Using association signal annotations to boost similarity network fusion. - Peifeng Ruan; Ya Wang; Ronglai Shen; Shuang Wang (Bioinform., 2019)

mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs. - Peifeng Ruan; Shuang Wang; Hua Liang (Bioinform., 2020)

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. - Peifeng Ruan; Shuang Wang (Briefings Bioinform., 2021)

MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale. - Ran Xu 002; Yuchen Zhuang; Yishan Zhong; Yue Yu 001; Xiangru Tang; Hang Wu; May D. Wang; Peifeng Ruan; Donghan Yang; Tao Wang 006; Guanghua Xiao; Carl Yang 001; et al. (CoRR, 2025)