Wouter Boomsma
Professor
Machine Learning
Universitetsparken 1
2100 København Ø
- 2024
- Published
A systematic analysis of regression models for protein engineering
Michael, Richard, Kæstel-Hansen, Jacob, Groth, Peter Mørch, Bartels, S., Salomon, J., Tian, P., Hatzakis, Nikos & Boomsma, Wouter, 2024, In: PLOS Computational Biology. 20, 5 May, 22 p., e1012061.Research output: Contribution to journal › Journal article › Research › peer-review
- 2023
- Published
Adaptive Cholesky Gaussian Processes
Bartels, S., Stensbo-Smidt, K., Moreno-Muñoz, P., Boomsma, Wouter, Frellsen, J. & Hauberg, S., 2023, In: Proceedings of Machine Learning Research. 206, p. 408--452 44 p.Research output: Contribution to journal › Conference article › Research › peer-review
- Published
Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition
Bartels, S., Boomsma, Wouter, Frellsen, J. & Garreau, D., 2023, In: Journal of Machine Learning Research. 24, p. 1-57 71.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components
Kampmeyer, Caroline, Grønbæk-Thygesen, Martin, Oelerich, N., Tatham, M. H., Cagiada, Matteo, Lindorff-Larsen, K., Boomsma, Wouter, Hofmann, K. & Hartmann-Petersen, Rasmus, 2023, In: Cellular and Molecular Life Sciences. 80, 6, 18 p., 143.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro
Jacobsen, Nina Louise, Bloch, Magnus Borup, Millard, P. S., Ruidiaz, Sarah Frederiksen, Elsborg, Jonas Damgaard, Boomsma, Wouter, Hendus-Altenburger, R., Hartmann-Petersen, Rasmus & Kragelund, Birthe Brandt, 2023, In: Protein Science. 32, 9, 16 p., e4733.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Rapid protein stability prediction using deep learning representations
Blaabjerg, Lasse Møller, Kassem, M. M., Good, L. L., Jonsson, Nicolas, Cagiada, Matteo, Johansson, Kristoffer Enøe, Boomsma, Wouter, Stein, Amelie & Lindorff-Larsen, Kresten, 2023, In: eLife. 12, 19 p., e82593.Research output: Contribution to journal › Journal article › Research › peer-review
- 2022
- Published
A context-dependent and disordered ubiquitin-binding motif
Dreier, Jesper Elmsted, Prestel, Andreas, Martins, J. M., Brøndum, S. S., Nielsen, Olaf, Garbers, Anna Engstrøm, Suga, H., Boomsma, Wouter, Rogers, Joseph Matthew, Hartmann-Petersen, Rasmus & Kragelund, Birthe Brandt, 2022, In: Cellular and molecular life sciences : CMLS. 79, 9, 21 p., 484.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Learning meaningful representations of protein sequences
Detlefsen, N. S., Hauberg, S. & Boomsma, Wouter, 2022, In: Nature Communications. 13, 1, p. 1-12 1914.Research output: Contribution to journal › Journal article › Research › peer-review
- 2021
- Published
Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients
Jimenez-Solem, E., Petersen, T. S., Hansen, C., Hansen, C., Lioma, C., Igel, C., Boomsma, W., Krause, O., Lorenzen, S., Selvan, R., Petersen, J., Nyeland, M. E., Ankarfeldt, M. Z., Virenfeldt, G. M., Winther-Jensen, M., Linneberg, A., Ghazi, M. M., Detlefsen, N., Lauritzen, A. D., Smith, A. G. & 15 others, , 2021, In: Scientific Reports. 11, 1, 12 p., 3246.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion
Pinholt, H. D., Bohr, S. S. R., Iversen, J. F., Boomsma, Wouter & Hatzakis, Nikos, 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 31, 7 p., e2104624118.Research output: Contribution to journal › Journal article › Research › peer-review
- 2020
- Published
Orchestration of signaling by structural disorder in class 1 cytokine receptors
Seiffert, P., Bugge, K., Nygaard, M., Haxholm, G. W., Martinsen, J. H., Pedersen, M. N., Arleth, Lise, Boomsma, Wouter & Kragelund, Birthe Brandt, 24 Aug 2020, In: Cell Communication and Signaling. 18, 1, 30 p., 132.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Context Matters in Disorder Based Protein Communication
Kragelund, Birthe Brandt, Prestel, Andreas, Wickmann, N., Martins, J., Boomsma, Wouter, Staby, L., Hendus-Altenburger, R. & Skriver, Karen, 2020, In: Biophysical Journal. 118, 3, suppl. 1, p. 491A 2407-Plat.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
