SYSIMIT

Papaxenopoulou, L. A., G. Zhao, S. Khailaie, K. Katsoulis-Dimitriou, I. Schmitz, E. Medina, H. Hatzikirou, and M. Meyer-Hermann (2022). "In silico predicted therapy against chronic Staphylococcus aureus infection leads to bacterial clearance in vivo." iScience: 105522. doi.org/10.1016/j.isci.2022.105522.

Setten, E., A. Castagna, J. M. Nava-Sedeño, J. Weber, R. Carriero, A. Reppas, V. Volk, J. Schmitz, W. Gwinner, H. Hatzikirou, F. Feuerhake, and M. Locati (2022). "Understanding fibrosis pathogenesis via modeling macrophage-fibroblast interplay in immune-metabolic context." Nat Commun 13(6499): 1–22. doi.org/10.1038/s41467-022-34241-5.

Graeser, M., F. Feuerhake, O. Gluz, V. Volk, M. Hauptmann, K. Jozwiak, M. Christgen, S. Kuemmel, E.-M. Grischke, H. Forstbauer, M. Braun, M. Warm, J. Hackmann, C. Uleer, B. Aktas, C. Schumacher, C. Kolberg-Liedtke, R. Kates, R. Wuerstlein, U. Nitz, H. H. Kreipe, and N. Harbeck (2021). "Immune cell composition and functional marker dynamics from multiplexed immunohistochemistry to predict response to neoadjuvant chemotherapy in the WSG-ADAPT-TN trial." Journal for ImmunoTherapy of Cancer 9(5): e002198. jitc.bmj.com/content/jitc/9/5/e002198.full.pdf.

Hermsen, M., V. Volk, J. H. Bräsen, D. J. Geijs, W. Gwinner, J. Kers, J. Linmans, N. S. Schaadt, J. Schmitz, E. J. Steenbergen, Z. Swiderska-Chadaj, B. Smeets, L. B. Hilbrands, F. Feuerhake, and J. A. W. M. van der Laak (2021). "Quantitative assessment of inflammatory infiltrates in kidney transplant biopsies using multiplex tyramide signal amplification and deep learning." Laboratory Investigation 101(8): 970-982. doi.org/10.1038/s41374-021-00601-w.

Merveille, O., T. Lampert, J. Schmitz, G. Forestier, F. Feuerhake, and C. Wemmert (2021). "An automatic framework for fusing information from differently stained consecutive digital whole slide images: A case study in renal histology." Comput Methods Programs Biomed 208: 106157. www.ncbi.nlm.nih.gov/pubmed/34091100.

Vasiljević, J., F. Feuerhake, C. Wemmert, and T. Lampert (2021). "Self adversarial attack as an augmentation method for immunohistochemical stainings." arXiv. arxiv.org/abs/2103.11362v1.

(2021). "Towards histopathological stain invariance by Unsupervised Domain Augmentation using generative adversarial networks." Neurocomputing 460: 277–291. doi.org/10.1016/j.neucom.2021.07.005.

Volk, V., S. J. Theobald, S. Danisch, S. Khailaie, M. Kalbarczyk, A. Schneider, J. Bialek-Waldmann, N. Krönke, Y. Deng, B. Eiz-Vesper, A. C. Dragon, C. von Kaisenberg, S. Lienenklaus, A. Bleich, J. Keck, M. Meyer-Hermann, F. Klawonn, W. Hammerschmidt, H.-J. Delecluse, C. Münz, F. Feuerhake, and R. Stripecke (2021). "PD-1 Blockade Aggravates Epstein–Barr Virus+ Post-Transplant Lymphoproliferative Disorder in Humanized Mice Resulting in Central Nervous System Involvement and CD4+ T Cell Dysregulations." Front Oncol 10. doi.org/10.3389/fonc.2020.614876.

Bug, D. N., Gregor; Grote, Anne; Feuerhake, Friedrich; Oswald, Eva; Schüler, Julia; Merhof, Dorit (2020). Image Quilting for Histological Image Synthesis. Bildverarbeitung für die Medizin 2020. P. D. T. M. D. Prof. Dr. Thomas Tolxdorff, Prof. Dr. Heinz Handels, Prof. Dr. Andreas Maier, Dr. Klaus H. Maier-Hein, Prof. Dr. Christoph Palm Springer Fachmedien Wiesbaden. www.springerprofessional.de/image-quilting-for-histological-image-synthesis/17693862.

