Thomas Wim Hamelryck

Thomas Wim Hamelryck

Professor

ORCID: 0000-0003-2917-3602

Publication year:
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26 - 50 out of 62Page size: 25
  1. 2012
  2. Published

    Bayesian methods in structural bioinformatics

    Hamelryck, Thomas Wim (ed.), Mardia, K. (ed.) & Ferkinghoff-Borg, J. (ed.), 2012, Springer. 377 p. (Statistics for Biology and Health).

    Research output: Book/Report › Book › Research › peer-review

  3. 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

  4. Published

    Mixtures of concentrated multivariate sine distributions with applications to bioinformatics

    Mardia, K. V., Kent, J. T., Zhang, Z., Taylor, C. C. & Hamelryck, Thomas Wim, 2012, In: Journal of Applied Statistics. 39, 11, p. 2475-2492 18 p.

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

  5. Published

    On the Physical Relevance and Statistical Interpretation of Knowledge-Based Potentials

    Borg, M., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2012, Bayesian Methods in Structural Bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer Publishing Company, p. 97-124 28 p. (Statistics for Biology and Health, Springer).

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

  6. 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

  7. 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

  8. Published

    Towards a general probabilistic model of protein structure: the reference ratio method

    Frellsen, J., Mardia, K. V., Borg, M., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2012, Bayesian methods in structural bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 125-134 10 p. (Statistics for Biology and Health).

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

  9. 2013
  10. Published

    A simple probabilistic model of multibody interactions in proteins

    Johansson, Kristoffer Enøe & Hamelryck, Thomas Wim, 2013, In: Proteins: Structure, Function, and Bioinformatics. 81, 8, p. 1340-1350 11 p.

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

  11. Published

    Combining the multicanonical ensemble with generative probabilistic models of local biomolecular structure

    Frellsen, J., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2013, Proceedings of the 59th World Statistics Congress of the International Statistical Institute, 2013 . Hague, p. 139-144 6 p.

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

  12. 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

  13. 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

  14. Published

    Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

    Antonov, L. D., Andreetta, C. & Hamelryck, Thomas Wim, 2013, Biomedical Engineering Systems and Technologies. Gabriel, J., Schier, J. & Huffel, S. V. (eds.). Springer Science+Business Media, Vol. 357. p. 222-235 14 p. (Communications in Computer and Information Science).

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

  15. 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

  16. 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

  17. 2014
  18. 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

  19. 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

  20. Published

    FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

    Christensen, A. S., Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2014, In: PeerJ. 2, e277.

    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. 2015
  23. Published

    Bayesian inference of protein structure from chemical shift data

    Bratholm, L. A., Christensen, A. S., Hamelryck, Thomas Wim & Jensen, Jan Halborg, 2015, In: PeerJ. 3, 19 p., e861.

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

  24. 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

  25. 2016
  26. 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

  27. Published

    Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template

    Johansson, Kristoffer Enøe, Johansen, Nicolai Tidemand, Christensen, S., Horowitz, S., Bardwell, J. C. A., Olsen, Johan Gotthardt, Willemoës, Martin, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J., Hamelryck, Thomas Wim & Winther, Jakob R., 2016, In: Journal of Molecular Biology. 428, 21, p. 4361-4377 17 p.

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

  28. 2017
  29. Published

    A Generative Angular Model of Protein Structure Evolution

    Golden, M., Garcia-Portugues, E., Sørensen, Michael, Mardia, K. V., Hamelryck, Thomas Wim & Hein, J., Aug 2017, In: Molecular Biology and Evolution. 34, 8, p. 2085-2100

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

  30. 2018
  31. Published

    MyPMFs: a simple tool for creating statistical potentials to assess protein structural models

    Postic, G., Hamelryck, Thomas Wim, Chomilier, J. & Stratmann, D., 2018, In: Biochimie. 151, p. 37-41 5 p.

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

  32. Published

    Probabilistic Programming for Voucher Information Extraction: Preliminary Practical Experiences

    Al-Sibahi, A. S., Hamelryck, Thomas Wim & Henglein, Fritz, 2018.

    Research output: Contribution to conference › Poster › Research

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