- Published
IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors
Millard, P. S., Bugge, K., Marabini, R., Boomsma, Wouter, Burow, Meike & Kragelund, Birthe Brandt, 2020, In: Protein Science. 29, 1, p. 169-183 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2019
- Published
Barnaba: software for analysis of nucleic acid structures and trajectories
Bottaro, S., Bussi, G., Pinamonti, G., Reisser, S., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2019, In: RNA. 25, 2, p. 219-231Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range
Hendus-Altenburger, R., Fernandes, Catarina, Bugge, K., Kunze, M. B. A., Boomsma, Wouter & Kragelund, Birthe Brandt, 2019, In: Journal of Biomolecular NMR. 73, 12, p. 713–725 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The PCNA interaction motifs revisited: thinking outside the PIP-box
Prestel, Andreas, Wichmann, N., Martins, J. M., Marabini, R., Kassem, N., Broendum, S. S., Otterlei, M., Nielsen, Olaf, Willemoës, Martin, Ploug, Michael, Boomsma, Wouter & Kragelund, Birthe Brandt, 2019, In: Cellular and Molecular Life Sciences. 76, 24, p. 4923-4943Research output: Contribution to journal › Journal article › Research › peer-review
- 2018
- Published
Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo
Kurut, A., Fonseca, R. & Boomsma, Wouter, 25 Jan 2018, In: Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical. 122, 3, p. 1195-1204Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias
Wang, Y., Tian, P., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2018, In: Journal of Physical Chemistry B. 122, 49, p. 11174-11185Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
A Monte Carlo study of the early steps of functional amyloid formation
Tian, P., Lindorff-Larsen, Kresten, Boomsma, Wouter, Jensen, Mogens Høgh & Otzen, D. E., 2016, In: P L o S One. 11, 1, 18 p., e0146096.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bayesian inference of protein ensembles from SAXS data
Antonov, L. D., Olsson, S., Boomsma, Wouter & Hamelryck, Thomas Wim, 2016, In: Physical Chemistry Chemical Physics. 18, 8, p. 5832-5838 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases
Boomsma, Wouter, Nielsen, S. V., Lindorff-Larsen, Kresten, Hartmann-Petersen, Rasmus & Ellgaard, Lars, 2016, In: PeerJ. 4, 18 p., e1725.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides
Safavi, Helena, Li, Q., Jackson, R. L., Song, A. S., Boomsma, Wouter, Bandyopadhyay, P. K., Gruber, C. W., Purcell, A. W., Yandell, M., Olivera, B. M. & Ellgaard, Lars, 2016, In: Proceedings of the National Academy of Sciences of the United States of America. 113, 12, p. 3227-3232 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Structure of the bacterial cytoskeleton protein bactofilin by NMR chemical shifts and sequence variation
Kassem, M. M., Wang, Y., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2016, In: Biophysical Journal. 110, 11, p. 2342-2348 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2015
- Published
Comparing molecular dynamics force fields in the essential subspace
Martin-García, F., Papaleo, E., Gomez-Puertas, P., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2015, In: PLoS ONE. 10, 3, 16 p., e0121114.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ENCORE: Software for Quantitative Ensemble Comparison
Tiberti, M., Papaleo, E., Bengtsen, T., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2015, In: PLoS Computational Biology. 11, 10, 16 p., e1004415.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Structure of a functional amyloid protein subunit computed using sequence variation
Tian, P., Boomsma, Wouter, Wang, Y., Otzen, D., Jensen, Mogens Høgh & Lindorff-Larsen, Kresten, 2015, In: Journal of the American Chemical Society. 137, 1, p. 22–25 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
What does evolution tell us about the structure of a functional amyloid protein?
