T. Liebisch, A. Drusko, B. Mathew, E. H. K. Stelzer, S. C. Fischer, F. Matthäus, Cell fate clusters in ICM organoids arise from cell fate heredity & division – a modelling approach, Sci. Rep. 10:22405, 2020.  

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) .

  

Messer M., Backhaus H., Fu T., Stroh A., Schneider G. (2020) A multi scale approach for testing and detecting peaks in time series. Statistics.  

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.  

Timon, L. B., Ekelmans, P., Konrad, S., Nold, A., & Tchumatchenko, T. (2022). Synaptic plasticity

controls the emergence of population-wide invariant representations in balanced network models. Physical Review Research, 4(1), 013162.

 

Bernaez Tim on, L., Ekelmans, P., Kraynyukova, N., Rose, T., Busse, L., & Tchumatchenko, T. (2022). How to incorporate biological insights into network models and why it matters. The Journal of Physiology    

 

Engineering Uniform Sampling of Graphs with a Prescribed Power-law Degree Sequence. Daniel Allendorf, Ulrich Meyer, Manuel Penschuck, Hung Tran, and Nick Wormald. SIAM Symposium on Algorithm Engineering and Experiments (ALENEX), 2022.

 

Parallel Global Edge Switching for the Uniform Sampling of Simple Graphs with Prescribed Degrees. Daniel Allendorf, Ulrich Meyer, Manuel Penschuck, and Hung Tran. 36th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2022.

 

Recent Advances in Scalable Network Generation. Manuel Penschuck, Ulrik Brandes, Michael Hamann, Sebastian Lamm, Ulrich Meyer, Ilya Safro, Peter Sanders, and Christian Schulz. In David A. Bader (Ed.): Massive Graph Analytics. 2022.

 

Efficiently generating geometric inhomogeneous and hyperbolic random graphs. Thomas Bläsius, Tobias Friedrich, Maximilian Katzmann, Ulrich Meyer, Manuel Penschuck, and Christopher Weyand. Network Science, 2022.

 

Generating Synthetic Graph Data from Random Network Models. Ulrich Meyer, and Manuel Penschuck. Algorithms for Big Data, 2022.

 

Sampling Rare Conformational Transitions with a Quantum Computer

Danial Ghamari, Philipp Hauke, Roberto Covino†, Pietro Faccioli† (†shared corresponding authors).

Scientific Reports 12, 16336 (2022) 

Information-theoretical measures identify accurate low-resolution representations of protein configurational space

Margherita Mele, Roberto Covino, Raffaello Potestio.

Soft Matter, 18, 7064-7074 (2022) 

Simulation-based inference of single-molecule force spectroscopy

Lars Dingeldein, Pilar Cossio, Roberto Covino. 

arXiv: 2209.10392

 

Co-Autorschaft Franziska Krämer bei Publikation zum Thema „Always On – Next generation marker-based vector concepts for high accuracy, high throughput genotyping of up to two independent transgenes” (Erstautor Frederic Strobl, Letztautor Ernst Stelzer), z.Z. im Peer-Review

 

