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
- 2013
- 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
- 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
- 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
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
- 2012
- Published
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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 2011
- 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
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
- 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
- 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
- 2010
- 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. 306Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
Stovgaard, K., Andreetta, C., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 429Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- 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
- 2009
- Published
A probabilistic approach to protein structure prediction: PHAISTOS in CASP8
Borg, M., Boomsma, Wouter, Ferkinghoff-Borg, J., Frellsen, J., Harder, T. P., Mardia, K., Røgen, P., Stovgaard, K. & Hamelryck, Thomas Wim, 2009, LASR 2009 — Statistical Tools for Challenges in Bioinformatics. Proceedings. Gusnanto, A., Mardia, K. V. & Fallaize, C. J. (eds.). University of Leeds, p. 65-70 6 p.Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
A probabilistic approach to protein structureprediction: PHAISTOS in CASP8
Borg, M., Boomsma, Wouter, Ferkinghoff-Borg, J., Frellsen, J., Harder, T. P., Mardia, K. V., Røgen, P., Stovgaard, K. & Hamelryck, Thomas Wim, 2009, In: School of Mathematics. p. 65-70Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A probabilistic model of RNA conformational space
Frellsen, J., Moltke, Ida, Thiim, M., Mardia, K. V., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 2009, In: PLoS Computational Biology. 5, 6, p. e1000406Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, Thomas Wim, Kauff, F., Wilczynski, B. & de Hoon, M. J. L., 2009, In: Bioinformatics. 25, 11, p. 1422-3 1 p.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 5765
Most downloads
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2307
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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
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