University of Western Ontario

London, Canada · 16 authors

University of Western Ontario (London, Canada): 16 authors and 75 papers in the de novo peptide sequencing catalog.

Departments

Department of Biochemistry
Department of Computer Science

Authors (16)

Julius John, Yi Liu, Amanda Doherty-Kirby, Christopher Hughes, Gilles Lajoie, Bin Ma, Bingran Shen, Changjiang Xu, Fang Han, Kaizhong Zhang, Ming Li, Shichao Wang, Xinlue Shen, Yan Yan, Yizhou Li, Yonghua Han

Papers (75)

High-accuracy glycan de novo prediction for N- and O-linked glycopeptides across multiple fragmentation techniques (2026, Nature Communications)
Spectra Fragment-Ion and Amino Acid Probability Prediction for Peptide Sequencing (2026)
AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
Tandem Mass Spectra Representation Design for Transformer-Based De Novo Peptide Sequencing (2026)
Zero-shot de novo peptide sequencing with open posttranslational modification discovery (2026, Nature Biotechnology)
Mass spectrometry-based de novo sequencing reveals non-canonical neoantigens with antitumor efficacy in hepatocellular carcinoma (2026, JHEP Reports)
A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle–Down, and De Novo Bottom–Up Mass Spectrometry (2025, Molecular & Cellular Proteomics)
Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child (2025, Proceedings of the National Academy of Sciences)
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases (2025, Nature Communications)
Zero-Shot De Novo Peptide Sequencing with Open Post-Translational Modification Discovery (2025, Research Square)
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra (2025, Journal of Bioinformatics and Computational Biology)
Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing (2024, arXiv)
1086 Sequencing antibodies from de novo to identify functional and neutralizing antibodies in human plasma after SARS-CoV-2 vaccination (2024, Regular and Young Investigator Award Abstracts)
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024, Molecular & Cellular Proteomics)
Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD) (2024, Analytical Chemistry)
De novo protein sequencing of antibodies for identification of neutralizing antibodies in human plasma post SARS-CoV-2 vaccination (2024, Nature Communications)
Ultra-sensitivity metaproteomics redefines the gut “dark metaproteome”, uncovering host-microbiome interactions and drug targets in intestinal inflammatory diseases (2024, bioRxiv)
NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing (2024, bioRxiv)
de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination (2024, bioRxiv)
A complete mass spectrometry-based immunopeptidomics pipeline for neoantigen identification and validation (2023, Research Square)
Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023, Nature Machine Intelligence)
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics (2023, Nature Communications)
DpNovo: A DEEP LEARNING MODEL COMBINED WITH DYNAMIC PROGRAMMING FOR DE NOVO PEPTIDE SEQUENCING (2023)
PaSER Novor: Real-time de novo sequencing for 4D-Proteomics applications (2023)
De novo sequencing of multiple tandem mass spectra of peptide containing SILAC labeling (2023)
De novo sequencing of multiple SILAC-based tandem mass spectra (2022, 2022 IEEE 21st International Conference on Cognitive Informatics & Cognitive Computing (ICCI*CC))
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning (2022, bioRxiv)
A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics (2022, Nature Communications)
A Personalized Mass Spectrometry–Based Assay to Monitor M-Protein in Patients with Multiple Myeloma (EasyM) (2021, Clinical Cancer Research)
Mass Spectrometry Provides a Highly Sensitive Noninvasive Means of Sequencing and Tracking M-Protein in the Blood of Multiple Myeloma Patients (2021, Journal of Proteome Research)
Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021, Nature Machine Intelligence)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2020, Nature Machine Intelligence)
Discrimination of Leucine and Isoleucine in De Novo peptide sequencing using deep neural networks (2020)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2019, bioRxiv)
DeepNovoV2: Better de novo peptide sequencing with deep learning (2019, arXiv)
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing (2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018, Nature Methods)
Protein identification with deep learning: from abc to xyz (2017, arXiv)
De novo peptide sequencing by deep learning (2017, Proceedings of the National Academy of Sciences)
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra (2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra (2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs (2016, BMC Bioinformatics)
De novo Peptide Sequencing (2016, Proteome Informatics)
De novo peptide sequencing using CID and HCD spectra pairs (2016, Proteomics)
Complete De Novo Assembly of Monoclonal Antibody Sequences (2016, Scientific Reports)
De Novo Sequencing Assisted Approach for Characterizing Mixture MS/MS Spectra (2016, IEEE Transactions on NanoBioscience)
Recent Developments in Computational Methods for De Novo Peptide Sequencing from Tandem Mass Spectrometry (MS/MS) (2015, Protein & Peptide Letters)
Algorithms for Peptide Identification from Mixture Tandem Mass Spectra (2015)
Novor: Real-Time Peptide de Novo Sequencing Software (2015, Journal of the American Society for Mass Spectrometry)
A Framework of De Novo Peptide Sequencing for Multiple Tandem Mass Spectra (2015, IEEE Transactions on NanoBioscience)
An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database (2015, Lecture Notes in Computer Science)
NovoPair: De novo peptide sequencing for tandem mass spectra pair (2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM))
NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra (2014, Lecture Notes in Computer Science)
An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra (2014, Lecture Notes in Computer Science)
NovoHCD: De novo Peptide Sequencing From HCD Spectra (2014, IEEE Transactions on NanoBioscience)
A multi-edge graph based de novo peptide sequencing method for HCD spectra (2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine)
DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE (2013, Journal of Bioinformatics and Computational Biology)
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012, Molecular & Cellular Proteomics)
De Novo Sequencing and Homology Searching (2012, Molecular & Cellular Proteomics)
Integrating de Novo Sequencing and Database Search for Peptide Identification (2012, Europe PMC (PubMed Central))
ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010, Journal of Bioinformatics and Computational Biology)
An Automata Approach to Match Gapped Sequence Tags Against Protein Database (2010, Lecture Notes in Computer Science)
Better score function for peptide identification with ETD MS/MS spectra (2010, BMC Bioinformatics)
De Novo Sequencing Methods in Proteomics (2009, Methods in Molecular Biology)
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009, Bioinformatics)
De Novo Interpretation of Tandem Mass Spectra (2009, Current Protocols in Bioinformatics)
Peptide De Novo Sequencing with MS/MS (2008, Encyclopedia of Algorithms)
Improving de novo sequencing accuracy for Ion Trap data in PEAKS software (2007)
Complexity and scoring function of MS/MS peptide de novo sequencing (2006, Computational Systems Bioinformatics)
AN AUTOMATA APPROACH TO MATCH GAPPED SEQUENCE TAGS AGAINST PROTEIN DATABASE (2005, International Journal of Foundations of Computer Science)
SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005, Journal of Bioinformatics and Computational Biology)
An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005, Journal of Computer and System Sciences)
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003, Rapid Communications in Mass Spectrometry)
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum (2003, Lecture Notes in Computer Science)

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