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Publikationen

2024

Lischer, C., M. Eberhardt, C. Flamann, J. Berges, E. Güse, A. Wessely, A. Weich, J. Retzlaff, J. Dörrie, N. Schaft, M. Wiesinger, J. März, B. Schuler-Thurner, H. Knorr, S. Gupta, K. P. Singh, G. Schuler, M. V. Heppt, E. A. T. Koch, N. D. van Kleef, J. J. Freen-van Heeren, A. W. Turksma, O. Wolkenhauer, B. Hohberger, C. Berking, H. Bruns, and J. Vera (2024). "Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy." Journal for ImmunoTherapy of Cancer 12(5): e008104. doi.org/10.1136/jitc-2023-008104.

Singh, S., S. Yadav, C. Cavallo, D. Mourya, I. Singh, V. Kumar, S. Shukla, P. Shukla, R. Chaudhary, G. P. Maurya, R. L. J. Müller, L. Rohde, A. Mishra, O. Wolkenhauer, S. Gupta, and A. Tripathi (2024). "Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model." npj Syst. Biol. Appl. 10(23): 1–15. doi.org/10.1038/s41540-024-00349-1.

2023

Hoch, M., J. Rauthe, K. Cesnulevicius, M. Schultz, D. Lescheid, O. Wolkenhauer, V. Chiurchiù, and S. Gupta (2023). "Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System." Int J Mol Sci 24(5): 4342. doi.org/10.3390/ijms24054342.

Hoch, M., S. Smita, K. Cesnulevicius, M. Schultz, D. Lescheid, O. Wolkenhauer, and S. Gupta (2023). "Network analyses reveal new insights into the effect of multicomponent Tr14 compared to single-component diclofenac in an acute inflammation model." J. Inflamm. 20(1): 1–15. doi.org/10.1186/s12950-023-00335-0.

Petzold, A., T. Steeb, A. Wessely, E. A. T. Koch, J. Vera, C. Berking, and M. V. Heppt (2023). "Is tebentafusp superior to combined immune checkpoint blockade and other systemic treatments in metastatic uveal melanoma? A comparative efficacy analysis with population adjustment." Cancer Treatment Reviews 115: 102543. doi.org/10.1016/j.ctrv.2023.102543.

Retzlaff, J., X. Lai, C. Berking, and J. Vera (2023). "Integration of transcriptomics data into agent-based models of solid tumor metastasis." Comput Struct Biotechnol J 21: 1930–1941. doi.org/10.1016/j.csbj.2023.02.014.

Schmitt, C., E. P. Hoefsmit, T. Fangmeier, N. Kramer, C. Kabakci, J. Vera González, J. M. Versluis, A. Compter, T. Harrer, H. Mijočević, S. Schubert, T. Hundsberger, A. M. Menzies, R. A. Scolyer, G. V. Long, L. E. French, C. U. Blank, and L. M. Heinzerling (2023). "Immune checkpoint inhibitor-induced neurotoxicity is not associated with seroprevalence of neurotropic infections." Cancer Immunol. Immunother. 72(11): 3475–3489. doi.org/10.1007/s00262-023-03498-0.

Tomsitz, D., T. Ruf, M. Heppt, R. Staeger, E. Ramelyte, R. Dummer, M. Garzarolli, F. Meier, E. Meier, H. Richly, T. Gromke, J. T. Siveke, C. Franklin, K.-C. Klespe, C. Mauch, T. Kilian, M. Seegräber, B. Schilling, L. E. French, C. Berking, and L. Heinzerling (2023). "Tebentafusp in Patients with Metastatic Uveal Melanoma: A Real-Life Retrospective Multicenter Study." Cancers 15(13): 3430. doi.org/10.3390/cancers15133430.

Tomsitz, D., T. Ruf, S. Zierold, L. E. French, and L. Heinzerling (2023). "Steroid-Refractory Immune-Related Adverse Events Induced by Checkpoint Inhibitors." Cancers 15(9): 2538. doi.org/10.3390/cancers15092538.

Zhang, L., S. Fan, J. Vera, and X. Lai (2023). "A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer." Comput Struct Biotechnol J 21: 34–45. doi.org/10.1016/j.csbj.2022.11.037.

