About me - ORCID
As of October 1st 2020, I am Assistant Professor at Chalmers University of Technology. More updates to come.
Job openings: PhD 1 and PhD 2
Affiliations
2020/10; Assistant Professor. Chalmers University of Technology, Department of Computer Science and Engineering, Section for Data Science and AI.
2016/03-2020/09; Postdoc. Computational Molecular Biology Group, Freie Universität Berlin. (w. Frank Noé)
2014/03-2016/02; Postdoc. Laboratory of Physical Chemistry, Eidgeniössische Technische Hochschule Zürich, Switzerland (w. Roland Riek)
2013/09-2016/02; Postdoc. Computational Structural Biology group, IRB, Universita della Svizzera italiana, Bellinzona, Switzerland. (w. Andrea Cavalli)
2013/04-2013/08; Postdoc. Bioinformatics Center, University of Copenhagen, Denmark.
2012/07; Visiting scholar at the Theobald lab, Biochemistry section, Brandeis University, Waltham, MA USA.
2010/04-2013/04; PhD. student at Structural Bioinformatics, University of Copenhagen, Denmark (supervisor: Thomas Hamelryck)
2008-10; Masters student at SBiN-Lab, University of Copenhagen, Denmark (supervisor: Flemming Poulsen, Kaare Teilum)
2007; Bachelor student at SBiN-Lab, University of Copenhagen, Denmark (supervisor: Flemming Poulsen)
2007; ERASMUS Student w. R. Konrat lab at MFPL in Vienna, Austria
Raich L, Meier K, Gunther J, Christ CD, Noe F*, Olsson S* "Discovery of a hidden transient state in all bromodomain families" pre-print
Peer-reviewed
Noe F*#, Olsson S#, Kohler J#, Hao W "Boltzmann Generators: Sampling Equilibrium States of Many-Body Systems with Deep Learning" Science (2019) 365, eaaw1147. doi: 10.1126/science.aaw1147pre-print
Olsson S*, Noe F* "Dynamic Graphical Models of Molecular Kinetics" Accepted Proc. Natl. Acad. Sci. U.S.A., (2019) doi; 10.1073/pnas.1901692116. pre-print
Wang L, Olsson S, Wehmeyer C, Perez A, Charron N, De Fabritiis G, Noe F*, Clementi C*. "Machine Learning of coarse-grained Molecular Dynamics Force Fields" ACS Central Science (2019). doi: 10.1021/acscentsci.8b00913. pre-print
Wehmeyer C*#, Scherer MK#, Hempel T#, Husic BE, Olsson S, Noe F "Introduction to Markov state modeling with the PyEMMA software" LiveComs (2018). doi: 10.33011/livecoms.1.1.5965
Gerber S#, Olsson S#, Noe F, Horenko I "A scalable approach to the computation of invariant measures for high-dimensional Markovian systems" Scientific Reports (2018) 8, 1796. doi: 10.1038/s41598-018-19863-4 . pre-print
Nichols P, Born A, Henen M, Strotz D, Orts J, Olsson S, Guntert P, Chi C, Vogeli B "The Exact NOE: Recent Advances" Molecules, 2017, 22, 7, 1176. doi: 10.3390/molecules22071176
Olsson S; Wu H; Paul F; Clementi C; Noe F "Combining Experimental and Simulation Data of Molecular Processes via Augmented Markov Models" Proc. Natl. Acad. Sci. U.S.A. (2017), 114(31), pp. 8265-8270. doi: 10.1073/pnas.1704803114
Olsson S; Noe F "Mechanistic models of chemical exchange induced relaxation in protein NMR" J. Am. Chem. Soc. (2017), 139 (1), pp 200-210. doi: 10.1021/jacs.6b09460
Olsson S; Strotz D; Vogeli B; Riek R; Cavalli A "The dynamic basis for signal propagation in human Pin1-WW." Structure, 2016, 24, pp. 1464-1475 doi: doi: 10.1016/j.str.2016.06.013
Antonov LD; Olsson S; Boomsma W; Hamelryck T. "Bayesian inference of protein ensembles from SAXS data" PCCP, 2016, 18, pp. 5832-5838. doi: 10.1039/C5CP04886A
