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Chillappagari, S., V. Garapati, P. Mahavadi, L. Naehrlich, B. T. Schmeck, M. L. Schmitz, and A. Guenther (2020). "Defective BACH1/HO-1 regulatory circuits in cystic fibrosis bronchial epithelial cells." Journal of Cystic Fibrosis.

Chua, R. L., S. Lukassen, S. Trump, B. P. Hennig, D. Wendisch, F. Pott, O. Debnath, L. Thürmann, F. Kurth, M. T. Völker, J. Kazmierski, B. Timmermann, S. Twardziok, S. Schneider, F. Machleidt, H. Müller-Redetzky, M. Maier, A. Krannich, S. Schmidt, F. Balzer, J. Liebig, J. Loske, N. Suttorp, J. Eils, N. Ishaque, U. G. Liebert, C. von Kalle, A. Hocke, M. Witzenrath, C. Goffinet, C. Drosten, S. Laudi, I. Lehmann, C. Conrad, L.-E. Sander, and R. Eils (2020). "COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis." Nat Biotechnol: 1–10.

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Hübner, K., D. Karwelat, E. Pietsch, I. Beinborn, S. Winterberg, K. Bedenbender, B. J. Benedikter, B. Schmeck, and E. Vollmeister (2020). "NF-κB-mediated inhibition of microRNA-149-5p regulates Chitinase-3-like 1 expression in human airway epithelial cells." Cell. Signalling 67: 109498.

Jung, A. L., M. M. Jorgensen, R. Baek, K. Griss, M. Han, K. A. D. Brinke, N. Timmesfeld, W. Bertrams, T. Greulich, R. Koczulla, S. Hippenstiel, N. Suttorp, and B. Schmeck (2020). "Surface Proteome of Plasma Extracellular Vesicles as Biomarkers for Pneumonia and Acute Exacerbation of Chronic Obstructive Pulmonary Disease." J Infect Dis 221(2): 325–335.

Karwelat, D., B. Schmeck, M. Ringel, B. J. Benedikter, K. Huebner, I. Beinborn, A. Maisner, L. N. Schulte, and E. Vollmeister (2020). "Influenza virus-mediated suppression of bronchial Chitinase-3-like 1 secretion promotes secondary pneumococcal infection." FASEB J.

Korfhage, N., M. Mühling, S. Ringshandl, A. Becker, B. Schmeck, and B. Freisleben (2020). "Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion." PLoS Comput Biol 16(9): e1008179.

Messner, C. B., V. Demichev, D. Wendisch, L. Michalick, M. White, A. Freiwald, K. Textoris-Taube, S. Vernardis, A.-S. Egger, M. Kreidl, D. Ludwig, C. Kilian, F. Agostini, A. Zelezniak, C. Thibeault, M. Pfeiffer, S. Hippenstiel, A. Hocke, C. von Kalle, A. Campbell, C. Hayward, D. J. Porteous, R. E. Marioni, C. Langenberg, and K. S. Lilley (2020). "Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection." CELL SYSTEMS 11(1): 11–+.

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Nikoghosyan, M., M. Schmidt, K. Margaryan, H. Loeffler-Wirth, A. Arakelyan, and H. Binder (2020). "SOMmelier-Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks." GENES 11(7).

Ochs, M., J. Hegermann, E. Lopez-Rodriguez, S. Timm, G. Nouailles, J. Matuszak, S. Simmons, M. Witzenrath, and W. M. Kuebler (2020). "On Top of the Alveolar Epithelium: Surfactant and the Glycocalyx." Int J Mol Sci 21(9).

Przybilla, J., P. Ahnert, H. Bogatsch, F. Bloos, F. M. Brunkhorst, M. Bauer, M. Loeffler, M. Witzenrath, N. Suttorp, and M. Scholz (2020). "Markov State Modelling of Disease Courses and Mortality Risks of Patients with Community-Acquired Pneumonia." JOURNAL OF CLINICAL MEDICINE 9(2).

Sanapala, S. R., B. M. S. Seco, J. Y. Baek, S. Awan, C. L. Pereira, and P. H. Seeberger (2020). "Chimeric oligosaccharide conjugate induces opsonic antibodies againstStreptococcus pneumoniaeserotypes 19A and 19F." Chem Sci 11(28): 7401–7407.

Santos, G., and J. Vera (2020). "The Role of Age, Neutrophil Infiltration and Antibiotics Timing in the Severity of Streptococcus pneumoniae Pneumonia. Insights from a Multi-Level Mathematical Model Approach." Int J Mol Sci 21(22): 8428.

Schirm, S., P. Ahnert, S. Berger, G. Nouailles, S.-M. Wienhold, H. Müller-Redetzky, N. Suttorp, M. Loeffler, M. Witzenrath, and M. Scholz (2020). "A biomathematical model of immune response and barrier function in mice with pneumococcal lung infection." PLoS One 15(12): e0243147.