2022

Hoang, Y., S. Gryzik, I. Hoppe, A. Rybak, M. Schädlich, I. Kadner, D. Walther, J. Vera, A. Radbruch, D. Groth, S. Baumgart, and R. Baumgrass (2022). "PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments." Front Immunol 0. doi.org/10.3389/fimmu.2022.849329.

Hoch, M., L. Ehlers, K. Bannert, C. Stanke, D. Brauer, V. Caton, G. Lamprecht, O. Wolkenhauer, R. Jaster, and M. Wolfien (2022). "In silico investigation of molecular networks linking gastrointestinal diseases, malnutrition, and sarcopenia." Front Nutr 9. doi.org/10.3389/fnut.2022.989453.

Hoch, M., S. Smita, K. Cesnulevicius, D. Lescheid, M. Schultz, O. Wolkenhauer, and S. Gupta (2022). "Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps." npj Systems Biology and Applications 8(1): 13. doi.org/10.1038/s41540-022-00222-z.

Lai, X., C. Keller, G. Santos, N. Schaft, J. Dörrie, and J. Vera (2022). "Multi-Level Computational Modeling of Anti-Cancer Dendritic Cell Vaccination Utilized to Select Molecular Targets for Therapy Optimization." Frontiers in Cell and Developmental Biology 9. www.frontiersin.org/article/10.3389/fcell.2021.746359.

Lai, X., J. Zhou, A. Wessely, M. Heppt, A. Maier, C. Berking, J. Vera, and L. Zhang (2022). "A disease network-based deep learning approach for characterizing melanoma." Int J Cancer 150(6): 1029–1044. doi.org/10.1002/ijc.33860.

Leavenworth, J. W., X. Lai, H. Miao, D. Wang, H. Zhao, and Y. Li (2022). "Editorial: Macrophage immunity and metabolism in cancer: Novel diagnostic and therapeutic strategies." Front Immunol 13. doi.org/10.3389/fimmu.2022.1113031.

Mohr, E., T. Hinnenthal, S. Gryzik, Y. Hoang, T. Lischke, J. Retzlaff, A. Mekonnen, F. Paul, A. Valleriani, A. Radbruch, J. Vera, and R. Baumgrass (2022). "Bin-based visualization of cytokine-co-expression patterns of IL-10-producing CD4 T cell subsets." Eur J Immunol n/a(n/a). doi.org/10.1002/eji.202249829.

Müller-Jensen, L., S. Zierold, J. M. Versluis, W. Boehmerle, P. Huehnchen, M. Endres, R. Mohr, A. Compter, C. U. Blank, T. Hagenacker, F. Meier, L. Reinhardt, A. Gesierich, M. Salzmann, J. C. Hassel, S. Ugurel, L. Zimmer, P. Banks, L. Spain, J. A. Soon, T. Enokida, M. Tahara, K. C. Kähler, R. Seggewiss-Bernhardt, C. Harvey, G. V. Long, F. Schöberl, L. von Baumgarten, T. Hundsberger, M. Schlaak, L. E. French, S. Knauss, and L. M. Heinzerling (2022). "Characteristics of immune checkpoint inhibitor-induced encephalitis and comparison with HSV-1 and anti-LGI1 encephalitis: A retrospective multicentre cohort study." Eur J Cancer 175: 224–235. doi.org/10.1016/j.ejca.2022.08.009.

Müller-Jensen, L., S. Zierold, J. M. Versluis, W. Boehmerle, P. Huehnchen, M. Endres, R. Mohr, A. Compter, C. U. Blank, T. Hagenacker, F. Meier, L. Reinhardt, A. Gesierich, M. Salzmann, J. C. Hassel, S. Ugurel, L. Zimmer, P. Banks, L. Spain, J. A. Soon, T. Enokida, M. Tahara, K. C. Kähler, R. Seggewiss-Bernhardt, C. Harvey, G. V. Long, F. Schöberl, L. von Baumgarten, T. Hundsberger, M. Schlaak, L. E. French, S. Knauss, and L. M. Heinzerling (2022). "Dataset of a retrospective multicenter cohort study on characteristics of immune checkpoint inhibitor-induced encephalitis and comparison with HSV-1 and anti-LGI1 encephalitis." Data in Brief: 108649. doi.org/10.1016/j.dib.2022.108649.

