris Cadow; Matteo Manica; Roland Mathis; Tiannan Guo; Ruedi Aebersold; María Rodríguez Martínez (Bioinform., 2021)

ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets. - Tiansheng Zhu; Hao Chen; Xishan Yan; Zhicheng Wu; Xiaoxu Zhou; Qi Xiao; Weigang Ge; Qiushi Zhang; Chao Xu; Luang Xu; Guan Ruan; Zhangzhi Xue; et al. (Bioinform., 2021)

DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins. - Zhangzhi Xue; Tiansheng Zhu; Fangfei Zhang; Cheng Zhang; Nan Xiang; Liujia Qian; Xiao Yi; Yaoting Sun; Wei Liu; Xue Cai; Linyan Wang; Xizhe Dai; et al. (Patterns, 2023)

BioKGBench: A Knowledge Graph Checking Benchmark of AI Agent for Biomedical Science. - Xinna Lin; Siqi Ma; Junjie Shan; Xiaojing Zhang; Shell Xu Hu; Tiannan Guo; Stan Z. Li; Kaicheng Yu (CoRR, 2024)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)

Airalogy: AI-empowered universal data digitization for research automation. - Zijie Yang; Qiji Zhou; Fang Guo; Sijie Zhang; Yexun Xi; Jinglei Nie; Yudian Zhu; Liping Huang; Chou Wu; Yonghe Xia; Xiaoyu Ma; Yingming Pu; et al. (CoRR, 2025)