Konstantinos Kalogeropoulos

9 papers in the catalog · Netherlands, Denmark

Konstantinos Kalogeropoulos: 9 papers in the catalog · Netherlands, Denmark · Delft University of Technology, Kavli Institute of Nanoscience · Works on InstaNexus, InstaNovo, InstaNovo+

Affiliations

Delft University of Technology · Department of Bionanoscience
Kavli Institute of Nanoscience
Technical University of Denmark · Center for Translational Protein Design
Technical University of Denmark · Department of Biotechnology and Biomedicine

Elsewhere

ORCID 0000-0003-3907-9281

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)
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 (3)

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

Methods and tools

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.

Jeroen Van Goey 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

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