Publications

A. Tomalka, O. Röhrle, J. C. Han, T. Pham, A. J. Taberner, und T. Siebert. Extensive eccentric contractions in intact cardiac trabeculae: revealing compelling differences in contractile behaviour compared to skeletal muscles. Proceedings of the Royal Society B, (286)1903:20190719, 2019. [PUMA: EXC2075 PN2 PN2A-1 selected] URL

Konstantin Gubaev, Viktor Zaverkin, Prashanth Srinivasan, Andrew Ian Duff, Johannes Kästner, und Blazej Grabowski. Performance of two complementary machine-learned potentials in modelling chemically complex systems. NPJ Computational Materials, (9):129, 2023. [PUMA: EXC2075 PN2 PN2-3(1) PN2-3A PN3 PN3-4 PN6 PN6-6 PN6A-1 selected] URL

André Tomalka, Maximilian Heim, Annika Klotz, Christian Rode, und Tobias Siebert. Ultrastructural and kinetic evidence support that thick filaments slide through the Z-disc. Interface : journal of the Royal Society, (19)197:20220642, The Royal Society, 2022. [PUMA: PN2 PN2A-1 EXC2075 selected] URL

Fleurianne Bertrand, Maximilian Brodbeck, und Tim Ricken. On robust discretization methods for poroelastic problems: Numerical examples and counter-examples. Examples and Counterexamples, (2):100087, Elsevier BV, November 2022. [PUMA: PN2-2A PN2 EXC2075 selected] URL

Daniela Stöhr, Jens O. Schmid, Tobias B. Beigl, Alexandra Mack, Daniela S. Maichl, Kai Cao, Beate Budai, Gavin Fullstone, Roland E. Kontermann, Thomas E. Mürdter, Stephen W. G. Tait, Cathrin Hagenlocher, Nadine Pollak, Peter Scheurich, und Markus Rehm. Stress-induced TRAILR2 expression overcomes TRAIL resistance in cancer cell spheroids. Cell Death & Differentiation, 27:3037–3052, 2020. [PUMA: PN2 EXC2075 selected] URL

Mohammad Azhdari, Seyed Morteza Seyedpour, Lena Lambers, Hans-Michael Tautenhahn, Franziska Tautenhahn, Tim Ricken, und Ghader Rezazadeh. Non-local three phase lag bio thermal modeling of skin tissue and experimental evaluation. International Communications in Heat and Mass Transfer, (149):107146, 2023. [PUMA: PN2-2A PN2 PN2-2(II) EXC2075 selected] URL

S. Adam, H. Anteneh, M. Hornisch, V. Wagner, J. Lu, N. Radde, P. Bashtrykov, J. Song, und A. Jeltsch. DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nature Communications, (11)1:1-15, Springer Science and Business Media LLC, 2020. [PUMA: PN2 PN2-9 EXC2075 PN2-1B selected]

Gavin Fullstone, Cristiano Guttà, Amatus Beyer, und Markus Rehm. The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. npj Systems Biology and Applications, (6)1:10--, 2020. [PUMA: PN2 EXC2075 selected] URL

Lena Lambers, Marlon Suditsch, Arndt Wagner, und Tim Ricken. A Multiscale and Multiphase Model of Function-Perfusion Growth Processes in the Human Liver. PAMM, (20)1Wiley, Januar 2021. [PUMA: PN2-2A PN2 EXC2075] URL

Gavin Fullstone, Tabea L. Bauer, Cristiano Guttà, Manuela Salvucci, Jochen H. M. Prehn, und Markus Rehm. The apoptosome molecular timer synergises with XIAP to suppress apoptosis execution and contributes to prognosticating survival in colorectal cancer. Cell Death & Differentiation, 27:2828–2842, 2020. [PUMA: PN2 EXC2075 PN2-1A selected] URL

Karsten Kuritz, Daniela Stöhr, Daniela Simone Maichl, Nadine Pollak, Markus Rehm, und Frank Allgöwer. Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities. Scientific Reports, (10)1:3619, Nature Publishing Group, Dezember 2020. [PUMA: PN2 EXC2075 selected] URL

Jan Range, Colin Halupczok, Jens Lohmann, Neil Swainston, Carsten Kettner, Frank T. Bergmann, Andreas Weidemann, Ulrike Wittig, Santiago Schnell, und Jürgen Pleiss. EnzymeML—a data exchange format for biocatalysis and enzymology. The FEBS Journal, (289)19:5864--5874, John Wiley & Sons, Ltd, Oktober 2022. [PUMA: PN2-6(II) PN2 EXC2075 selected] URL

André Tomalka, Sven Weidner, Daniel Hahn, Wolfgang Seiberl, und Tobias Siebert. Power Amplification Increases With Contraction Velocity During Stretch-Shortening Cycles of Skinned Muscle Fibers. Frontiers in Physiology, (12)Frontiers Media SA, März 2021. [PUMA: PN2 PN2A-1 EXC2075 selected] URL

André Tomalka, Sven Weidner, Daniel Hahn, Wolfgang Seiberl, und Tobias Siebert. Cross-Bridges and Sarcomeric Non-cross-bridge Structures Contribute to Increased Work in Stretch-Shortening Cycles. In Tobias Siebert (Hrsg.), Frontiers in Physiology, (11)Frontiers Media SA, Juli 2020. [PUMA: PN2 PN2A-1 EXC2075 selected] URL

Bruno Christ, Maximilian Collatz, Uta Dahmen, Karl-Heinz Herrmann, Sebastian Höpfl, Matthias König, Lena Lambers, Manja Marz, Daria Meyer, Nicole Radde, Jürgen R. Reichenbach, Tim Ricken, und Hans-Michael Tautenhahn. Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function. Frontiers in Physiology, (12)Frontiers Media SA, November 2021. [PUMA: PN2-2A PN2 EXC2075 selected] URL

Vincent Wagner, Sebastian Höpfl, Viviane Klingel, Maria C. Pop, und Nicole E. Radde. An inverse transformation algorithm to infer parameter distributions from population snapshot data. In Ioannis P. Androulakis Maria Klapa, Daniel P. Howsmon (Hrsg.), IFAC-PapersOnLine, (55)23:86-91, 2022. [PUMA: PN2 PN2-9 EXC2075 PN2-1B selected] URL

Lena Lambers, André Mielke, und Tim Ricken. Semi-automated Data-driven FE Mesh Generation and Inverse Parameter Identification for a Multiscale and Multiphase Model of Function-Perfusion Processes in the Liver. PAMM, (21)12021. [PUMA: PN2-2A PN2 misc EXC2075]

Vincent Wagner, Benjamin Castellaz, Marco Oesting, und Nicole Radde. Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation. Bioinformatics, (38)18:4352-4359, Oxford University Press, 2022. [PUMA: PN2 PN2-9 PN5 EXC2075 PN2-1B merged selected]

Matthew Millard, David W Franklin, und Walter Herzog. A three filament mechanistic model of musculotendon force and impedance. bioRxiv, Cold Spring Harbor Laboratory, 2023. [PUMA: PN2 PNX EXC2075] URL

Julio Vera, Xin Lai, Andreas Baur, Michael Erdmann, Shailendra Gupta, Cristiano Guttà, Lucie Heinzerling, Markus V Heppt, Philipp Maximilian Kazmierczak, Manfred Kunz, Christopher Lischer, Brigitte M Pützer, Markus Rehm, Christian Ostalecki, Jimmy Retzlaff, Stephan Witt, Olaf Wolkenhauer, und Carola Berking. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Briefings in Bioinformatics, Oktober 2022. [PUMA: PN2 EXC2075 PN2-1A selected] URL