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MV Barbarossa and J Fuhrmann, Germany's next shutdown - possible scenarios and outcomes, Influenza and Other Respiratory Viruses (2020) https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.12827  

J Fuhrmann and MV Barbarossa, The significance of case detection ratios for predictions on the outcome of an epidemic - a message from mathematical modelers. Arch Public Health 78, 63 (2020). https://doi.org/10.1186/s13690-020-00445-8 . 

  

MV Barbarossa, J Fuhrmann, J Meinke, S Krieg, HV Varma, N Castelletti, and Th Lippert, Modeling the spread of COVID-19 in Germany: Early assessment and possible scenarios, PLoS ONE 15(9): e0238559(2020). 

J Bracher, D Wolffram, J Deuschel, K Görgen, JL Ketterer, A Ullrich, S Abbot, MV Barbarossa, et al., Short-term forecasting of COVID-19 in Germany and Poland during the second wave – a preregistered study, submitted (2020).  

MV Barbarossa, N Bogya, A Dénes, G Röst, H Vinod Varma, Zs Vizi, Fleeing lockdown and its impact on the size of epidemic outbreaks in the source and target regions - a COVID-19 lesson, submitted (2020) .

  

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Straub B., Schneider G. (2020) A model for the study of the increase in stimulus and change point detection with small and variable spiking delays.  Neural Computation 32, 1277-1321.  

Ratke, Krämer and Strobl (2020) – Simultaneous Live Imaging of Multiple Insect Embryos in Sample Chamber-Based Light Sheet Fluorescence Microscopes – JoVE – (doi: 10.3791/61713) 

Beata Turoňová, Mateusz Sikora, Christoph Schürmann, Wim J. H. Hagen, Sonja Welsch, Florian E. C. Blanc, Sören von Bülow, Michael Gecht, Katrin Bagola, Cindy Hörner, Ger van Zandbergen, Jonathan Landry, Nayara Trevisan Doimo de Azevedo, Shyamal Mosalaganti, Andre Schwarz, Roberto Covino, Michael D. Mühlebach, Gerhard Hummer, Jacomine Krijnse Locker, and Martin Beck. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges - Science 370(6513) 203 (2020).

 

Schätzle, Hannah, et al. "Functional Diversity of TonB-Like Proteins in the Heterocyst-Forming Cyanobacterium Anabaena sp. PCC 7120." Msphere 6.6 (2021): e00214-21. 

Pereyra, Drusko, Krämer, Strobl, Stelzer and Matthäus (2021) – QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis – BMC Bioinformatics – (doi: 10.1186/s12859-021-04474-0).  

L. Hof, T. Moreth, M. Koch, T. Liebisch, M. Kurtz, J. Tarnick, S.M. Lissek, M.M.A. Verstegen, L.J.W. van der Laan, M. Huch, F. Matthäus, E.H.K. Stelzer, F. Pampaloni, Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis, BMC Biology 19(37), 2021.  

EHK Stelzer, F Strobl, BJ Chang, F Preusser, S. Preibisch, K. McDole, R. Fiolka. „Light sheet fluorescence microscopy.”  Nature Reviews Methods Primers 1, Art. no. 73, 2021.  

F Strobl, EHK Stelzer. “A deterministic genotyping workflow reduces waste of transgenic individuals by two-thirds” - Scientific reports 11, Art. No. 15325, 2021.  

M. V. Barbarossa, N. Bogya, A. Dénes, G. Röst, H. Vinod Varma and Zs. Vizi, Fleeing lockdown and its impact on the size of epidemic outbreaks in the source and target regions - a COVID-19 lesson, Sci Rep 11, 9233 (2021) open access.  

M. V. Barbarossa and J. Fuhrmann, Germany's next shutdown - possible scenarios and outcomes, Influenza and Other Respi Viruses 15(3):326-330 (2021) open access.  

M. V. Barbarossa and J. Fuhrmann, Compliance with NPIs and possible deleterious effects on mitigation of an epidemic outbreak, Infectious Disease Modelling 6: 859-874 (2021) open access.  

