Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. - Xinning Jiang; Xiaogang Jiang; Guanghui Han; Mingliang Ye; Hanfa Zou (BMC Bioinform., 2007)

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. - Jian Ren 002; Zexian Liu; Xinjiao Gao; Changjiang Jin; Mingliang Ye; Hanfa Zou; Longping Wen; Zhaolei Zhang; Yu Xue 001; Xuebiao Yao (Nucleic Acids Res., 2010)

MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides. - Jiawei Mao; He Zhu; Luyao Liu; Zheng Fang; Mingming Dong; Hongqiang Qin; Mingliang Ye (Bioinform., 2022)

GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis. - Zheng Fang; Mingming Dong; Hongqiang Qin; Mingliang Ye (Genom. Proteom. Bioinform., 2024)