Bin Ma
36 papers in the catalog · Canada
Bin Ma: 36 papers in the catalog · Canada · Rapid Novor Inc., University of Waterloo · Works on ADEPTS, Anti-PfEMP1 plasma antibody MS sequencing, Champs
Affiliations
- Rapid Novor Inc.
- University of Waterloo · David R. Cheriton School of Computer Science
- University of Waterloo · School of Computer Science
- University of Western Ontario · Department of Computer Science
- Western University
Elsewhere
Papers
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
- 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)
- 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)
- 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)
- de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination (2024, bioRxiv)
- PaSER Novor: Real-time de novo sequencing for 4D-Proteomics applications (2023)
- 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)
- Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing (2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
- An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra (2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
- De novo Peptide Sequencing (2016, Proteome Informatics)
- De Novo Sequencing Assisted Approach for Characterizing Mixture MS/MS Spectra (2016, IEEE Transactions on NanoBioscience)
- Novor: Real-Time Peptide de Novo Sequencing Software (2015, Journal of the American Society for Mass Spectrometry)
- An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database (2015, Lecture Notes in Computer Science)
- An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra (2014, Lecture Notes in Computer Science)
- 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)
Methods and tools
ADEPTS, Anti-PfEMP1 plasma antibody MS sequencing, Champs, De novo assisted mixture spectrum characterization, De novo interpretation protocol (Current Protocols), De novo peptide sequencing (Proteome Informatics chapter), De novo sequencing and homology searching, De novo sequencing methods in proteomics (review), De novo sequencing of mixture spectra (Liu thesis), DeNovoPTM, EasyM M-protein monitoring, Gapped sequence tag automata matching, Living proteomics benchmark, M-protein de novo sequencing and tracking, Novor, PEAKS, PEAKS DB, PaSER Novor, Peptide de novo sequencing with MS/MS (Encyclopedia of Algorithms), Polyclonal IgG neutralizing antibody discovery, R-met C-terminal labeling de novo sequencing, SPIDER, uMetaP / novoMP