University of Southern California
Los Angeles, USA, Los Angeles · 9 authors
University of Southern California (Los Angeles, USA, Los Angeles): 9 authors and 43 papers in the de novo peptide sequencing catalog.
Departments
- Department of Biology, Department of Mathematics
- Departments of Mathematics, Computer Science and Molecular Biology
- Keck School of Medicine
- Molecular and Computational Biology Program, Department of Biological Sciences
Papers (43)
- Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2025, ICLR 2025)
- NovoBench: Benchmarking Deep Learning-based De Novo Sequencing Methods in Proteomics (2024, NeurIPS 2024)
- Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2024, bioRxiv)
- NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics (2024, arXiv)
- AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information (2024, arXiv)
- De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments (2020, Cell Systems)
- De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments (2019, bioRxiv)
- Top-down analysis of protein samples by de novo sequencing techniques (2016, Bioinformatics)
- De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015, Journal of Proteome Research)
- De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014, Journal of Proteome Research)
- Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo‐peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms (2014, Rapid Communications in Mass Spectrometry)
- UniNovo: a universal tool for de novo peptide sequencing (2013, Bioinformatics)
- Constrained De Novo Sequencing of Conotoxins (2012, Journal of Proteome Research)
- De novo peptide sequencing and spectral alignment algorithm via tandem mass spectrometry (2012)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Journal of Computational Biology)
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2011, Molecular & Cellular Proteomics)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Lecture Notes in Computer Science)
- Constrained De Novo Sequencing of Peptides with Application to Conotoxins (2011, Lecture Notes in Computer Science)
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2010, Lecture Notes in Computer Science)
- Dereplication and de novo sequencing of nonribosomal peptides (2009, Nature Methods)
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009, Molecular & Cellular Proteomics)
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009, Molecular & Cellular Proteomics)
- Automated de novo protein sequencing of monoclonal antibodies (2008, Nature Biotechnology)
- Multi-spectra peptide sequencing and its applications to multistage mass spectrometry (2008, Bioinformatics)
- A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry (2008, Journal of Proteome Research)
- De Novo Sequencing of Nonribosomal Peptides (2008, Lecture Notes in Computer Science)
- Sequence similarity‐driven proteomics in organisms with unknown genomes by LC‐MS/MS and automated de novo sequencing (2007, PROTEOMICS)
- Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007, Molecular & Cellular Proteomics)
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007, Analytical Chemistry)
- Protein identification by spectral networks analysis (2007, Proceedings of the National Academy of Sciences)
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007, Journal of Proteome Research)
- MODELING AND CHARACTERIZATION OF MULTI-CHARGE MASS SPECTRA FOR PEPTIDE SEQUENCING (2006, Journal of Bioinformatics and Computational Biology)
- Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches (2006, Journal of Proteome Research)
- An Efficient Algorithm for De Novo Peptide Sequencing (2005, Adaptive and Natural Computing Algorithms)
- CHARACTERIZATION OF MULTI-CHARGE MASS SPECTRA FOR PEPTIDE SEQUENCING (2005, Proceedings of the 4th Asia-Pacific Bioinformatics Conference)
- Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry (2005, Journal of Proteome Research)
- InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005, Analytical Chemistry)
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005, Analytical Chemistry)
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry)
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004, Drug Discovery Today: BIOSILICO)
- A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry (2003, Journal of Computational Biology)
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001, Journal of Computational Biology)
- De novo peptide sequencing via tandem mass spectrometry (1999, Journal of Computational Biology)