Jeroen Van Goey

10 papers in the catalog · UK

Jeroen Van Goey: 10 papers in the catalog · UK · InstaDeep Ltd · Works on Awesome De Novo Peptide Sequencing catalog, InstaNexus, InstaNovo

Affiliations

InstaDeep Ltd

Elsewhere

ORCID 0000-0003-4480-5567 · OpenAlex

Papers

Learning from tandem mass spectra at scale with a self-supervised foundation model for proteomics (2026, bioRxiv)
InstaNovo-P: a de novo peptide sequencing model for phosphoproteomics (2026, Nature Communications)
Awesome De Novo Peptide Sequencing (2026, Zenodo)
A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
Generalizable Direct Protein Sequencing With InstaNexus (2026, Molecular & Cellular Proteomics)
De novo peptide sequencing rescoring and FDR estimation with Winnow (2025, arXiv)
Generalizable direct protein sequencing with InstaNexus (2025, bioRxiv)
InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics (2025, bioRxiv)
InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025, Nature Machine Intelligence)
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023, bioRxiv)

Theses supervised (5)

INSearch: AI-native framework for large scale proteomic database search via contrastive joint embeddings and transformer-based scoring function (2026), by Tasneem Midhat Mustafa Attaallah
Sparse Autoencoders for Interpretability of InstaNovo (2026), by Mohammed Esameldin Adam Nagi
Diffusion-based Foundation Model For Mass Spectrometry Via Self-Supervised Learning on Unlabelled Data (2026), by Vicent Mwanda
Advancing De Novo Glycopeptide Sequencing with InstaNovo in Glycoproteomics (2025), by Isaac H.J. Houngue
Enhancing Peptide Mass Spectra Encoder through Pretraining using Contrastive Predictive Coding (2024), by Abel Legese Shibiru

Methods and tools

Awesome De Novo Peptide Sequencing catalog, InstaNexus, InstaNovo, InstaNovo+, InstaNovo-FM, InstaNovo-P, Living proteomics benchmark, Winnow

Co-authors (92)

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.

Konstantinos Kalogeropoulos strength 0.61, 9 shared
Timothy P. Jenkins strength 0.61, 9 shared
Erwin M. Schoof strength 0.50, 7 shared
Kevin Eloff strength 0.43, 6 shared
Nicolas Lopez Carranza strength 0.43, 6 shared
Rachel Catzel strength 0.37, 5 shared
Amandla Mabona strength 0.34, 5 shared
Jemma Daniel strength 0.27, 3 shared
Andreas Hougaard Laustsen strength 0.27, 4 shared
Anne Ljungars strength 0.27, 4 shared
Alberto Santos strength 0.25, 3 shared
Marco Reverenna strength 0.25, 3 shared
Darian Stephan Wolff strength 0.15, 2 shared
Elpida Lytra strength 0.15, 2 shared
Maike Wennekers Nielsen strength 0.15, 2 shared
Marie V. Lukassen strength 0.15, 2 shared
Pasquale D. Colaianni strength 0.15, 2 shared
Jakob Berg Jespersen strength 0.12, 2 shared
Karim Beguir strength 0.12, 2 shared
Marcin J. Skwark strength 0.12, 2 shared
Oliver Morell strength 0.12, 2 shared
Sam P. B. van Beljouw strength 0.12, 2 shared
Stan J. J. Brouns strength 0.12, 2 shared
Ulrich auf dem Keller strength 0.12, 2 shared
Wesley Williams strength 0.12, 2 shared
Annekatrine Kirketerp-Møller strength 0.11, 2 shared
Chiara Francavilla strength 0.11, 2 shared
Henrik Servais Janssen Knudsen strength 0.11, 1 shared
Ida Sofie Goldschmidt strength 0.11, 2 shared
Jennifer Ferguson strength 0.11, 2 shared
Jesper Lauridsen strength 0.11, 2 shared
Lennart Martens strength 0.11, 2 shared
Pathmanaban Ramasamy strength 0.11, 2 shared
Paul Fullwood strength 0.11, 2 shared
Sam van Puyenbroeck strength 0.11, 2 shared
Tine Claeys strength 0.11, 2 shared
Vahap Canbay strength 0.11, 2 shared
Divanisha Patel strength 0.09, 1 shared
Isaac H.J. Houngue strength 0.09, 1 shared
Mechiel Nieuwoudt strength 0.09, 1 shared

Seen in the charts

Back to the full map