V. Thallmair, L. Schultz, W. Zhao, S. J. Marrink, D. Oliver, S. Thallmair, Two Cooperative Binding Sites Sensitize PI(4,5)P2 Recognition by the Tubby Domain, Sci. Adv. 8, eabp9471 (2022), doi: 10.1126/sciadv.abp9471. - J. Volarić, S. Thallmair, B. L. Feringa, W. Szymanski, Photoswitchable, Water-soluble Bis-azobenzene Cross-linkers with Enhanced Properties for Biological Applications, ChemPhotoChem 6, e202200170 (2022), doi: 10.1002/cptc.202200170. - B. Fábián, S. Thallmair, G. Hummer, Small Ionic Radii Limit Time Step in Martini 3 Molecular Dynamics Simulations, J. Chem. Phys. 157, 034101 (2022), doi: 10.1063/5.0095523. - J. Losa, S. Leupold, D. Alonso-Martinez, P. Vainikka, S. Thallmair, K. M. Tych, S. J. Marrink, M. Heinemann, Perspective: A Stirring Role for Metabolism in Cells, Mol. Syst. Biol. 18, e10822 (2022), doi: 10.15252/msb.202110822. - P. Kobauri, N. S. Galenkamp, A. M. Schulte, J. de Vries, N. A. Simeth, G. Maglia, S. Thallmair, D. Kolarski, W. Szymanski, B. L. Feringa, Hypothesis-Driven, Structure-Based Design in Photopharmacology: The Case of eDHFR Inhibitors, J. Med. Chem. 65, 4798 (2022), doi: 10.1021/acs.jmedchem.1c01962. - F. Azadi-Chegeni, S. Thallmair, M. E. Ward, G. Perin, S. J. Marrink, M.Baldus, T. Morosinotto, A. Pandit, Protein Dynamics and Lipid Affinity of Monomeric Zeaxanthin- Binding LHCII in Thylakoid Membranes, Biophys. J. 121, 396 (2022), doi: 10.1016/j.bpj.2021.12.039.

 

Alessandro T Gifford, Benjamin Lahner, Sari Saba-Sadiya, Martina G Vilas, Alex Lascelles, Aude Oliva, Kendrick Kay, Gemma Roig, Radoslaw M Cichy. The Algonauts Project 2023 Challenge: How the Human Brain Makes Sense of Natural Scenes. arXiv preprint

Marco Seiler und Anja Sturm “Contact process on a dynamical long range percolation”, Electronic Journal of Probability, 28: 1-36 (2023)

 

Frederic Strobl, Julia Ratke, Franziska Krämer, Ana Utta, Sigrun Becker and Ernst H.K. Stelzer (2023) – Next generation marker-based vector concepts for rapid and unambiguous identification of single and double homozygous transgenic organisms – Biology Open – (doi: 10.1242/bio.060015)

 

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.

 

T. Liebisch, A. Drusko, B. Mathew, E. H. K. Stelzer, S. C. Fischer, F. Matthäus, Cell fate clusters in ICM organoids arise from cell fate heredity & division – a modelling approach, Sci. Rep. 10:22405, 2020.

 

Gübert J.*, Schneider G.*, Hahn-Klimroth M., Dierkes P. (2023) Nocturnal behavioral patterns of African ungulates in zoos Ecology and Evolution. 13:e10777 *equal contribution

 

Visual features are processed before navigational affordances in the human brain. K Dwivedi, S Sadiya, MP Balode, G Roig, RM Cichy. (2024) Scientific Reports 14 (1), 5573

 

Different Algorithms (Might) Uncover Different Patterns: A Brain-Age Prediction Case Study. T Ettling, S Saba-Sadiya, G Roig. 2023 IEEE International Conference on Bioinformatics and Biomedicine

 

L. Borges-Araújo, A. C. Borges Araújo, T. Ozturk, D. P. Ramirez-Echemendia, B. Fábián, T. Carpenter, S. Thallmair, J. Barnoud, H. Ingólfsson, G. Hummer, D. P. Tieleman, S. Marrink, P. C. Souza, M. Melo, “Martini 3 coarse-grained force field for cholesterol,” J. Chem. Theory Comput. 19, 7387-7404 (2023). [https://doi.org/10.1021/acs.jctc.3c00547]

H. Jung, R. Covino, A. Arjun, C. Leitold, C. Dellago, P. G. Bolhuis, G. Hummer, “Machine-guided path sampling to discover mechanisms of molecular self-organization,” Nat. Comput. Sci. 3, 334-345 (2023). [https://doi.org/10.1038/s43588-023-00428-z]

B. Fábián, S. Thallmair, G. Hummer, “Optimal bond-constraint topology for molecular dynamics simulations of cholesterol,” J. Chem. Theory Comput. 19, 1592-1601 (2023). [https://doi.org/10.1021/acs.jctc.2c01032]