Vogeli B; Olsson S; Guntert P; Riek R "The exact NOE as an alternative in ensemble structure determination" Biophys. J., 2016, 110, pp. 113-126. doi: 10.1016/j.bpj.2015.11.031
Sgrignani J; Olsson S; Ekonomiuk D; Genini D; Krause R; Catapano CV; Cavalli A "Molecular determinants for unphosphorylated STAT3 dimerization by integrative modeling" Biochemistry, 2015, 54, pp. 5489-5501 doi: 10.1021/bi501529x
Olsson S; Cavalli A. "Quantification of entropy-loss in replica-averaged modeling." J. Chem. Theory Comput., 2015, 11, pp. 3973-3977 doi: 10.1021/acs.jctc.5b00579
Vogeli B; Olsson S; Riek R; Guntert P "Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics" J. Struct. Biol., 2015, 191, pp. 306-317 doi: 10.1016/j.jsb.2015.07.008. Associated Data in Brief content doi: 10.1016/j.dib.2015.08.020
Olsson S; Ekonomiuk D; Sgrignani J; Cavalli A "Molecular dynamics of biomolecules through direct analysis of dipolar couplings" J. Am. Chem. Soc., 2015, 137, pp. 6270-6278. doi: 10.1021/jacs.5b01289
Olsson S; Vogeli B; Cavalli A; Boomsma W; Ferkinghoff-Borg J; Lindorff-Larsen K; Hamelryck T. "Probabilistic Determination of Native State Ensembles of Proteins." J. Chem. Theory Comput., 2014, 10 (8), pp 3484-3491. doi: 10.1021/ct5001236
Olsson S; Frellsen J; Boomsma W; Mardia KV; Hamelryck T. "Inference of structure ensembles of flexible biomolecules from sparse, averaged data." PLoS ONE, 2013, 8(11): e79439, doi: 10.1371/journal.pone.0079439
Boomsma W; Frellsen J; Harder T; Bottaro S; Johansson KE; Tian P; Stovgaard K; Andreetta C; Olsson S; Valentin J; Antonov LD; Christiansen AS ;Borg M; Jensen JH; Lindorff-Larsen K;Ferkinghoff-Borg J; Hamelryck T. "PHAISTOS: A Framework for Markov Chain Monte Carlo Simulation and Inference of Protein Structure" J. Comput. Chem., 2013, 34 pp. 1697-1705 doi: 10.1002/jcc.23292
Harder T; Borg M; Bottaro S; Boomsma W; Olsson S; Ferkinghoff-Borg J; Hamelryck T, "An efficient null model for conformational fluctuations in proteins" Structure, 2012, 20, pp. 1028-1039. doi: 10.1016/j.str.2012.03.020
Olsson S; Boomsma W; Frellsen J; Bottaro S; Harder T; Ferkinghoff-Borg J; Hamelryck T, "Generative probabilistic models extend the scope of inferential structure determination" J. Magn. Reson., 2011, 213, pp. 182-186 doi: 10.1016/j.jmr.2011.08.039 GPM.pdf GPM_suppl.pdf
Contributions to conference proceedings:
Olsson S; Hamelryck T. "On the significance of the reference ratio method in inferential structure determination of biomolecules." Proceedings of the 32nd Leeds Annual Statistical Research Workshop Statistical Models and Methods for non-Euclidean Data with Current Scientific Applications, 2013, pp. 65-68. PDF. full proceedings.
Grants and honors
2017; Alexander von Humboldt postdoctoral fellowship
2016-2017; DRS POINT-MarieCurie COFUND Fellowship
2014-2016; Individual Postdoc grant from the Danish Council for Independent Research (Awarded amount: DKK 1.672.593)
2007; ERASMUS Stipend from the European Union
Contributions to open-source software
Phaistos - Markov chain Monte Carlo framework for protein simulations.
Almost - Molecular dynamics framework for biomolecular simulations.
PyEMMA - a python library for estimation, validation and analysis of Markov state models.