Hoore, M., S. Khailaie, G. Montaseri, T. Mitra, and M. Meyer-Hermann (2020). "Mathematical Model Shows How Sleep May Affect Amyloid-beta Fibrillization." Biophys J 119(4): 862–872. doi.org/10.1016/j.bpj.2020.07.011.

Khailaie, S., G. Montaseri, and M. Meyer-Hermann (2020). "An Adaptive Control Scheme for Interleukin-2 Therapy." iScience 23(11): 101663. doi.org/10.1016/j.isci.2020.101663.

Schaadt, N. S., R. Schönmeyer, G. Forestier, N. Brieu, P. Braubach, K. Nekolla, M. Meyer-Hermann, and F. Feuerhake (2020). "Graph-based description of tertiary lymphoid organs at single-cell level." PLoS Comput Biol 16(2): e1007385. journals.plos.org/ploscompbiol/article.

Slabik, C., M. Kalbarczyk, S. Danisch, R. Zeidler, F. Klawonn, V. Volk, N. Krönke, F. Feuerhake, C. Ferreira de Figueiredo, R. Blasczyk, H. Olbrich, S. J. Theobald, A. Schneider, A. Ganser, C. von Kaisenberg, S. Lienenklaus, A. Bleich, W. Hammerschmidt, and R. Stripecke (2020). "CAR-T Cells Targeting Epstein-Barr Virus gp350 Validated in a Humanized Mouse Model of EBV Infection and Lymphoproliferative Disease." Mol Ther Oncolytics 18: 504–524. doi.org/10.1016/j.omto.2020.08.005.

Danisch, S., Slabik, C., Cornelius, A., Albanese, M., Tagawa, T., Chen, Y. A., Kronke, N., Eiz-Vesper, B., Lienenklaus, S., Bleich, A., Theobald, S. J., Schneider, A., Ganser, A., von Kaisenberg, C., Zeidler, R., Hammerschmidt, W., Feuerhake, F. and Stripecke, R. (2019). "Spatiotemporally Skewed Activation of Programmed Cell Death Receptor 1-Positive T Cells after Epstein-Barr Virus Infection and Tumor Development in Long-Term Fully Humanized Mice." Am J Pathol 189(3): 521-539. www.ncbi.nlm.nih.gov/pubmed/30593822.

Grote, A., Schaadt, N. S., Forestier, G., Wemmert, C. and Feuerhake, F. (2019). "Crowdsourcing of Histological Image Labeling and Object Delineation by Medical Students." IEEE Trans Med Imaging 38(5): 1284-1294. www.ncbi.nlm.nih.gov/pubmed/30489264.

Mascheroni, P., Lopez Alfonso, J. C., Kalli, M., Stylianopoulos, T., Meyer-Hermann, M. and Hatzikirou, H. (2019). "On the Impact of Chemo-Mechanically Induced Phenotypic Transitions in Gliomas." Cancers (Basel) 11(5). www.ncbi.nlm.nih.gov/pubmed/31137643.

Danisch, S., Slabik, C., Cornelius, A., Albanese, M., Tagawa, T., Chen, Y. A., Kronke, N., Eiz-Vesper, B., Lienenklaus, S., Bleich, A., Theobald, S. J., Schneider, A., Ganser, A., von Kaisenberg, C., Zeidler, R., Hammerschmidt, W., Feuerhake, F.Stripecke, R., 2018. Spatiotemporally Skewed Activation of Programmed Cell Death Receptor 1-Positive T Cells after Epstein-Barr Virus Infection and Tumor Development in Long-Term Fully Humanized Mice. Am J Pathol. doi.org/10.1016/j.ajpath.2018.11.014

Lopez Alfonso, J. C., Parsai, S., Joshi, N., Godley, A., Shah, C., Koyfman, S. A., Caudell, J. J., Fuller, C. D., Enderling, H.Scott, J. G., 2018. Temporally feathered intensity-modulated radiation therapy: A planning technique to reduce normal tissue toxicity. Med Phys, 45(7), 3466-3474. doi.org/10.1002/mp.12988

Meyer-Hermann, M., 2018. Estimation of the cancer risk induced by therapies targeting stem cell replication and treatment recommendations. Sci Rep, 8(1), 11776. doi.org/10.1038/s41598-018-29967-6

