Wout Bittremieux

13 papers in the catalog · Belgium, USA, Bloomington, La Jolla

Wout Bittremieux: 13 papers in the catalog · Belgium, USA, Bloomington, La Jolla · Biomedical Informatics Research Center Antwerp, Indiana University · Works on 2018 YPIC unknown protein characterization, AI proteomics perspective, Casanovo

Affiliations

Biomedical Informatics Research Center Antwerp
Indiana University · Computer Science
University of Antwerp · Adrem Data Lab
University of Antwerp · Department of Computer Science
University of California San Diego · Skaggs School of Pharmacy and Pharmaceutical Sciences
University of Washington

Elsewhere

ORCID 0000-0002-3105-1359 · OpenAlex

Papers

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)
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)
2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample (2019, Journal of Proteome Research)

Methods and tools

2018 YPIC unknown protein characterization, AI proteomics perspective, Casanovo, Casanovo Foundation, CasanovoGUI, Deep Learning Methods for De Novo Peptide Sequencing, Living proteomics benchmark

Co-authors (121)

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.

William Stafford Noble strength 1.59, 11 shared
Melih Yilmaz strength 1.39, 10 shared
William E. Fondrie 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
Andy Lin strength 0.50, 1 shared
Lindsay Pino strength 0.50, 1 shared
Bo Wen strength 0.47, 4 shared
Michael J. MacCoss strength 0.35, 3 shared
Michael Riffle strength 0.35, 3 shared
Rowan Nelson strength 0.29, 2 shared
Marina Pominova strength 0.22, 3 shared
Kai Li strength 0.20, 1 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
Jacob H. Russell strength 0.14, 1 shared
Nicholas M. Riley strength 0.14, 1 shared
Cheng Chang strength 0.04, 2 shared
Haixu Tang strength 0.04, 2 shared
Ming Li strength 0.04, 2 shared
Siqi Sun strength 0.04, 2 shared
Tiannan Guo strength 0.04, 2 shared
Yingying Sun strength 0.04, 2 shared
Yu Wang strength 0.04, 2 shared
Zhongzhi Luan strength 0.04, 2 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 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

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