J. Heidecke and M. V. Barbarossa; When ideas go viral – complex bifurcations in a two-stage transmission model, in Trends in Biomathematics, Chaos and Control in Epidemics, Ecosystems and Cells, Edited by R. Mondaini, Springer Nature (2021).  

J Bracher, D Wolffram, J Deuschel, K Görgen, JL Ketterer, A Ullrich, et al. A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave, Nature communications 12 (1), 1-16 (2021) open access.

A Coulibaly, SY Velásquez, N Kassner, J Schulte, MV Barbarossa, HA Lindner, STAT3 governs the HIF-1α response in IL-15 primed human NK cells. Scientific Reports 11 (7023) open access.  

Ghamari D, Hauke P, Covino R^†, and Faccioli P^†. Sampling rare conformational transitions with a quantum computer. arXiv: 2201:11781 (^†shared corresponding authors).

Jung H*, Covino R*, Arjun A, Bolhuis P, and Hummer G (2021) Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments. arXiv 2105.06673 (*shared first authors).

Iruegas R, Dosch J, Sikora M, Hummer G, Covino R, and Ebersberger I (2021) The evolutionary making of SARS-CoV-2 (bioRxiv preprint).

Väth K, Mattes C, Reinhard J, Covino R, Stumpf H, Hummer G, and Ernst R (2021) Systematic cysteine-crosslinking in native membranes establishes the transmembrane architecture in Ire1 clusters. Journal of Cell Biology 220 (8).  

Sikora M*, Blanc FEC*, von Bülow S*, Gecht M*, Covino R*, and Hummer G (2021) Maps of SARS-CoV-2 spike epitopes not shielded by glycans. PLoS Computational Biology 17(4) e1008790 (*shared first authors).  

P. A. Vainikka, S. Thallmair, P. C. T. Souza, S. J. Marrink, Martini 3 coarse-grained model for type III deep eutectic solvents: Thermodynamic, structural, and extraction properties, ACS Sustainable Chem. Eng. 9, 17338 (2021), doi: 10.1021/acssuschemeng.1c06521.   

C. Ramírez Palacios, H. Wijma, S. Thallmair, S. J. Marrink, D. B. Janssen, Computational prediction of ω-transaminase specificity by a combination of docking and molecular dynamics simulations, J. Chem. Inf. Model. 61, 5569 (2021), doi: 10.1021/acs.jcim.1c00617.

Q. Meng, C. Ramírez Palacios, N. Capra, M. Hooghwinkel, S. Thallmair, H. Rozeboom, A.-M. Thunnissen, H. Wijma, S. J. Marrink, D. B. Janssen, Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines, ACS Catal. 11, 10733 (2021), doi: 10.1021/acscatal.1c02053.

S. Thallmair, M. Javanainen, B. Fábián, H. Martinez-Seara, S. J. Marrink, Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations, J. Phys. Chem. B 125, 9537 (2021), doi: 10.1021/acs.jpcb.1c03665.

P. Kobauri, W. Szymanski, F. Cao, S. Thallmair, S. J. Marrink, M. D. Witte, F. J. Dekker*, B. L. Feringa, Biaryl Sulfonamides as Cisoid Azosteres for Photopharmacology, Chem. Commun. 57, 4126 (2021), doi: 10.1039/D1CC00950H.  

P. C. T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, F. Grunewald, I. Patmanidis, H. Abdizadeh, B. M. H. Bruininks, T. A. Wassenaar, P. C. Kroon, J. Melcr, V. Nieto, V. Corradi, H. M. Khan, J. Domański, M. Javanainen, H. Martinez-Seara, N. Reuter, R. B. Best, I. Vattulainen, L. Monticelli, X. Periole, D. P. Tieleman, A. H. de Vries, S. J. Marrink, Martini 3: A General Purpose Force Field for Coarse-Grain Molecular Dynamics, Nat. Methods 18, 382 (2021), doi: 10.1038/s41592-021-01098-3.