Meyer-Hermann, M., Binder, S. C., Mesin, L.Victora, G. D., 2018. Computer Simulation of Multi-Color Brainbow Staining and Clonal Evolution of B Cells in Germinal Centers. Front. Immunol., 9. doi.org/10.3389/fimmu.2018.02020

Montaseri, G., Boianelli, A., Hernandez-Vargas, E. A.Meyer-Hermann, M., 2018. PK/PD-based adaptive tailoring of oseltamivir doses to treat within-host influenza viral infections. Prog. Biophys. Mol. Biol., 139, 31-42. doi.org/10.1016/j.pbiomolbio.2018.07.007

Theobald, S. J., Khailaie, S., Meyer-Hermann, M., Volk, V., Olbrich, H., Danisch, S., Gerasch, L., Schneider, A., Sinzger, C., Schaudien, D., Lienenklaus, S., Riese, P., Guzman, C. A., Figueiredo, C., von Kaisenberg, C., Spineli, L. M., Glaesener, S., Meyer-Bahlburg, A., Ganser, A., Schmitt, M., Mach, M., Messerle, M.Stripecke, R., 2018. Signatures of T and B Cell Development, Functional Responses and PD-1 Upregulation After HCMV Latent Infections and Reactivations in Nod.Rag.Gamma Mice Humanized With Cord Blood CD34+ Cells. Front. Immunol., 9. doi.org/10.3389/fimmu.2018.02734

Alfonso, J.C.L., Talkenberger, K., Seifert, M., Klink, B., Hawkins-Daarud, A., Swanson, K.R., Hatzikirou, H., Deutsch, A., 2017. The biology and mathematical modelling of glioma invasion: a review. J R Soc Interface 14. doi.org/10.1098/rsif.2017.0490

Hatzikirou, H., López Alfonso, J.C., Leschner, S., Weiss, S., Meyer-Hermann, M., 2017. Therapeutic Potential of Bacteria against Solid Tumors. Cancer Res. 77, 1553–1563. doi.org/10.1158/0008-5472.CAN-16-1621

Khailaie, S., Rowshanravan, B., Robert, P.A., Walker, L.S.K., Sansom, D.M., Meyer-Hermann, M., 2017. Quantitative characterization of CTLA4 trafficking and turnover using a combined in vitro and in silico approach. bioRxiv 106898. doi.org/10.1101/106898

Nava-Sedeño, J.M., Hatzikirou, H., Klages, R., Deutsch, A., 2017a. Cellular automaton models for time-correlated random walks: derivation and analysis. Sci Rep 7, 16952. doi.org/10.1038/s41598-017-17317-x

Nava-Sedeño, J.M., Hatzikirou, H., Peruani, F., Deutsch, A., 2017b. Extracting cellular automaton rules from physical Langevin equation models for single and collective cell migration. J Math Biol. doi.org/10.1007/s00285-017-1106-9

Schaadt, N.S., Alfonso, J.C.L., Schönmeyer, R., Grote, A., Forestier, G., Wemmert, C., Krönke, N., Stoeckelhuber, M., Kreipe, H.H., Hatzikirou, H., Feuerhake, F., 2017. Image analysis of immune cell patterns in the human mammary gland during the menstrual cycle refines lymphocytic lobulitis. Breast Cancer Res Treat 1–11. doi.org/10.1007/s10549-017-4239-z

Volk, V., Reppas, A.I., Robert, P.A., Spineli, L.M., Sundarasetty, B.S., Theobald, S.J., Schneider, A., Gerasch, L., Deves Roth, C., Klöss, S., Koehl, U., von Kaisenberg, C., Figueiredo, C., Hatzikirou, H., Meyer-Hermann, M., Stripecke, R., 2017. Multidimensional Analysis Integrating Human T-Cell Signatures in Lymphatic Tissues with Sex of Humanized Mice for Prediction of Responses after Dendritic Cell Immunization. Front Immunol 8, 1709. doi.org/10.3389/fimmu.2017.01709

Alfonso, J.C.L., Köhn-Luque, A., Stylianopoulos, T., Feuerhake, F., Deutsch, A., Hatzikirou, H., 2016a. Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights. Sci Rep 6, 37283. doi.org/10.1038/srep37283

