BS
Baozhen Shan
bioinformaticsProteomicscs.LGq-bio.BMTandem Mass SpectrometryGlycopeptidesDatabases, Proteindeep learningde novo sequencingmass spectrometry
On Valency
published · living versionsW_r57atzen·v1 · currentpublished
NovoCRF: Globally Normalized De Novo Peptide Sequencing on a Prefix-Mass Lattice
with Rui Qiao, Lei Xin
1 version
Preprints & journals
38 papers in the corpus · 2008–2026High-accuracy glycan de novo prediction for N- and O-linked glycopeptides across multiple fragmentation techniques.42864315 · Zhang, Qianqiu, Mao, Zeping, Chen, Yuling et al.2026 · 0 citationsNature communications. 2026;17(1)
Mass spectrometry-based de novo sequencing reveals non-canonical neoantigens with antitumor efficacy in hepatocellular carcinoma.41861674 · Xing, Xiaohua, Liu, Mingxin, Ouyang, Jiahe et al.2026 · 0 citationsJHEP reports : innovation in hepatology. 2026;8(4):101775
Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle-Down, and De Novo Bottom-Up Mass Spectrometry.41093274 · Xin, Lei, Li, Wenting, Zhang, Shuyang et al.2025 · 2 citationsMolecular & cellular proteomics : MCP. 2025;24(11):101088
Proteoform search from protein database with top-down mass spectra.41044386 · Li, Kunyi, Shan, Baozhen, Xin, Lei et al.2025 · 0 citationsNature computational science. 2025;5(11):998-1009
De Novo sequencing-assisted homology search for DIA data analysis enables low abundance peptide variants discovery10.1101/2025.05.30.657054v2 · Qiao, R., Li, H., Bian, H. et al.2025 · 1 citationbioRxiv
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing.40615171 · Tran, Ngoc Hieu, Qiao, Rui, Mao, Zeping et al.2026 · 1 citationMolecular & cellular proteomics : MCP. 2025;24(6):100939
Quantitative Site-Specific Glycoproteomics Reveals Glyco-Signatures for Breast Cancer Diagnosis.39810347 · Yang, Yi, Zhao, Dan, Luo, Ji et al.2025 · 5 citationsAnalytical chemistry. 2025;97(1):114-121
Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing2411.15684v7 · Zheng Ma, Zeping Mao, Ruixue Zhang et al.2024 · 1 citationarXiv
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing.39321875 · Tran, Ngoc Hieu, Qiao, Rui, Mao, Zeping et al.2024 · 14 citationsMolecular & cellular proteomics : MCP. 2024;23(11):100849
Quantitative site-specific glycoproteomics by ZenoTOF reveals glyco-signatures for breast cancer diagnosis10.1101/2024.09.08.611557v1 · Yang, Y., Zhao, D., Luo, J. et al.2024 · 0 citationsbioRxiv
Pursuing Impactful Quantitative Proteomics Using QC-Channels in Every Spectrum and Trend-Design in Experiment.38416724 · Lai, Xianyin, Qi, Guihong, Kovach, Chris et al.2024 · 1 citationJournal of the American Society for Mass Spectrometry. 2024;35(4):674-682
Author Correction: Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics.38267455 · Sun, Weiping, Zhang, Qianqiu, Zhang, Xiyue et al.2024 · 0 citationsNature communications. 2024;15(1):701
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics.37422459 · Sun, Weiping, Zhang, Qianqiu, Zhang, Xiyue et al.2023 · 58 citationsNature communications. 2023;14(1):4046
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.37435391 · Kirkpatrick, Joanna, Stemmer, Paul M, Searle, Brian C et al.2023 · 2 citationsJournal of biomolecular techniques : JBT. 2023;34(2)
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning10.1101/2022.07.05.497667v3 · Tran, N. H., Peng, C., Lei, Q. et al.2022 · 3 citationsbioRxiv
A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics.35672356 · Xin, Lei, Qiao, Rui, Chen, Xin et al.2023 · 101 citationsNature communications. 2022;13(1):3108
Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.34521906 · Zohora, Fatema Tuz, Rahman, M Ziaur, Tran, Ngoc Hieu et al.2021 · 11 citationsScientific reports. 2021;11(1):18249
ChimST: An Efficient Spectral Library Search Tool for Peptide Identification from Chimeric Spectra in Data-Dependent Acquisition.31603795 · Zhang, Wenju, Liang, Zhewei, Chen, Xin et al.2022 · 3 citationsIEEE/ACM transactions on computational biology and bioinformatics. 2021;18(4):1416-1425
