William Stafford Noble
20 papers in the catalog · USA
William Stafford Noble: 20 papers in the catalog · USA · University of Washington, University of Washington · Works on 9-species multi-species benchmark, Ab-seq benchmark (MS antibody sequencing), Casanovo
Affiliations
- University of Washington
- University of Washington · Department of Genome Sciences
- University of Washington · Paul G. Allen School of Computer Science and Engineering
Elsewhere
Papers
- 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)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025, Cell Systems)
- A procedure for controlling the false discovery rate of de novo peptide sequencing (2025, bioRxiv)
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025, bioRxiv)
- A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2025, Nature Methods)
- Foundation model for mass spectrometry proteomics (2025, arXiv)
- Deep Learning Methods for De Novo Peptide Sequencing (2024, Mass Spectrometry Reviews)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv)
- Wrangling a de novo sequencing benchmark (2024, Springer Nature Communities (Behind the Paper))
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models (2024, Scientific Data)
- Accounting for Digestion Enzyme Bias in Casanovo (2024, Journal of Proteome Research)
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models (2024, ChemRxiv)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024, Nature Communications)
- A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2024, bioRxiv)
- A learned score function improves the power of mass spectrometry database search (2024, bioRxiv)
- 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)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, bioRxiv)
Methods and tools
9-species multi-species benchmark, Ab-seq benchmark (MS antibody sequencing), Casanovo, Casanovo Foundation, Casanovo-DB, CasanovoGUI, Cascadia, De novo FDR control procedure, Deep Learning Methods for De Novo Peptide Sequencing, Living proteomics benchmark, Wrangling a de novo sequencing benchmark