Pützer, B. M., and K. Sabapathy (2022). "Editorial: Multidisciplinary Approaches in Exploring Cancer Heterogeneity, TME and Therapy Resistance: Perspectives for Systems Medicine." Frontiers in Cell and Developmental Biology 10. www.frontiersin.org/article/10.3389/fcell.2022.842596.

Schulz, T. U., S. Zierold, M. M. Sachse, G. Pesch, D. Tomsitz, K. Schilbach, K. C. Kähler, L. E. French, and L. Heinzerling (2022). "Health-related quality of life (EuroQol 5D-5L) in patients with autoimmunity in the context of immunotherapy: A large dataset comprising cancer patients after cessation of checkpoint inhibitor therapy and patients with autoimmune diseases." Data in Brief 45: 108676. doi.org/10.1016/j.dib.2022.108676.

Schulz, T. U., S. Zierold, M. M. Sachse, G. Pesch, D. Tomsitz, K. Schilbach, K. C. Kähler, L. E. French, and L. Heinzerling (2022). "Health-related quality of life (EuroQol 5D-5L) in patients with autoimmunity in the context of immunotherapy: A large dataset comprising cancer patients after cessation of checkpoint inhibitor therapy and patients with autoimmune diseases." Data in Brief 45: 108676. doi.org/10.1016/j.dib.2022.108676.

Tomsitz, D., M. Schlaak, S. Zierold, G. Pesch, T. U. Schulz, G. Müller, C. Zecha, L. E. French, and L. Heinzerling (2022). "Development of Lymphopenia during Therapy with Immune Checkpoint Inhibitors Is Associated with Poor Outcome in Metastatic Cutaneous Melanoma." Cancers 14(13): 3282. doi.org/10.3390/cancers14133282.

Vera, J., X. Lai, A. Baur, M. Erdmann, S. Gupta, C. Guttà, L. Heinzerling, M. V. Heppt, P. M. Kazmierczak, M. Kunz, C. Lischer, B. M. Pützer, M. Rehm, C. Ostalecki, J. Retzlaff, S. Witt, O. Wolkenhauer, and C. Berking (2022). "Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence." Briefings Bioinf. doi.org/10.1093/bib/bbac433.

Zierold, S., L. S. Akcetin, E. Gresser, A. M. Maier, A. König, R. Kramer, S. Theurich, D. Tomsitz, M. Erdmann, L. E. French, M. Rudelius, and L. Heinzerling (2022). "Checkpoint-inhibitor induced Polyserositis with Edema." Cancer Immunology, Immunotherapy. doi.org/10.1007/s00262-022-03211-7.

2021

Bailey, C.G., Gupta, S., Metierre, C., Amarasekera, P.M.S., O'Young, P., Kyaw, W., Laletin, T., Francis, H., Semaan, C., Sharifi Tabar, M., Singh, K.P., Mullighan, C.G., Wolkenhauer, O., Schmitz, U. and Rasko, J.E.J. (2021). "Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer." Cell Mol Life Sci. www.ncbi.nlm.nih.gov/pubmed/34657170.

Faas, M., Ipseiz, N., Ackermann, J., Culemann, S., Grüneboom, A., Schröder, F., Rothe, T., Scholtysek, C., Eberhardt, M., Böttcher, M., Kirchner, P., Stoll, C., Ekici, A., Fuchs, M., Kunz, M., Weigmann, B., Wirtz, S., Lang, R., Hofmann, J., Vera, J., Voehringer, D., Michelucci, A., Mougiakakos, D., Uderhardt, S., Schett, G. and Krönke, G. (2021). "IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation." Immunity 54(11): 2531–2546.e2535. doi.org/10.1016/j.immuni.2021.09.010.

Hornschuh, M., Wirthgen, E., Wolfien, M., Singh, K.P., Wolkenhauer, O. and Dabritz, J. (2021). "The role of epigenetic modifications for the pathogenesis of Crohn's disease." Clinical Epigenetics 13(1): 108. www.ncbi.nlm.nih.gov/pubmed/33980294.