Tian, P., Boomsma, Wouter, Wang, Y., Otzen, D. E., Jensen, Mogens Høgh & Lindorff-Larsen, Kresten, 2015, In: Biophysical Journal. 108, 2, Supplement 1, p. 227a 1 p.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
- 2014
- Published
Combining experiments and simulations using the maximum entropy principle
Boomsma, Wouter, Ferkinghoff-Borg, J. & Lindorff-Larsen, Kresten, 2014, In: PLoS Computational Biology. 10, 2, 9 p., e1003406.Research output: Contribution to journal › Journal article › Research › peer-review
Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I
Petrlova, J., Bhattacherjee, A., Boomsma, Wouter, Wallin, S., Lagerstedt, J. O. & Irbäck, A., 2014, In: Protein Science. 23, 11, p. 1559-1571 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts
Boomsma, Wouter, Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, Thomas Wim, Lindorff-Larsen, Kresten & Vendruscolo, M., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13852-13857 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method
Valentin, J., Andreetta, C., Boomsma, Wouter, Bottaro, S., Ferkinghoff-Borg, J., Frellsen, J., Mardia, K. V., Tian, P. & Hamelryck, Thomas Wim, 2014, In: Proteins: Structure, Function, and Bioinformatics. 82, 2, p. 288-299 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Probabilistic determination of native state ensembles of proteins
Olsson, S., Vögeli, B. R., Cavalli, A., Boomsma, Wouter, Ferkinghoff-Borg, J., Lindorff-Larsen, Kresten & Hamelryck, Thomas Wim, 2014, In: Journal of Chemical Theory and Computation. 10, 8, p. 3484-3491 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Robust estimation of diffusion-optimized ensembles for enhanced sampling
Tian, P., Jónsson, S. Æ., Ferkinghoff-Borg, J., Krivov, S. V. .., Lindorff-Larsen, Kresten, Irbäck, A. & Boomsma, Wouter, 2014, In: Journal of Chemical Theory and Computation. 10, 2, p. 543–553 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2013
- Published
A sticky cage can slow down folding
Boomsma, Wouter & Lindorff-Larsen, Kresten, 2013, In: Biophysical Journal. 104, 5, p. 964-965 2 p.Research output: Contribution to journal › Comment/debate › Research
- Published
Inference of structure ensembles of flexible biomolecules from sparse, averaged data
Olsson, S., Frellsen, J., Boomsma, Wouter, Mardia, K. V. & Hamelryck, Thomas Wim, 2013, In: PLoS ONE. 8, 11, 7 p., e79439.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure
Boomsma, Wouter, Frellsen, J., Harder, T. P., Bottaro, S., Johansson, Kristoffer Enøe, Tian, P., Stovgaard, K., Andreetta, C., Olsson, S., Valentin, J., Antonov, L. D., Christensen, A. S., Borg, M., Jensen, Jan Halborg, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2013, In: Journal of Computational Chemistry. 34, 19, p. 1697-1705 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Christensen, A. S., Linnet, T. E., Borg, M., Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2013, In: PLoS ONE. 8, 12, 10 p., e84123.Research output: Contribution to journal › Journal article › Research › peer-review
- 2012
- Published
An efficient null model for conformational fluctuations in proteins
Harder, T. P., Bottaro, S., Boomsma, Wouter, Olsson, S., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2012, In: Structure. 20, 6, p. 1028-1039 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast large-scale clustering of protein structures using Gauss integrals
Harder, T. P., Borg, M., Boomsma, Wouter, Røgen, P. & Hamelryck, Thomas Wim, 2012, In: Bioinformatics. 28, 4, p. 510-515 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Subtle Monte Carlo updates in dense molecular systems
