Wouter Boomsma

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Thomas HamelryckDpt. of computer science / Dpt. of biology, University of CopenhagenVerified email at binf.ku.dk
Kresten Lindorff-LarsenLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenVerified email at bio.ku.dk
Jes FrellsenAssociate Professor, Technical University of Denmark (DTU)Verified email at dtu.dk
Jesper Ferkinghoff-BorgAssociate Professor, Research Director, Novo Nordisk A/SVerified email at novonordisk.com
Sandro BottaroPeptoneVerified email at peptone.io
Simon OlssonAssistant Professor, Chalmers University of TechnologyVerified email at chalmers.se
Kanti MardiaSENIOR RESARCH PROFESSOR ,UNIVERSITY OF LEEDS AND UNIVERSITY OF OXFORDVerified email at leeds.ac.uk
Pengfei TianProtein Design ScientistVerified email at nih.gov
Tim HarderResearch Scientist at Philips ResearchVerified email at philips.com
Christian AndreettaUniv. of Copenhagen, Denmark, and Uni Computing, Uni Research, NorwayVerified email at uni.no
Birthe B. KragelundProfessor of protein biophysics, University of CopenhagenVerified email at bio.ku.dk
Kristoffer Enøe JohanssonDepartment of Biology, University of CopenhagenVerified email at bio.ku.dk
Yong WangZhejiang UniversityVerified email at zju.edu.cn
Eske WillerslevCentre for GeoGenetics, University of CopenhagenVerified email at snm.ku.dk
Kasper MunchBioinformatics Research Centre, Aarhus UniversityVerified email at daimi.au.dk
Rasmus NielsenUC Berkeley, University of CopenhagenVerified email at bio.ku.dk
Charles C TaylorUniversity of LeedsVerified email at maths.leeds.ac.uk
Mogens H. JensenProfessor of Complex Systems, Niels Bohr InstituteVerified email at nbi.dk
Elena PapaleoDanish Cancer Society Research Center and Technical University of DenmarkVerified email at cancer.dk
Taco CohenQualcomm AI ResearchVerified email at qti.qualcomm.com

Wouter Boomsma

Professor, Department of Computer Science, University of Copenhagen

Verified email at di.ku.dk

Machine learning Structural Bioinformatics Biomolecular simulations


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Ancient biomolecules from deep ice cores reveal a forested southern Greenland E Willerslev, E Cappellini, W Boomsma, R Nielsen, MB Hebsgaard, ... Science 317 (5834), 111-114, 2007	495	2007
3d steerable cnns: Learning rotationally equivariant features in volumetric data M Weiler, M Geiger, M Welling, W Boomsma, TS Cohen Advances in Neural Information Processing Systems 31, 2018	346	2018
Statistical assignment of DNA sequences using Bayesian phylogenetics K Munch, W Boomsma, JP Huelsenbeck, E Willerslev, R Nielsen Systematic biology 57 (5), 750-757, 2008	206	2008
A generative, probabilistic model of local protein structure W Boomsma, KV Mardia, CC Taylor, J Ferkinghoff-Borg, A Krogh, ... Proceedings of the National Academy of Sciences 105 (26), 8932-8937, 2008	189	2008
Combining experiments and simulations using the maximum entropy principle W Boomsma, J Ferkinghoff-Borg, K Lindorff-Larsen PLoS computational biology 10 (2), e1003406, 2014	165	2014
Structure of a functional amyloid protein subunit computed using sequence variation P Tian, W Boomsma, Y Wang, DE Otzen, MH Jensen, K Lindorff-Larsen Journal of the American Chemical Society 137 (1), 22-25, 2015	97	2015
Comparing molecular dynamics force fields in the essential subspace F Martín-García, E Papaleo, P Gomez-Puertas, W Boomsma, ... PLoS One 10 (3), e0121114, 2015	93	2015
Potentials of mean force for protein structure prediction vindicated, formalized and generalized T Hamelryck, M Borg, M Paluszewski, J Paulsen, J Frellsen, C Andreetta, ... PloS one 5 (11), e13714, 2010	91	2010
Beyond rotamers: a generative, probabilistic model of side chains in proteins T Harder, W Boomsma, M Paluszewski, J Frellsen, KE Johansson, ... BMC bioinformatics 11, 1-13, 2010	79	2010
Fast phylogenetic DNA barcoding K Munch, W Boomsma, E Willerslev, R Nielsen Philosophical Transactions of the Royal Society B: Biological Sciences 363 …, 2008	79	2008
Spherical convolutions and their application in molecular modelling W Boomsma, J Frellsen Advances in neural information processing systems 30, 2017	75	2017
The PCNA interaction motifs revisited: thinking outside the PIP-box A Prestel, N Wichmann, JM Martins, R Marabini, N Kassem, SS Broendum, ... Cellular and Molecular Life Sciences 76, 4923-4943, 2019	64	2019
ENCORE: software for quantitative ensemble comparison M Tiberti, E Papaleo, T Bengtsen, W Boomsma, K Lindorff-Larsen PLoS computational biology 11 (10), e1004415, 2015	63	2015
Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients E Jimenez-Solem, TS Petersen, C Hansen, C Hansen, C Lioma, C Igel, ... Scientific reports 11 (1), 1-12, 2021	62	2021
Inference of structure ensembles of flexible biomolecules from sparse, averaged data S Olsson, J Frellsen, W Boomsma, KV Mardia, T Hamelryck PloS one 8 (11), e79439, 2013	56	2013
Bayesian inference of protein ensembles from SAXS data LD Antonov, S Olsson, W Boomsma, T Hamelryck Physical Chemistry Chemical Physics 18 (8), 5832-5838, 2016	52	2016
PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure W Boomsma, J Frellsen, T Harder, S Bottaro, KE Johansson, P Tian, ... Journal of computational chemistry 34 (19), 1697-1705, 2013	48	2013
Probabilistic determination of native state ensembles of proteins S Olsson, BR Vögeli, A Cavalli, W Boomsma, J Ferkinghoff-Borg, ... Journal of Chemical Theory and Computation 10 (8), 3484-3491, 2014	42	2014
Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides H Safavi-Hemami, Q Li, RL Jackson, AS Song, W Boomsma, ... Proceedings of the National Academy of Sciences 113 (12), 3227-3232, 2016	41	2016
Learning meaningful representations of protein sequences NS Detlefsen, S Hauberg, W Boomsma Nature communications 13 (1), 1914, 2022	38	2022

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