Wouter Boomsma

Wouter Boomsma

Professor

ORCID: 0000-0002-8257-3827

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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Published

    Graphical models and directional statistics capture protein structure

    Boomsma, Wouter, Kent, J. T., Mardia, K. V., Taylor, C. C. & Hamelryck, Thomas Wim, 2006, Interdisciplinary Statistics and Bioinformatics. Barber, S., Baxter, P. D., Mardia, K. V. & Walls, R. E. (eds.). Leeds University Press, p. 91-94 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  7. 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

  8. Published

    Implicit Variational Inference for High-Dimensional Posteriors

    Uppal, A., Stensbo-Smidt, K., Boomsma, Wouter & Frellsen, J., 2023, Advances in Neural Information Processing Systems 36 pre-proceedings (NeurIPS 2023). NeurIPS Proceedings, 24 p. (Advances in Neural Information Processing Systems, Vol. 36).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  9. 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

  10. Published

    Iterative ratio method: a formal justification for the potentials of mean force

    Valentin, J., Andreetta, C., Paluszewski, M., Borg, M., Frellsen, J., Paulsen, J., Boomsma, Wouter, Bottaro, S., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011. 1 p.

    Research output: Contribution to conference › Poster › Research

  11. 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

  12. 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

  13. 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

  14. 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. 11174-11185

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Multiple sequence alignment using SAGA: investigating the effects of operator scheduling, population seeding, and crossover operators

    Thomsen, R. & Boomsma, Wouter, 2004, Applications of Evolutionary Computing: EvoWorkshops 2004: EvoBIO, EvoCOMNET, EvoHOT, EvoISAP, EvoMUSART, and EvoSTOC, Coimbra, Portugal, April 5-7, 2004. Proceedings. Raidl, G. R. (ed.). Springer, p. 113-122 10 p. (Lecture notes in computer science, Vol. 3005).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  16. 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

  17. 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

  18. Published

    Phaistos user manual

    Boomsma, Wouter, Bottaro, S., Hamelryck, Thomas Wim, Frellsen, J., Andreetta, C., Borg, M., Harder, T., Johansson, Kristoffer Enøe, Stovgaard, K. & Tian, P., 2013, 90 p.

    Research output: Book/Report › Book › Education

  19. 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

  20. 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

  21. 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

  22. Published

    Probabilistic models of local biomolecular structure and their applications

    Boomsma, Wouter, Frellsen, J. & Hamelryck, Thomas Wim, 2012, Bayesian methods in structural bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 233-254 22 p. (Statistics for Biology and Health, Springer).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  23. Published

    Protein Structure: Probabilistic Modeling and Simulation

    Boomsma, Wouter, 2008, Department of Biology: Museum Tusculanum. 106 p.

    Research output: Book/Report › Ph.D. thesis › Research

  24. 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

  25. Published

    Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

    Hamelryck, Thomas Wim, Boomsma, Wouter, Ferkinghoff-Borg, J., Foldager, J. I., Frellsen, J., Haslett, J. & Theobald, D., 2015, Geometry driven statistics. Dryden, I. L. & Kent, J. T. (eds.). Wiley, p. 356-376 21 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

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