WB
Wouter Boomsma
cs.LGbioinformaticsModels, Molecularq-bio.BMNMRstat.MLModels, StatisticalAlgorithmsIDPMachine Learning
On Valency
published · living versionsW_yaar2ca2·v1 · currentpublished
BEND 2.0: Benchmarking the Capabilities Needed to Design DNA
with Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli, Panagiotis Antoniadis +4
1 version
Preprints & journals
71 papers in the corpus · 2005–2026RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts2610.11761v1 · Frederikke Isa Marin, Panagiotis Antoniadis, Dionysia Danai Brilli et al.2026 · 0 citationsarXiv
APOSM: Pairwise preference learning improves generative small-molecule design10.64898/2026.06.06.730554v1 · Dreisler, M. W., Michael, R., Hatzakis, N. S. et al.2026 · 0 citationsbioRxiv
The Importance of UBQLN2 Ubiquitylation for Its Turnover and Localization.41428212 · Grønbæk-Thygesen, Martin, Kampmeyer, Caroline, Eschger, Paula et al.2026 · 2 citationsBiochemistry. 2026;65(1):52-63
UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions2512.10515v2 · Han Tang, Alexander Tong, Wouter Boomsma2025 · 1 citationarXiv
Supervised Learning of Protein Melting Temperature: Cross-Species vs. Species-Specific Prediction.40653882 · López, Sebastián García, Salomon, Jesper, Boomsma, Wouter2025 · 1 citationProteins. 2025;93(12):2158-2166
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation2506.05596v2 · Jes Frellsen, Maher M. Kassem, Tone Bengtsen et al.2025 · 1 citationarXiv
Gene finding revisited: improved robustness through structured decoding from learned embeddings2505.03377v1 · Frederikke I. Marin, Dennis Pultz, Wouter Boomsma2025 · 0 citationsarXiv
Foundation models of protein sequences: A brief overview.39983412 · Bjerregaard, Andreas, Groth, Peter Mørch, Hauberg, Søren et al.2025 · 16 citationsCurrent opinion in structural biology. 2025;91:103004
SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions.39511177 · Blaabjerg, Lasse M, Jonsson, Nicolas, Boomsma, Wouter et al.2024 · 23 citationsNature communications. 2024;15(1):9646
Probabilistic Multiple Sequence Alignment using Spatial Transformations10.1101/2024.10.12.617969v1 · Garcia Lopez, S., Hauberg, S., Boomsma, W.2024 · 1 citationbioRxiv
Supervised learning of protein melting temperatures: cross-species vs species-specific prediction10.1101/2024.10.12.617972v2 · Garcia Lopez, S., Salomon, J., Boomsma, W.2024 · 0 citationsbioRxiv
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences2406.04739v2 · Miguel Gonz'alez-Duque, Richard Michael, Simon Bartels et al.2024 · 5 citationsarXiv
A systematic analysis of regression models for protein engineering.38701099 · Michael, Richard, Kæstel-Hansen, Jacob, Mørch Groth, Peter et al.2024 · 12 citationsPLoS computational biology. 2024;20(5):e1012061
A Continuous Relaxation for Discrete Bayesian Optimization2404.17452v1 · Richard Michael, Simon Bartels, Miguel Gonz'alez-Duque et al.2024 · 2 citationsarXiv
Kermut: Composite kernel regression for protein variant effects2407.00002v3 · Peter M\orch Groth, Mads Herbert Kerrn, Lars Olsen et al.2024 · 7 citationsarXiv
A joint embedding of protein sequence and structure enables robust variant effect predictions10.1101/2023.12.14.571755v1 · Blaabjerg, L. M., Jonsson, N., Boomsma, W. et al.2023 · 1 citationbioRxiv
BEND: Benchmarking DNA Language Models on biologically meaningful tasks2311.12570v4 · Frederikke Isa Marin, Felix Teufel, Marc Horlacher et al.2023 · 31 citationsarXiv
Deep learning assisted single particle tracking for automated correlation between diffusion and function.38014323 · Kæstel-Hansen, Jacob, de Sautu, Marilina, Saminathan, Anand et al.2025 · 51 citationsbioRxiv : the preprint server for biology. 2023
Implicit Variational Inference for High-Dimensional Posteriors2310.06643v3 · Anshuk Uppal, Kristoffer Stensbo-Smidt, Wouter Boomsma et al.2023 · 2 citationsarXiv
Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro.37463013 · Jacobsen, Nina L, Bloch, Magnus, Millard, Peter S et al.2023 · 2 citationsProtein science : a publication of the Protein Society. 2023;32(9):e4733
FLOP: Tasks for Fitness Landscapes Of Protein wildtypes10.1101/2023.06.21.545880v2 · Groth, P. M., Michael, R., Salomon, J. et al.2023 · 4 citationsbioRxiv
Assessing the performance of protein regression models10.1101/2023.06.18.545472v2 · Michael, R., Kaestel-Hansen, J., Groth, P. M. et al.2023 · 5 citationsbioRxiv
Rapid protein stability prediction using deep learning representations.37184062 · Blaabjerg, Lasse M, Kassem, Maher M, Good, Lydia L et al.2023 · 175 citationseLife. 2023;12
Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components.37160462 · Kampmeyer, Caroline, Grønbæk-Thygesen, Martin, Oelerich, Nicole et al.2023 · 13 citationsCellular and molecular life sciences : CMLS. 2023;80(6):143
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters2302.13711v3 · Marloes Arts, Jes Frellsen, Wouter Boomsma2023 · 2 citationsarXiv
