William E. Fondrie

10 papers in the catalog · USA

William E. Fondrie: 10 papers in the catalog · USA · Talus Bioscience · Works on Casanovo, Casanovo Foundation, Deep Learning Methods for De Novo Peptide Sequencing

Affiliations

Talus Bioscience

Elsewhere

ORCID 0000-0002-1554-3716 · OpenAlex

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)
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)
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

Casanovo, Casanovo Foundation, Deep Learning Methods for De Novo Peptide Sequencing, Living proteomics benchmark

Co-authors (65)

Ranked by Newman fractional collaboration strength, so a pair on a two-author paper counts for more than a pair on a 50-author consortium paper.

Melih Yilmaz strength 1.39, 10 shared
William Stafford Noble strength 1.39, 10 shared
Wout Bittremieux strength 1.39, 10 shared
Sewoong Oh strength 1.24, 8 shared
Justin Sanders strength 0.58, 5 shared
Carlo F. Melendez strength 0.58, 4 shared
Varun Ananth strength 0.56, 5 shared
Rowan Nelson strength 0.29, 2 shared
Bo Wen strength 0.27, 3 shared
Marina Pominova strength 0.22, 3 shared
Daniela Klaproth-Andrade strength 0.17, 3 shared
Chris Hsu strength 0.15, 2 shared
Gwenneth Straub strength 0.15, 2 shared
Lingwen Xu strength 0.15, 2 shared
Michael J. MacCoss strength 0.15, 2 shared
Michael Riffle strength 0.15, 2 shared
Jacob H. Russell strength 0.14, 1 shared
Nicholas M. Riley strength 0.14, 1 shared
Alfred Nilsson strength 0.02, 1 shared
Baozhen Shan strength 0.02, 1 shared
Benjamin A. Neely strength 0.02, 1 shared
Bin Ma strength 0.02, 1 shared
Ceder Dens strength 0.02, 1 shared
Charlotte Adams strength 0.02, 1 shared
Cheng Chang strength 0.02, 1 shared
Cheng Ge strength 0.02, 1 shared
Chenyu Yao strength 0.02, 1 shared
Christian Nix strength 0.02, 1 shared
Di Zhang strength 0.02, 1 shared
Ekapol Chuangsuwanich strength 0.02, 1 shared
Guillaume Deflandre strength 0.02, 1 shared
Haipeng Wang strength 0.02, 1 shared
Haixu Tang strength 0.02, 1 shared
Jeroen Van Goey strength 0.02, 1 shared
Jingbo Zhou strength 0.02, 1 shared
Joel Lapin strength 0.02, 1 shared
Julien Gagneur strength 0.02, 1 shared
Jun Xia strength 0.02, 1 shared
Kaiyuan Liu strength 0.02, 1 shared
Konstantinos Kalogeropoulos strength 0.02, 1 shared

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