Thomas Wim Hamelryck

Thomas Wim Hamelryck

Professor

ORCID: 0000-0003-2917-3602

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  1. Published

    Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model

    Thygesen, Christian Bahne, Al-Sibahi, A. S., Steenmanns, C. S., Sanz Moreta, Lys, Sørensen, A. B. & Hamelryck, Thomas Wim, 2021, International Conference on Machine Learning, 18-24 July 2021, Virtual. PMLR, p. 10258-10267 (Proceedings of Machine Learning Research, Vol. 139).

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

  2. 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 proceeding › Conference abstract in proceedings › Research

  3. 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

  4. Published

    Evolving hidden Markov models for protein secondary structure prediction

    Won, K. J., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2005, The 2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005: Proceedings. IEEE, Vol. 3. p. 33-40 8 p.

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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Published

    GISA: using Gauss Integrals to identify rare conformations in protein structures

    Grønbæk, Christian, Hamelryck, Thomas Wim & Røgen, P., 2020, In: PeerJ. 8, 16 p., e9159.

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

  10. 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

  11. 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

  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

    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

  14. Published

    Langevin diffusions on the torus: estimation and applications

    García-Portugués, E., Sørensen, Michael, Mardia, K. V. & Hamelryck, Thomas Wim, 2019, In: Statistics and Computing. 29, 1, p. 1-22 22 p.

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

  15. Published

    Mixture Models for Spherical Data with Applications to Protein Bioinformatics

    Mardia, K. V., Barber, S., Burdett, P. M., Kent, J. T. & Hamelryck, Thomas Wim, 2022, Directional Statistics for Innovative Applications: A Bicentennial Tribute to Florence Nightingale. Springer, p. 15-32 (Forum for Interdisciplinary Mathematics).

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

  16. 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

  17. Published

    Mocapy++ - a toolkit for inference and learning in dynamic Bayesian networks

    Paluszewski, M. & Hamelryck, Thomas Wim, 2010, In: BMC Bioinformatics. 11, Suppl 1, 6 p., 126.

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

  18. 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

  19. 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

  20. 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

  21. 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

  22. Published

    Persistent Topology of Protein Space

    Hamilton, W., Borgert, J. E., Hamelryck, Thomas Wim & Marron, J. S., 2022, Research in Computational Topology 2. Springer, p. 223-244 (Association for Women in Mathematics Series, Vol. 30).

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

  23. 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

  24. 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

  25. 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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