S. von Bülow, M. Sikora, F. E. C. Blanc, R. Covino, G. Hummer, “Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants,” PLOS Comput. Biol. 19, e1010822 (2023). [https://doi.org/10.1371/journal.pcbi.1010822]

 

Muñoz-García, J. & Ares, S. (2016). Formation and maintenance of nitrogen-fixing cell patterns in filamentous cyanobacteria PNAS 113 (22) 6218-6223;  https://doi.org/10.1073/pnas.1524383113

Malatinszky D, Steuer R, Jones PR. (2017). A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. Plant Physiol. 173 (1): 509-523. doi: 10.1104/pp.16.01487. Epub 2016 Nov 29. PMID: 27899536; PMCID: PMC5210747

Bandyopadhyay A, Ye Z,Benedikty Z, Trtilek M, Pakrasi HB. (2021) Antenna Modification Leads to Enhanced Nitrogenase Activity in a High Light-Tolerant Cyanobacterium. mBio 12:e03408-21. https://doi.org/10.1128/mbio.03408-21

Kuniyoshi et. al. (2011) 2-oxoglutarate enhances NtcA binding activity to promoter regions of the microcystin synthesis gene clusters. FEBS Letters, 585 (24): 3921-3926, https://doi.org/10.1016/j.febslet.2011.10.034

Wilcox, M., Mitchison, G. J. & Smith, R. J. (1973). Pattern formation in the blue-green alga Anabaena. I. Controlled proheterocyst regression. J. Cell Sci. 13 637-649

 

Woo, T, Liang, X, Evans, D, Fernandez, O, Kretschmer, F, Reiter S and Laurent, G. (2023). The Dynamics of PaKern Matching in Camouflaging CuKlefish. Nature.

 

Ghamari D, Covino R, Faccioli P (2023) Sampling a rare protein transition with a hybrid classical-quantum computing algorithm. arXiv: 2311.15891 – in press in the Journal of Chemical Theory and Computation.

 

Lazzeri G, Jung H, Bolhuis P G, Covino R (2023) Molecular free energies, rates, and mechanisms from data-efficient path sampling simulations. Journal of Chemical Theory and Computation 19, 24, 9060–9076. DOI: 10.1021/acs.jctc.3c00821.

 

Nishimura T‡, Lazzeri G, Covino R‡, Tooze S (2023) Unique Amphipathic α-helix Drives Membrane Insertion and Enzymatic Activity of ATG3. Science Advances 9, eadhi281 (‡ shared corresponding author).

 

Jung H*, Covino R*, Arjun A, Leitlold C, Dellago C, Bolhuis P, Hummer G (2023) Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 3, 334-345 (* shared first author).

 

Dingeldein L, Cossio P, Covino R (2023) Simulation-based inference of single-molecule force spectroscopy. Machine Learning Science and Technology 4 025009.

 

von Bülow S, Sikora M, Blanc FEC, Covino R, Hummer G (2023) Maps of SARS-CoV-2 spike epitopes not shielded by glycans. PLoS Computational Biology 19(1) e1010822

 

Li Y, Arghittu S M, Dietz M S, Hasse D, Ferraris D M, Freund P, Barth H, Niemann H H, Covino R‡, Heilemann M‡ (2023) Single-molecule FRET and molecular dynamics simulations reveal early activation steps of MET receptor by Listeria monocytogenes. bioRxiv: 10.1101/2023.12.22.572978.

Hornegger H, Muratovic A, Anisimova A, Burgeois B, Spinetti E, Covino R, Madl T, Karagöz E (2023) IGF2BP1 phosphorylation regulates ribonucleoprotein condensate formation by impairing low-affinity protein and RNA interactions. bioRxiv: 10.1101/2023.12.05.570121v1.

Manger S, Arghittu S M, Sprankel L, Meier-Credo J, Wieland K, Bublak D, Schwalm M, Knapp S, Langer J, Covino R‡, Frangakis A‡ (2023) P116 from Mycoplasma is a self-sufficient lipid uptake and delivery machinery. bioRxiv: 10.1101/2023.10.24.563710.

