Wouter Boomsma

Wouter Boomsma

Professor


  1. 2023
  2. 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 journalConference articlepeer-review

  3. 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 proceedingArticle in proceedingsResearchpeer-review

  4. 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 journalJournal articlepeer-review

  5. 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 journalJournal articlepeer-review

  6. 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 journalJournal articlepeer-review

  7. 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 journalJournal articlepeer-review

  8. 2022
  9. 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 journalJournal articlepeer-review

  10. 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 journalJournal articlepeer-review

  11. 2021
  12. 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, de Bruijne, Marleen, Ibragimov, Bulat, Petersen, Jens, Lillholm, Martin, Middleton, Jon Anthony, Mogensen, S. H., Thorsen-Meyer, H., Perner, Anders, Helleberg, M., Kaas-Hansen, Benjamin Skov, Bonde, M., Bonde, A., Pai, A., Nielsen, Mads & Sillesen, Martin Hylleholt, 2021, In: Scientific Reports. 11, 1, 12 p., 3246.

    Research output: Contribution to journalJournal articlepeer-review

  13. 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 journalJournal articlepeer-review

  14. 2020
  15. 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 journalJournal articlepeer-review

  16. 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 journalConference abstract in journalpeer-review

  17. 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 journalJournal articlepeer-review

  18. 2019
  19. 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. 219-231

    Research output: Contribution to journalJournal articlepeer-review

  20. 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 journalJournal articlepeer-review

  21. 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. 4923-4943

    Research output: Contribution to journalJournal articlepeer-review

  22. 2018
  23. 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. 1195-1204

    Research output: Contribution to journalJournal articlepeer-review

  24. Published

    3D steerable CNNs: Learning rotationally equivariant features in volumetric data

    Weiler, M., Geiger, M., Welling, M., Boomsma, Wouter & Cohen, T., 2018, Proceedings of the 32nd International Conference on Neural Information Processing Systems. derc ed. NIPS Proceedings, Vol. 2018. p. 10381-10392 12 p. (Advances in Neural Information Processing Systems, Vol. 31).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  25. Published

    Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

    Wang, Yong, Tian, P., Boomsma, Wouter & Lindorff-Larsen, Kresten, 2018, In: Journal of Physical Chemistry B. 122, 49, p. 11174-11185

    Research output: Contribution to journalJournal articlepeer-review

  26. 2017
  27. Published

    Spherical convolutions and their application in molecular modelling

    Boomsma, Wouter & Frellsen, J., 2017, Neural Information Processing Systems 2017. Guyon, I., Luxburg, U. V., Bengio, S., Wallach, H., Fergus, R., Vishwanathan, S. & Garnett, R. (eds.). NIPS Proceedings, 11 p. (Advances in Neural Information Processing Systems, Vol. 30).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  28. 2016
  29. 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 journalJournal articlepeer-review

  30. 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 journalJournal articlepeer-review

  31. 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 journalJournal articlepeer-review

  32. 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 journalJournal articlepeer-review

  33. 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 journalJournal articlepeer-review

  34. 2015
  35. 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 journalJournal articlepeer-review

  36. 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 journalJournal articlepeer-review

  37. 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 proceedingBook chapterResearchpeer-review

  38. Published

    Structure of a functional amyloid protein subunit computed using sequence variation

    Tian, P., Boomsma, Wouter, Wang, Yong, 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 journalJournal articlepeer-review

  39. 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 journalConference abstract in journalpeer-review

  40. 2014
  41. 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 journalJournal articlepeer-review

  42. 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 journalJournal articlepeer-review

  43. 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 journalJournal articlepeer-review

  44. 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 journalJournal articlepeer-review

  45. 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 journalJournal articlepeer-review

  46. 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 journalJournal articlepeer-review

  47. 2013
  48. 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 journalComment/debate

  49. 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 journalJournal articlepeer-review

  50. 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 journalJournal articlepeer-review

  51. 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/ReportBook

  52. 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 journalJournal articlepeer-review

  53. 2012
  54. 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 journalJournal articlepeer-review

  55. 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 journalJournal articlepeer-review

  56. 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 proceedingBook chapterResearchpeer-review

  57. 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 journalJournal articlepeer-review

  58. 2011
  59. Published

    Efficient, non-disruptive local moves for Monte Carlo sampling of proteins

    Bottaro, S., Boomsma, Wouter, Johansson, Kristoffer Enøe, Andreetta, C., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2011, Next Generation Statistics in Biosciences: Proceedings of the 30th Leeds Annual Statistical Research (LASR) Workshop. Mardia, K. V., Gusnanto, A., Riley, A. D. & Voss, J. (eds.). University of Leeds, p. 127 1 p.

    Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsResearch

  60. 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 journalLetterpeer-review

  61. 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 conferencePosterResearch

  62. 2010
  63. 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. 306

    Research output: Contribution to journalJournal articlepeer-review

  64. 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 journalJournal articlepeer-review

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