Fast Algorithms for Extended Regular Expression Matching and Searching. - Lucian Ilie; Baozhen Shan; Sheng Yu 001 (STACS, 2003)

Stochastic Context-Free Graph Grammars for Glycoprotein Modelling. - Baozhen Shan (CIAA, 2004)

Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry. - Baozhen Shan; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (APBC, 2007)

Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry. - Baozhen Shan; Bin Ma 002; Kaizhong Zhang; Gilles A. Lajoie (J. Bioinform. Comput. Biol., 2008)

Better score function for peptide identification with ETD MS/MS spectra. - Xiaowen Liu; Baozhen Shan; Lei Xin; Bin Ma 002 (BMC Bioinform., 2010)

DISC: DISulfide linkage Characterization from tandem mass spectra. - Yi Liu 039; Weiping Sun; Baozhen Shan; Kaizhong Zhang (Bioinform., 2017)

Protein identification with deep learning: from abc to xyz. - Ngoc Hieu Tran; Zachariah Levine; Lei Xin; Baozhen Shan; Ming Li (CoRR, 2017)

De novo peptide sequencing by deep learning. - Ngoc Hieu Tran; Xianglilan Zhang; Lei Xin; Baozhen Shan; Ming Li (Proc. Natl. Acad. Sci. USA, 2017)

DeepIso: A Deep Learning Model for Peptide Feature Detection. - Fatema Tuz Zohora; Ngoc Hieu Tran; Xianglilan Zhang; Lei Xin; Baozhen Shan; Ming Li (CoRR, 2018)

DeepNovoV2: Better de novo peptide sequencing with deep learning. - Rui Qiao 001; Ngoc Hieu Tran; Ming Li 001; Lei Xin; Baozhen Shan; Ali Ghodsi 001 (CoRR, 2019)

PointIso: Point Cloud Based Deep Learning Model for Detecting Arbitrary-Precision Peptide Features in LC-MS Map through Attention Based Segmentation. - Fatema Tuz Zohora; M. Ziaur Rahman; Ngoc Hieu Tran; Lei Xin; Baozhen Shan; Ming Li (CoRR, 2020)

Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines. - Ngoc Hieu Tran; Rui Qiao 001; Lei Xin; Xin Chen; Baozhen Shan; Ming Li 001 (Nat. Mach. Intell., 2020)

Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices. - Rui Qiao 001; Ngoc Hieu Tran; Lei Xin; Xin Chen; Ming Li 001; Baozhen Shan; Ali Ghodsi 001 (Nat. Mach. Intell., 2021)

ChimST: An Efficient Spectral Library Search Tool for Peptide Identification from Chimeric Spectra in Data-Dependent Acquisition. - Wenju Zhang; Zhewei Liang; Xin Chen; Lei Xin; Baozhen Shan; Zhigang Luo; Ming Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

De novo sequencing of multiple SILAC-based tandem mass spectra. - Fang Han; Baozhen Shan; Kaizhong Zhang (ICCI*CC, 2022)