Kettel P, Marosits L, Spinetti E, Rechberger M, Radler P, Niedermoser I, Fischer I, Versteeg G A, Loose M, Covino R, Karagoz G E (2023) Stress-induced clustering of the UPR sensor IRE1 is driven by disordered regions within its ER lumenal domain. bioRxiv: 10.1101/2023.03.30.534746v1.

L. Borges-Araújo, A. Borges-Araújo, T. Ozturk, D. P. Ramirez-Echemendia, B. Fábián, T.

S. Carpenter, S. Thallmair, J. Barnoud, H. I. Ingólfsson, G. Hummer, D. P. Tieleman, S. J.

Marrink, P. C. T. Souza, M. N. Melo, Martini 3 Coarse-Grained Force Field for

Cholesterol, J. Chem. Theory Comput. 19, 7387 (2023), doi: 10.1021/acs.jctc.3c00547.

 

V. Thallmair, L. Schultz, S. Evers, T. Jolie, C. Goecke, M. G. Leitner, S. Thallmair, D.

Oliver, Localization of the Tubby Domain, a PI(4,5)P2 Biosensor, to E-Syt3-rich ER-PM

Junctions, J. Cell Sci. 136, jcs260848 (2023), doi: 10.1242/jcs.260848.

 

S. Emmert, G. Quargnali, S. Thallmair, P. Rivera-Fuentes, A Locally Activatable Sensor

for Robust Quantification of Organellar Glutathion, Nat. Chem. 15, 1415 (2023), doi:

10.1038/s41557-023-01249-3.    

 

B. Fábián, S. Thallmair, G. Hummer, Optimal bond-constraint topology for molecular

dynamics simulations of cholesterol, J. Chem. Theory Comput. 19, 1592 (2023), doi:

10.1021/acs.jctc.2c01032.

 

R. Alessandri, S. Thallmair, C. Gil Herrero, R. Mera-Adasme, S. J. Marrink, P. C. T. Souza,

A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding

Simulations, in "A Practical Guide to Recent Advances in Multiscale Modeling and

Simulation of Biomolecules" edited by Y. Wang, R. Zhou, AIP Publishing, Melville, New

York, pp. 1-1—1-34 (2023), doi: 10.1063/9780735425279_001.

 

Parallel and I/O-Efficient Algorithms for Non-Linear Preferential Attachment. D. Allendorf, U. Meyer, M. Penschuck, and H. Tran. SIAM Symposium on Algorithm Engineering and Experiments (ALENEX), 2023.

 

Certifying Induced Subgraphs in Large Graphs. U. Meyer, H. Tran, and K. Tsakalidis. 17^th International Conference and Workshops on Algorithms and Computation (WALCOM), 2023. Full version accepted for Journal of Graph Algorithms and Applications (JGAA).

 

Parallel global edge switching for the uniform sampling of simple graphs with prescribed degrees. D. Allendorf, U. Meyer, M. Penschuck, and H. Tran. Journal of Parallel and Distributed Computing (JPDC), 2023

 

PACE Solver Description: Exact (GUTHMI) and Heuristic (GUTHM). A. Leonhardt, H. Dell, A. Haak, F. Kammer, J. Meintrup, U. Meyer, and M. Penschuck. 18th International Symposium on Parameterized and Exact Computation (IPEC), 2023

 

Spatial Invasion of Cooperative Parasites. V. Brouard, C. Pokalyuk, M. Seiler, and H. Tran. 2023, submitted.

 

Insights into (k, ρ)-shortcutting algorithms. A. Leonhardt, U. Meyer, and M. Penschuck. 2023/24, submitted.

 

Ekelmans P, Kraynyukova N, Tchumatchenko T (2023) Targeting operational regimes of interest in recurrent neural networks. PLOS Computational Biology 19(5): e1011097. https://doi.org/10.1371/journal.pcbi.1011097