Wouter Boomsma

University of Copenhagen — Denmark

Biochemistry, Genetics and Molecular Biology · Life Sciences

31h-index3.6kcitations98works3.12yr avg
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Research Topics

Protein Structure and Dynamics(49), Enzyme Structure and Function(21), RNA and protein synthesis mechanisms(13), Machine Learning in Bioinformatics(13), Genomics and Phylogenetic Studies(12)

Publications98 total

The Importance of UBQLN2 Ubiquitylation for Its Turnover and Localization
Biochemistry·2025
UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions
arXiv (Cornell University)·2025Open Access
The importance of UBQLN2 ubiquitylation for its turnover and localization
2025· 1 citedOpen Access
Supervised Learning of Protein Melting Temperature: Cross‐Species vs. Species‐Specific Prediction
Proteins Structure Function and Bioinformatics·2025Open Access
Author response for "Supervised Learning of Protein Melting Temperature: Cross-Species vs. Species-Specific Prediction"
2025
Gene finding revisited: improved robustness through structured decoding from learned embeddings
arXiv (Cornell University)·2025Open Access
Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function
Nature Methods·2025· 16 citedOpen Access
Foundation models of protein sequences: A brief overview
Current Opinion in Structural Biology·2025· 3 citedOpen Access
SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions
Nature Communications·2024· 15 citedOpen Access
Supervised learning of protein melting temperatures: cross-species vs species-specific prediction
2024Open Access
Probabilistic Multiple Sequence Alignment using Spatial Transformations
2024· 1 citedOpen Access
Kermut: Composite kernel regression for protein variant effects
2024· 3 citedOpen Access
A systematic analysis of regression models for protein engineering
PLoS Computational Biology·2024· 10 citedOpen Access
A Continuous Relaxation for Discrete Bayesian Optimization
arXiv (Cornell University)·2024· 2 citedOpen Access
Kermut: Composite kernel regression for protein variant effects
arXiv (Cornell University)·2024Open Access
Deep learning assisted single particle tracking for automated correlation between diffusion and function
2024· 3 citedOpen Access
Kermut: Composite kernel regression for protein variant effects
2024
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences
2024· 1 citedOpen Access
A joint embedding of protein sequence and structure enables robust variant effect predictions
2023Open Access
BEND: Benchmarking DNA Language Models on biologically meaningful tasks
arXiv (Cornell University)·2023· 27 citedOpen Access
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Frequent Co-authors

Kresten Lindorff‐Larsen(17), Thomas Hamelryck(15), Jesper Ferkinghoff‐Borg(11), Jes Frellsen(9), Pengfei Tian(7), Sandro Bottaro(7), Simon Olsson(6), Kristoffer E. Johansson(5), Birthe B. Kragelund(5), Mikael Borg(5), Tim Harder(5), Christian Andreetta(4), Eske Willerslev(3), Rasmus Nielsen(3), Kanti V. Mardia(3), Lasse M. Blaabjerg(3), Maher M. Kassem(3), Nicolas Jonsson(3), Matteo Cagiada(3), Amelie Stein(3)