Bottaro, S., Boomsma, Wouter, Johansson, Kristoffer Enøe, Andreetta, C., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2012, In: Journal of Chemical Theory and Computation. 8, 2, p. 695-702 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2011
- Published
Generative probabilistic models extend the scope of inferential structure determination
Olsson, S., Boomsma, Wouter, Frellsen, J., Bottaro, S., Harder, T. P., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011, In: Journal of Magnetic Resonance. 213, 1, p. 182-186 5 p.Research output: Contribution to journal › Letter › Research › peer-review
- 2010
- Published
Beyond rotamers: a generative, probabilistic model of side chains in proteins
Harder, T., Boomsma, Wouter, Paluszewski, M., Frellsen, J., Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 306Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Potentials of mean force for protein structure prediction vindicated, formalized and generalized
Hamelryck, Thomas Wim, Borg, M., Paluszewski, M., Paulsen, J., Frellsen, J., Andreetta, C., Boomsma, Wouter, Bottaro, S. & Ferkinghoff-Borg, J., 2010, In: PLoS ONE. 5, 11, 11 p., e13714.Research output: Contribution to journal › Journal article › Research › peer-review
- 2009
- Published
A probabilistic approach to protein structureprediction: PHAISTOS in CASP8
Borg, M., Boomsma, Wouter, Ferkinghoff-Borg, J., Frellsen, J., Harder, T. P., Mardia, K. V., Røgen, P., Stovgaard, K. & Hamelryck, Thomas Wim, 2009, In: School of Mathematics. p. 65-70Research output: Contribution to journal › Journal article › Research › peer-review
- 2008
- Published
A generative, probabilistic model of local protein structure
Boomsma, Wouter, Mardia, K. V., Taylor, C. C., Ferkinghoff-Borg, J., Krogh, Anders & Hamelryck, Thomas Wim, 2008, In: Proceedings of the National Academy of Science of the United States of America. 105, 26, p. 8932-8937 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast phylogenetic DNA barcoding
Terkelsen, K. M., Boomsma, Wouter, Willerslev, Eske & Nielsen, Rasmus, 2008, In: Philosophical Transactions of the Royal Society of London. Biological Sciences. 363, 1512, p. 3997-4002 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Statistical assignment of DNA sequences using Bayesian phylogenetics
Terkelsen, K. M., Boomsma, Wouter, Huelsenbeck, J. P., Willerslev, Eske & Nielsen, Rasmus, 2008, In: Systematic Biology. 57, 5, p. 750-757 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2007
- Published
Ancient biomolecules from deep ice cores reveal a forested southern Greenland.
Willerslev, E., Cappellini, E., Boomsma, W. K., Nielsen, R., Hebsgaard, M. B., Brand, T. B., Hofreiter, M., Bunce, M., Poinar, H. N., Dahl-Jensen, D., Johnsen, S. J., Steffensen, J. P., Bennike, O., Schwenninger, J-L., Nathan, R., Armitage, S., de Hoog, C-J., Alfimov, V., Christl, M., Beer, J. & 10 others, , 2007, In: Science. 317, 5834, p. 111-114 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2005
- Published
Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
Boomsma, Wouter & Hamelryck, Thomas Wim, 2005, In: BMC Bioinformatics. 6, 10 p., 159.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 40103911
Most downloads
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2309
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Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
1431
downloads
Potentials of mean force for protein structure prediction vindicated, formalized and generalized
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
1431
downloads
Inference of structure ensembles of flexible biomolecules from sparse, averaged data
Research output: Contribution to journal › Journal article › Research › peer-review
Published