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
- 2024
- Published
AI Implementation and Capability Development in Manufacturing: An Action Research Case
Eklöf, Jon, Snis, U. L., Hamelryck, Thomas Wim, Grima, A. & Rønning, Ola, 2024, Proceedings of the 57th Hawaii International Conference on System Sciences - HICSS 2024. Hawaii International Conference on System Sciences, 10 p.Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Accepted/In press
Abstraction, mimesis and the evolution of deep learning
Eklöf, Jon, Hamelryck, Thomas Wim, Last, C., Grima, A. & Snis, U. L., 2024, (Accepted/In press) In: AI and Society. 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2022
- 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
- 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
- 2021
- Published
Time-efficient Bayesian Inference for a (Skewed) von Mises Distribution on the Torus in a Deep Probabilistic Programming Language
Rønning, Ola, Ley, C., Mardia, K. V. & Hamelryck, Thomas Wim, 2021, 2021 IEEE International Conference on Multisensor Fusion and Integration for Intelligent Systems (MFI). IEEE, p. 1-8Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- 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
- 2020
- 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
- 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
- Published
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
- 2019
- 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
- Published
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
- 2018
- 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
- 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
- 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
- 2017
- 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. 2085-2100Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- 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
- 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
- 2015
- 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
- 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
- 2014
- 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
- 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
- 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
- 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
- 2013
- 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
- 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
ID: 5765
Most downloads
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2307
downloads
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
1784
downloads
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
Published -
1468
downloads
A probabilistic model of RNA conformational space
Research output: Contribution to journal › Journal article › Research › peer-review
Published