Melih Yilmaz
13 papers in the catalog · USA
Melih Yilmaz: 13 papers in the catalog · USA · University of Washington, University of Washington · Works on Ab-seq benchmark (MS antibody sequencing), Casanovo, Casanovo Foundation
Affiliations
- University of Washington
- University of Washington · Paul G. Allen School of Computer Science and Engineering
Elsewhere
Papers
- 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)
- 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)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv)
- 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)
- 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
Ab-seq benchmark (MS antibody sequencing), Casanovo, Casanovo Foundation, Casanovo-DB, Deep Learning Methods for De Novo Peptide Sequencing, Living proteomics benchmark