University of California San Diego
San Diego, USA, La Jolla, USA · 21 authors
University of California San Diego (San Diego, USA, La Jolla, USA): 21 authors and 30 papers in the de novo peptide sequencing catalog.
Departments
- Bioinformatics Program
- California Institute for Telecommunications and Information Technology
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering
- Center for Microbiome Innovation
- Department of Computer Science and Engineering
- Department of Electrical and Computer Engineering and Department of Computer Science and Engineering
- Department of Pharmacology
- Integrated Space Stem Cell Orbital Research (ISSCOR) Center
- Skaggs School of Pharmacy and Pharmaceutical Sciences
Papers (30)
- AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo (2026, bioRxiv)
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
- Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer (2025, Journal of Proteome Research)
- SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data (2025, Journal of Proteomics)
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025, bioRxiv)
- Foundation model for mass spectrometry proteomics (2025, arXiv)
- Deep Learning Methods for De Novo Peptide Sequencing (2024, Mass Spectrometry Reviews)
- Accounting for Digestion Enzyme Bias in Casanovo (2024, Journal of Proteome Research)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024, Nature Communications)
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023, Nature Communications)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023, bioRxiv)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, ICML 2022)
- PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing (2022, Research Square)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, bioRxiv)
- De novo sequencing of proteins by mass spectrometry (2020, Expert Review of Proteomics)
- De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments (2020, Cell Systems)
- De Novo MS/MS Sequencing of Native Human Antibodies (2017, Journal of Proteome Research)
- UniNovo: a universal tool for de novo peptide sequencing (2013, Bioinformatics)
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013, Journal of Proteome Research)
- Shotgun Protein Sequencing with Meta-contig Assembly (2012, Molecular & Cellular Proteomics)
- 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)
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007, Journal of Proteome Research)
- Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches (2006, Journal of Proteome Research)
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005, Analytical Chemistry)
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry)
- De novo peptide sequencing via tandem mass spectrometry (1999, Journal of Computational Biology)
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997, Rapid Communications in Mass Spectrometry)