Thomas Wim Hamelryck
Professor
Computational and RNA Biology
Ole Maaløes Vej 5
2200 København N.
Programming Languages and Theory of Computing
Universitetsparken 5
2100 København Ø
- Published
Toroidal Diffusions and Protein Structure Evolution
Garcia Portugues, E., Golden, M., Sørensen, Michael, Mardia, K. V., Hamelryck, Thomas Wim & Hein, J., 2018, Applied Directional Statistics: Modern Methods and Case Studies. Ley, C. & Verdebout, H. (eds.). CRC Press, 34 p.Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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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
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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. 2085-2100Research output: Contribution to journal › Journal article › Research › peer-review
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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
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An Overview of Bayesian Inference and Graphical Models
Hamelryck, Thomas Wim, 2012, Bayesian Methods in Structural Bioinformatics. Hamelryck, T., Mardia, K. & Ferkinghoff-Borg, J. (eds.). Springer, p. 3-48 46 p. (Statistics for Biology and Health, Springer).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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Probabilistic models and machine learning in structural bioinformatics
Hamelryck, Thomas Wim, 2009, In: Statistical Methods in Medical Research. 18, 5, p. 505-26 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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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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
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Sampling Realistic Protein Conformations Using Local Structural Bias
Hamelryck, Thomas Wim, Kent, J. T. & Krogh, Anders, 2006, In: PLoS ONE. 2, 9, p. e131Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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
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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
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
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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
- Published
A statistical view on the reference ratio method
Mardia, K., Frellsen, J., Borg, M., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2011. 6 p.Research output: Contribution to conference › Paper › Research
- 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
- 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
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A Probabilistic Programming Approach to Protein Structure Superposition
Sanz Moreta, Lys, Al-Sibahi, A. S., Theobald, D., Bullock, W., Rommes, B. N., Manoukian, Andreas & Hamelryck, Thomas Wim, 2019, 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019. Baruzzo, G., Daberdaku, S., Di Camillo, B., Furini, S., Giordano, E. D. & Nicosia, G. (eds.). IEEE, 5 p. 8791469Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Bayesian protein superposition using Hamiltonian Monte Carlo
Sanz Moreta, Lys, Al-Sibahi, A. S. & Hamelryck, Thomas Wim, Oct 2020, Proceedings - IEEE 20th International Conference on Bioinformatics and Bioengineering, BIBE 2020. IEEE, p. 1-11 9288019Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
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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
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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
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
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A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]
Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., Tusnady, G. & 3 others, , 2020, In: F1000Research. 9, 27 p., 278.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 5765
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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
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1788
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Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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1469
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A probabilistic model of RNA conformational space
Research output: Contribution to journal › Journal article › Research › peer-review
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