Alfonso, J.C.L., Schaadt, N.S., Schönmeyer, R., Brieu, N., Forestier, G., Wemmert, C., Feuerhake, F., Hatzikirou, H., 2016b. In-silico insights on the prognostic potential of immune cell infiltration patterns in the breast lobular epithelium. Sci Rep 6, 33322. doi.org/10.1038/srep33322

Binder, S.C., Eckweiler, D., Schulz, S., Bielecka, A., Nicolai, T., Franke, R., Häussler, S., Meyer-Hermann, M., 2016. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Sci Rep 6, 22212. doi.org/10.1038/srep22212

Boianelli, A., Sharma-Chawla, N., Bruder, D., Hernandez-Vargas, E.A., 2016. Oseltamivir PK/PD Modeling and Simulation to Evaluate Treatment Strategies against Influenza-Pneumococcus Coinfection. Front Cell Infect Microbiol 6, 60. doi.org/10.3389/fcimb.2016.00060

Ghanbari, A., Dehghany, J., Schwebs, T., Müsken, M., Häussler, S., Meyer-Hermann, M., 2016. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms. Sci Rep 6, 32097. doi.org/10.1038/srep32097

Apou, G., Feuerhake, F., Forestier, G., Naegel, B., Wemmert, C., 2015. Synthesizing whole slide images, in: 2015 9th International Symposium on Image and Signal Processing and Analysis (ISPA). Presented at the 2015 9th International Symposium on Image and Signal Processing and Analysis (ISPA), pp. 154–159. doi.org/10.1109/ISPA.2015.7306050

Binder, S.C., Hernandez-Vargas, E.A., Meyer-Hermann, M., 2015. Reducing complexity: An iterative strategy for parameter determination in biological networks. Computer Physics Communications 190, 15–22. doi.org/10.1016/j.cpc.2015.01.001

Boianelli, A., Nguyen, V.K., Ebensen, T., Schulze, K., Wilk, E., Sharma, N., Stegemann-Koniszewski, S., Bruder, D., Toapanta, F.R., Guzmán, C.A., Meyer-Hermann, M., Hernandez-Vargas, E.A., 2015. Modeling Influenza Virus Infection: A Roadmap for Influenza Research. Viruses 7, 5274–5304. doi.org/10.3390/v7102875

Hatzikirou, H., Alfonso, J.C.L., Mühle, S., Stern, C., Weiss, S., Meyer-Hermann, M., 2015. Cancer therapeutic potential of combinatorial immuno- and vasomodulatory interventions. J R Soc Interface 12. doi.org/10.1098/rsif.2015.0439

Kempf, H., Bleicher, M., Meyer-Hermann, M., 2015. Spatio-Temporal Dynamics of Hypoxia during Radiotherapy. PLoS ONE 10, e0133357. doi.org/10.1371/journal.pone.0133357

Nguyen, V.K., Binder, S.C., Boianelli, A., Meyer-Hermann, M., Hernandez-Vargas, E.A., 2015. Ebola virus infection modeling and identifiability problems. Front Microbiol 6, 257. doi.org/10.3389/fmicb.2015.00257

Sukhorukov, V.M., Meyer-Hermann, M., 2015. Structural Heterogeneity of Mitochondria Induced by the Microtubule Cytoskeleton. Sci Rep 5, 13924. doi.org/10.1038/srep13924

Haering, M., Hördt, A., Meyer-Hermann, M., Hernandez-Vargas, E.A., 2014. Computational study to determine when to initiate and alternate therapy in HIV infection. Biomed Res Int 2014, 472869. doi.org/10.1155/2014/472869

Meyer-Hermann, M., 2014. Overcoming the dichotomy of quantity and quality in antibody responses. J. Immunol. 193, 5414–5419. doi.org/10.4049/jimmunol.1401828

Zhao, G., Dharmadhikari, G., Maedler, K., Meyer-Hermann, M., 2014. Possible role of interleukin-1β in type 2 diabetes onset and implications for anti-inflammatory therapy strategies. PLoS Comput. Biol. 10, e1003798. doi.org/10.1371/journal.pcbi.1003798

Kempf, H., Hatzikirou, H., Bleicher, M., Meyer-Hermann, M., 2013. In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids. PLoS Comput. Biol. 9, e1003295. doi.org/10.1371/journal.pcbi.1003295