MembraneFold: Visualising transmembrane protein structure and topology10.1101/2022.12.06.518085v1 · Gutierrez, S., Tyczynski, W. G., Boomsma, W. et al.2022 · 21 citationsbioRxiv
A context-dependent and disordered ubiquitin-binding motif.35974206 · Dreier, Jesper E, Prestel, Andreas, Martins, João M et al.2022 · 14 citationsCellular and molecular life sciences : CMLS. 2022;79(9):484
Learning meaningful representations of protein sequences.35395843 · Detlefsen, Nicki Skafte, Hauberg, Søren, Boomsma, Wouter2022 · 168 citationsNature communications. 2022;13(1):1914
Adaptive Cholesky Gaussian Processes2202.10769v3 · Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Munoz et al.2022 · 0 citationsProceedings of The 26th International Conference on Artificial Intelligence and Statistics (2023)
Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion.34321355 · Pinholt, Henrik D, Bohr, Søren S-R, Iversen, Josephine F et al.2021 · 83 citationsProceedings of the National Academy of Sciences of the United States of America. 2021;118(31)
Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition2107.10587v1 · Simon Bartels, Wouter Boomsma, Jes Frellsen et al.2021 · 1 citationarXiv
Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients.33547335 · Jimenez-Solem, Espen, Petersen, Tonny S, Hansen, Casper et al.2021 · 80 citationsScientific reports. 2021;11(1):3246
Orchestration of signaling by structural disorder in class 1 cytokine receptors.32831102 · Seiffert, Pernille, Bugge, Katrine, Nygaard, Mads et al.2021 · 30 citationsCell communication and signaling : CCS. 2020;18(1):132
IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.31642121 · Millard, Peter S, Bugge, Katrine, Marabini, Riccardo et al.2020 · 19 citationsProtein science : a publication of the Protein Society. 2020;29(1):169-183
Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range.31598803 · Hendus-Altenburger, Ruth, Fernandes, Catarina B, Bugge, Katrine et al.2020 · 50 citationsJournal of biomolecular NMR. 2019;73(12):713-725
The PCNA interaction motifs revisited: thinking outside the PIP-box.31134302 · Prestel, Andreas, Wichmann, Nanna, Martins, Joao M et al.2019 · 112 citationsCellular and molecular life sciences : CMLS. 2019;76(24):4923-4943
(q,p)-Wasserstein GANs: Comparing Ground Metrics for Wasserstein GANs1902.03642v1 · Anton Mallasto, Jes Frellsen, Wouter Boomsma et al.2019 · 9 citationsarXiv
Barnaba: software for analysis of nucleic acid structures and trajectories.30420522 · Bottaro, Sandro, Bussi, Giovanni, Pinamonti, Giovanni et al.2019 · 93 citationsRNA (New York, N.Y.). 2019;25(2):219-231
Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias.30141937 · Wang, Yong, Tian, Pengfei, Boomsma, Wouter et al.2019 · 5 citationsThe journal of physical chemistry. B. 2018;122(49):11174-11185
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data1807.02547v2 · Maurice Weiler, Mario Geiger, Max Welling et al.2018 · 231 citationsarXiv
Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories10.1101/345678v3 · Bottaro, S., Bussi, G., Pinamonti, G. et al.2018 · 2 citationsbioRxiv
Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo.29260565 · Kurut, Anıl, Fonseca, Rasmus, Boomsma, Wouter2018 · 6 citationsThe journal of physical chemistry. B. 2018;122(3):1195-1204
Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.27276252 · Kassem, Maher M, Wang, Yong, Boomsma, Wouter et al.2017 · 17 citationsBiophysical journal. 2016;110(11):2342-2348
Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides.26957604 · Safavi-Hemami, Helena, Li, Qing, Jackson, Ronneshia L et al.2016 · 59 citationsProceedings of the National Academy of Sciences of the United States of America. 2016;113(12):3227-32
Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases.26966660 · Boomsma, Wouter, Nielsen, Sofie V, Lindorff-Larsen, Kresten et al.2016 · 33 citationsPeerJ. 2016;4:e1725
Bayesian inference of protein ensembles from SAXS data.26548662 · Antonov, L D, Olsson, S, Boomsma, W et al.2017 · 56 citationsPhysical chemistry chemical physics : PCCP. 2016;18(8):5832-8
A Monte Carlo Study of the Early Steps of Functional Amyloid Formation.26745180 · Tian, Pengfei, Lindorff-Larsen, Kresten, Boomsma, Wouter et al.2016 · 9 citationsPloS one. 2016;11(1):e0146096
ENCORE: Software for Quantitative Ensemble Comparison.26505632 · Tiberti, Matteo, Papaleo, Elena, Bengtsen, Tone et al.2016 · 89 citationsPLoS computational biology. 2015;11(10):e1004415
Comparing molecular dynamics force fields in the essential subspace.25811178 · Martín-García, Fernando, Papaleo, Elena, Gomez-Puertas, Paulino et al.2016 · 89 citationsPloS one. 2015;10(3):e0121114
Structure of a functional amyloid protein subunit computed using sequence variation.25415595 · Tian, Pengfei, Boomsma, Wouter, Wang, Yong et al.2016 · 105 citationsJournal of the American Chemical Society. 2015;137(1):22-5
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