Husain, B., Kirchberger, M.C., Erdmann, M., Schüpferling, S., Abolhassani, A.-R., Fröhlich, W., Berking, C. and Heinzerling, L. (2021). "Inflammatory markers in autoimmunity induced by checkpoint inhibitors." Journal of Cancer Research and Clinical Oncology 147(6): 1623-1630. doi.org/10.1007/s00432-021-03550-5.

Lai, X., Dreyer, F.S., Cantone, M., Eberhardt, M., Gerer, K.F., Jaitly, T., Uebe, S., Lischer, C., Ekici, A., Wittmann, J., Jack, H.M., Schaft, N., Dorrie, J. and Vera, J. (2021). "Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy." Theranostics 11(3): 1412-1428. doi.org/10.7150/thno.53092.

Logotheti, S., Richter, C., Murr, N., Spitschak, A., Marquardt, S. and Putzer, B.M. (2021). "Mechanisms of Functional Pleiotropy of p73 in Cancer and Beyond." Front Cell Dev Biol 9: 737735. www.ncbi.nlm.nih.gov/pubmed/34650986.

Marquardt, S., Pavlopoulou, A., Takan, I., Dhar, P., Pützer, B.M. and Logotheti, S. (2021). "A Systems-Based Key Innovation-Driven Approach Infers Co-option of Jaw Developmental Programs During Cancer Progression." Front Cell Dev Biol 0. doi.org/10.3389/fcell.2021.682619.

Sauerer, T., Lischer, C., Weich, A., Berking, C., Vera, J. and Dorrie, J. (2021). "Single-Molecule RNA Sequencing Reveals IFNgamma-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines." Frontiers in Microbiology 12: 785662. www.ncbi.nlm.nih.gov/pubmed/35003017.

Vera, J., Lischer, C., Nenov, M., Nikolov, S., Lai, X. and Eberhardt, M. (2021). "Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic." International Journal of Molecular Sciences 22(2): 547. doi.org/10.3390/ijms22020547.

Wagner, N., Eberhardt, M., Vera, J., Cuomo, F., Blume, K., Galster, S., Achenbach, S., Laffert, B., Kahlert, H., Schuler, G., Berking, C. and Baur, A. (2021). "Plasma-derived extracellular vesicles discriminate type-1 allergy subjects from non-allergic controls." World Allergy Organ J 14(9): 100583. www.ncbi.nlm.nih.gov/pubmed/34659629.

2020

Logotheti, S., S. Marquardt, S. K. Gupta, C. Richter, B. A. H. Edelhäuser, D. Engelmann, J. Brenmoehl, C. Söhnchen, N. Murr, M. Alpers, K. P. Singh, O. Wolkenhauer, D. Heckl, A. Spitschak, and B. M. Pützer (2020). "LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1." Theranostics 10(21). doi.org/10.7150/thno.44176.

Logotheti, S., S. Marquardt, C. Richter, R. Sophie Hain, N. Murr, I. Takan, A. Pavlopoulou, and B. M. Pützer (2020). "Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk." Cancers (Basel) 12(12): 3789. doi.org/10.3390/cancers12123789.

Serhan, C. N., S. K. Gupta, M. Perretti, C. Godson, E. Brennan, Y. Li, O. Soehnlein, T. Shimizu, O. Werz, V. Chiurchiù, A. Azzi, M. Dubourdeau, S. S. Gupta, P. Schopohl, M. Hoch, D. Gjorgevikj, F. M. Khan, D. Brauer, A. Tripathi, K. Cesnulevicius, D. Lescheid, M. Schultz, E. Särndahl, D. Repsilber, R. Kruse, A. Sala, J. Z. Haeggström, B. D. Levy, J. G. Filep, and O. Wolkenhauer (2020). "The Atlas of Inflammation Resolution (AIR)." Mol Aspects Med 74: 100894. doi.org/10.1016/j.mam.2020.100894.

Singh, N., M. Eberhardt, O. Wolkenhauer, J. Vera, and S. K. Gupta (2020). "An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma." BMC Bioinformatics 21(1): 1–17. doi.org/10.1186/s12859-020-03656-6.