Publications

Students publications

Nicolò Cogno Cogno, N. et al., “A 3D Agent-Based Model of Lung Fibrosis”. Symmetry, 2022 DOI
Cogno, N. et al., “An Agent-Based Model of Radiation-Induced Lung Fibrosis” Int. J. Mol. Sci., 2022 DOI
Cogno, N. et al., “Mechanistic model of radiotherapy-induced lung fibrosis using coupled 3D agent-based and Monte Carlo simulations”. Commun Med (Lond), 2024 DOI
Cogno, N. et al., “Recipes for calibration and validation of agent-based models in cancer biomedicine”. ArXiv, 2023 DOI
Maruthi Kumar Mamberti, Stefania, et al. “The Chromatin Architectural Protein CTCF Is Critical for Cell Survival upon Irradiation-Induced DNA Damage.” International Journal of Molecular Sciences, 2022 DOI
Pabba, Maruthi Kumar, et al. “Replisome loading reduces chromatin motion independent of DNA synthesis.” bioRxiv, 2023. DOI
Pabba, MK et al., “DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.” Histochem Cell Biol. 2024 DOI
Ritter, C., Lee, J. Y., Pham, M. T., Pabba, M. K., Cardoso, M. C., Bartenschlager, R., & Rohr, K., “Multi-detector fusion and Bayesian smoothing for tracking viral and chromatin structures.” Medical Image Analysis, 2024 DOI
Maria Arroyo, Corella S Casas-Delucchi, Maruthi K Pabba, et al., “Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome”, Nucleic Acids Research, 2024 DOI
Pabba, M. et al. “Super-resolution compatible DNA labeling technique reveals chromatin mobility and organization changes during differentiation.” bioRxiv, 2025 DOI
Romero, H., Amiri, A., Pabba, M. K. et al. “Chromatin organization controls nuclear stiffness.” bioRxiv, 2025 DOI
Jorge Lerma Romero Lerma Romero JA, et al. “Binding pocket stabilization by high-throughput screening of yeast display libraries.” Front Mol Biosci., 2022 DOI
Lerma Romero JA, et al. “Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening”. Methods Mol Biol., 2023 DOI
Lerma Romero JA, et al. “A protein engineering approach towards understanding FKBP51 conformational dynamics and mechanisms of ligand binding”. Protein Eng Des Sel., 2023 DOI
Andreas Zhadan Arroyo, M., Hastert, F.D. et al. “Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation.” Nat Commun, 2022 DOI
Hastert, F., Weber, J., Bauer, C., Zhadan, A., et al. “TET dioxygenases localize at splicing speckles and promote RNA splicing”bioRxiv, 2025 DOI
Vanessa Buffa Buffa, V., Knaup, F.H., et al.“Analysis of the Selective Antagonist SAFit2 as a Chemical Probe for the FK506-Binding Protein” ACS pharmacology & translational science, 2023 DOI
Alina Kuzembayeva Lehr, François-Xavier; Kuzembayeva, Alina et al., “Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering.” ACS Synthetic Biology, 2021 DOI
Lisa-Marie Maurer & Daniel Kelvin Kraus, L. et al., “Development of a novel tobramycin dependent riboswitch.” Nucleic Acids Research, 2023 DOI
Lisa-Marie Maurer Vockenhuber, M. P., Hoetzel, J., Maurer, L. M. et al., “A Novel RNA Aptamer as Synthetic Inducer of DasR Controlled Transcription.” ACS synthetic biology, 2024 DOI
Daniel Kelvin Kelvin, D. et al., “Synthetic Dual-Input Hybrid Riboswitches─Optimized Genetic Regulators in Yeast” ACS Synth Biol. 2025
Gréta Szabó Gréta V. Szabo and Thomas P. Burg, “Time Resolved Cryo-Correlative Light and Electron Microscopy”, Advanced Functional Materials, 2024 DOI
Thiem, DB, Szabo, G., Burg, TP “Model-Based Optimization of Solid-Supported Micro-Hotplates for Microfluidic Cryofixation”Micromachines (Basel), 2024 DOI
Klara Eisenhauer Eisenhauer, K. et al. “Scaling the Functional Nanopore (FuN) Screen: Systematic Evaluation of Self-Assembling Membrane Peptides and Extension with a K+-Responsive Fluorescent Protein Sensor” ACS Synth Biol., 2024 DOI
Simon Greulich Vinh, Trinh Quang et al. “Light reflection spectra as a tool for direct and real-time determination of biomass and pigments in the microalgae Microchloropsis salina” Lighting Research & Technology, 2021 DOI
Pappert, I., Greulich, S. et al.“Protein Expression in Synechococcus PCC 7002: A Quantitative Comparison of Promoters and Integration Sites.” Journal of Advances in Biology & Biotechnology, 2023 DOI
Simon Greulich and Ralf Kaldenhoff: “Staxanthin synthesis in Synechococcus PCC7002: Optimization and Product Secretion to Culture Medium”. J. of Adv. Res., 2024 DOI
Niko Faul Faul, N. et al. “Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives”. J Struc Biol, 2025 DOI
Mojiri, S., Dobbs, J., Faul, N., Burg, T.P. et al. “Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy”. biorxiv, 2025 DOI
Maik Molderings Engelmann, N., Molderings, M., Koeppl, H. “Tuning Ultrasensitivity in Genetic Logic Gates Using Antisense RNA Feedback”. ACS Synthetic Biology, 2025 DOI
Arooj Sajjad Fehlinger, S., Cui, K., Sajjad, A. et al. “Fluctuation induced network patterns in active matter with spatially correlated noise”. Soft Matter, 2025 DOI
Angela Kühn T. M. Geiger, M. Walz, C. Meyners, A. Kuehn et al.“Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51)”, Angew. Chem. Int. Ed. 2024 DOI
Olga Becker Bruckhoff RW, Becker O, Steinhilber D, Suess B. “Potential and Optimization of Mammalian Splice Riboswitches for the Regulation of Exon Skipping-Dependent Gene Expression and Isoform Switching within the ALOX5 Gene”, ACS Synthetic Biology, 2025 DOI