William E. Fondrie

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Carafe2 enables high quality <i>in silico</i> spectral library generation for timsTOF data-independent acquisition proteomics

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-31 · 2 citations

• <b>A living proteomics benchmark for comprehensive </b><b>evaluation of deep learning-based </b><b><i>de novo</i></b><b> peptide </b><b>sequencing tools</b>

  Figshare · 2026-03-12

• <b>A living proteomics benchmark for comprehensive </b><b>evaluation of deep learning-based </b><b><i>de novo</i></b><b> peptide </b><b>sequencing tools</b>

  Figshare · 2026-03-12

• Improvements to Casanovo, a Deep Learning <i>De Novo</i> Peptide Sequencer

  Journal of Proteome Research · 2025-12-30 · 1 citations

• Improvements to Casanovo, a deep learning <i>de novo</i> peptide sequencerPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-26 · 2 citations

• Foundation model for mass spectrometry proteomicsPreprint

  ArXiv.org · 2025-05-16 · 2 citations

• Open-Source and FAIR Research Software for Proteomics

  Journal of Proteome Research · 2025-04-23 · 15 citations

• Open-source and FAIR Research Software for ProteomicsPreprint

  ChemRxiv · 2024-12-09 · 1 citations

• Deep Learning Methods for <i>De Novo</i> Peptide Sequencing

  Mass Spectrometry Reviews · 2024-11-29 · 25 citations

• Deep learning methods for de novo peptide sequencingPreprint

  ChemRxiv · 2024-10-07

• Accounting for Digestion Enzyme Bias in Casanovo

  Journal of Proteome Research · 2024-08-30 · 8 citations

• Sequence-to-sequence translation from mass spectra to peptides with a transformer model

  Nature Communications · 2024-07-30 · 95 citations