A Facile Immunopeptidomics Workflow for Capturing the HLA-I Ligandome with PEAKS XPro10.1101/2021.05.20.444976v1 · Hoffman, K. S., Shan, B., Krieger, J. R.2021 · 2 citationsbioRxiv
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study10.1101/2020.11.20.391300v1 · Neely, B. A., Stemmer, P., Searle, B. C. et al.2020 · 2 citationsbioRxiv
PointIso: Point Cloud Based Deep Learning Model for Detecting Arbitrary-Precision Peptide Features in LC-MS Map through Attention Based Segmentation2009.07250v1 · Fatema Tuz Zohora, M Ziaur Rahman, Ngoc Hieu Tran et al.2020 · 0 citationsarXiv
Personalized workflow to identify optimal T-cell epitopes for peptide-based vaccines against COVID-192003.10650v1 · Rui Qiao, Ngoc Hieu Tran, Baozhen Shan et al.2020 · 9 citationsarXiv
DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map.31748623 · Zohora, Fatema Tuz, Rahman, M Ziaur, Tran, Ngoc Hieu et al.2020 · 78 citationsScientific reports. 2019;9(1):17168
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines10.1101/620468v3 · Tran, N. H., Qiao, R., Xin, L. et al.2019 · 44 citationsbioRxiv
DeepNovoV2: Better de novo peptide sequencing with deep learning1904.08514v2 · Rui Qiao, Ngoc Hieu Tran, Lei Xin et al.2019 · 14 citationsarXiv
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry.30573815 · Tran, Ngoc Hieu, Qiao, Rui, Xin, Lei et al.2019 · 375 citationsNature methods. 2019;16(1):63-66
DeepIso: A Deep Learning Model for Peptide Feature Detection1801.01539v1 · Fatema Tuz Zohora, Ngoc Hieu Tran, Xianglilan Zhang et al.2017 · 2 citationsarXiv
DISC: DISulfide linkage Characterization from tandem mass spectra.29069330 · Liu, Yi, Sun, Weiping, Shan, Baozhen et al.2018 · 5 citationsBioinformatics (Oxford, England). 2017;33(23):3861-3870
Protein identification with deep learning: from abc to xyz1710.02765v1 · Ngoc Hieu Tran, Zachariah Levine, Lei Xin et al.2017 · 3 citationsarXiv
De novo peptide sequencing by deep learning.28720701 · Tran, Ngoc Hieu, Zhang, Xianglilan, Xin, Lei et al.2019 · 448 citationsProceedings of the National Academy of Sciences of the United States of America. 2017;114(31):8247-8252
Complete De Novo Assembly of Monoclonal Antibody Sequences.27562653 · Tran, Ngoc Hieu, Rahman, M Ziaur, He, Lin et al.2018 · 158 citationsScientific reports. 2016;6:31730
GlycoMaster DB: software to assist the automated identification of N-linked glycopeptides by tandem mass spectrometry.25113421 · He, Lin, Xin, Lei, Shan, Baozhen et al.2015 · 84 citationsJournal of proteome research. 2014;13(9):3881-95
Through the eye of an electrospray needle: mass spectrometric identification of the major peptides and proteins in the milk of the one-humped camel (Camelus dromedarius).23832934 · Alhaider, Abdulqader, Abdelgader, Abdel Galil, Turjoman, Abdullah Arif et al.2014 · 28 citationsJournal of mass spectrometry : JMS. 2013;48(7):779-94
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.23376229 · Perez-Riverol, Yasset, Hermjakob, Henning, Kohlbacher, Oliver et al.2014 · 19 citationsJournal of proteomics. 2013;87:134-8
PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.22186715 · Zhang, Jing, Xin, Lei, Shan, Baozhen et al.2012 · 1,084 citationsMolecular & cellular proteomics : MCP. 2012;11(4):M111.010587
PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications.21609001 · Han, Xi, He, Lin, Xin, Lei et al.2011 · 178 citationsJournal of proteome research. 2011;10(7):2930-6
Better score function for peptide identification with ETD MS/MS spectra.20122213 · Liu, Xiaowen, Shan, Baozhen, Xin, Lei et al.2010 · 48 citationsBMC bioinformatics. 2010;11 Suppl 1:S4
Complexities and algorithms for glycan sequencing using tandem mass spectrometry.18324747 · Shan, Baozhen, Ma, Bin, Zhang, Kaizhong et al.2008 · 28 citationsJournal of bioinformatics and computational biology. 2008;6(1):77-91
Career total: 60 works. 38 are in this corpus.
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