Timothy P. Jenkins

12 papers in the catalog · Denmark

Timothy P. Jenkins: 12 papers in the catalog · Denmark · Technical University of Denmark, Technical University of Denmark · Works on AI-model database search framework, Ab-seq benchmark (MS antibody sequencing), InstaNexus

Affiliations

Technical University of Denmark
Technical University of Denmark · Center for Translational Protein Design
Technical University of Denmark · Department of Biotechnology and Biomedicine

Elsewhere

ORCID 0000-0003-2979-5663 · 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)
A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics (2026, Journal of Proteome Research)
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)
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025, Cell Systems)
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)
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv)
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023, bioRxiv)

Methods and tools

AI-model database search framework, Ab-seq benchmark (MS antibody sequencing), InstaNexus, InstaNovo, InstaNovo+, InstaNovo-FM, InstaNovo-P, Living proteomics benchmark, Winnow

Co-authors (107)

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 1.05, 12 shared
Jeroen Van Goey strength 0.94, 10 shared
Kevin Eloff strength 0.76, 7 shared
Erwin M. Schoof strength 0.50, 7 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
Melih Yilmaz strength 0.13, 3 shared
William Stafford Noble strength 0.13, 3 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
Anand Patel strength 0.11, 2 shared
Annekatrine Kirketerp-Møller strength 0.11, 2 shared
Chiara Francavilla strength 0.11, 2 shared
Geir Kjetil Sandve strength 0.11, 2 shared
Henrik Servais Janssen Knudsen strength 0.11, 1 shared
Ida Sofie Goldschmidt strength 0.11, 2 shared
Igor Snapkow strength 0.11, 2 shared
Jan Terje Andersen strength 0.11, 2 shared
Jennifer Ferguson strength 0.11, 2 shared
Jesper Lauridsen strength 0.11, 2 shared
Khang Lê Quý strength 0.11, 2 shared
Lennart Martens strength 0.11, 2 shared
Maria Chernigovskaya strength 0.11, 2 shared

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