Schmidt, M., L. Hopp, A. Arakelyan, H. Kirsten, C. Engel, K. Wirkner, K. Krohn, R. Burkhardt, J. Thiery, M. Loeffler, H. Loeffler-Wirth, and H. Binder (2020). "The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health." Front Big Data 3.

Thalheim, T., L. Hopp, M. Herberg, S. Siebert, C. Kerner, M. Quaas, M. R. Schweiger, G. Aust, and J. Galle (2020). "Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells." Int J Mol Sci 21(6).


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Dabrowski, A. N., Shrivastav, A., Conrad, C., Komma, K., Weigel, M., Dietert, K., Gruber, A. D., Bertrams, W., Wilhelm, J., Schmeck, B., Reppe, K., N'Guessan, P. D., Aly, S., Suttorp, N., Hain, T. and Zahlten, J. (2019). "Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota." Front Immunol 10: 2106.

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Jensen, A. V., Baunbaek Egelund, G., Bang Andersen, S., Petersen, P. T., Benfield, T., Witzenrath, M., Rohde, G., Ravn, P., Faurholt-Jepsen, D. and Members of the, C. s. g. e. t. a. (2019). "The Glycemic Gap and 90-Day Mortality in Community-acquired Pneumonia. A Prospective Cohort Study." Ann Am Thorac Soc 16(12): 1518-1526.

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Lindhauer, N. S., Bertrams, W., Poppel, A., Herkt, C. E., Wesener, A., Hoffmann, K., Greene, B., Van Der Linden, M., Vilcinskas, A., Seidel, K. and Schmeck, B. (2019). "Antibacterial activity of a Tribolium castaneum defensin in an in vitro infection model of Streptococcus pneumoniae." Virulence 10(1): 902-909.

Loeffler-Wirth, H., Kreuz, M., Hopp, L., Arakelyan, A., Haake, A., Cogliatti, S. B., Feller, A. C., Hansmann, M. L., Lenze, D., Moller, P., Muller-Hermelink, H. K., Fortenbacher, E., Willscher, E., Ott, G., Rosenwald, A., Pott, C., Schwaenen, C., Trautmann, H., Wessendorf, S., Stein, H., Szczepanowski, M., Trumper, L., Hummel, M., Klapper, W., Siebert, R., Loeffler, M., Binder, H. and German Cancer Aid consortium Molecular Mechanisms for Malignant, L. (2019). "A modular transcriptome map of mature B cell lymphomas." Genome Med 11(1): 27.

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Nikoghosyan, M., Hakobyan, S., Hovhannisyan, A., Loeffler-Wirth, H., Binder, H. and Arakelyan, A. (2019). "Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians - A Machine Learning Approach." Front Genet 10: 394.

Regier, Y., Komma, K., Weigel, M., Kraiczy, P., Laisi, A., Pulliainen, A. T., Hain, T. and Kempf, V. A. J. (2019). "Combination of microbiome analysis and serodiagnostics to assess the risk of pathogen transmission by ticks to humans and animals in central Germany." Parasites & Vectors 12(1): 11.

Scheller, N., Herold, S., Kellner, R., Bertrams, W., Jung, A. L., Janga, H., Greulich, T., Schulte, L. N., Vogelmeier, C. F., Lohmeyer, J. and Schmeck, B. (2019). "Proviral MicroRNAs Detected in Extracellular Vesicles From Bronchoalveolar Lavage Fluid of Patients With Influenza Virus-Induced Acute Respiratory Distress Syndrome." J Infect Dis 219(4): 540-543.

Schulte, L. N., Bertrams, W., Stielow, C. and Schmeck, B. (2019). "ncRNAs in Inflammatory and Infectious Diseases." Methods Mol Biol 1912: 3-32.

Wienhold, S. M., Lienau, J. and Witzenrath, M. (2019). "Towards Inhaled Phage Therapy in Western Europe." Viruses 11(3).


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Dietert, K., Nouailles, G., Gutbier, B., Reppe, K., Berger, S., Jiang, X., Schauer, A. E., Hocke, A. C., Herold, S., Slevogt, H., Witzenrath, M., Suttorp, N. and Gruber, A. D. (2018). "Digital Image Analyses on Whole-Lung Slides in Mouse Models of Acute Pneumonia." American Journal of Respiratory Cell and Molecular Biology 58(4): 440-448.

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Gutbier, B., Schönrock, S. M., Ehrler, C., Haberberger, R., Dietert, K., Gruber, A. D., Kummer, W., Michalick, L., Kuebler, W. M., Hocke, A. C., Szymanski, K., Letsiou, E., Lüth, A., Schumacher, F., Kleuser, B., Mitchell, T. J., Bertrams, W., Schmeck, B., Treue, D., Klauschen, F., Bauer, T. T., Tönnies, M., Weissmann, N., Hippenstiel, S., Suttorp, N., Witzenrath, M. and Group, C. S. (2018). "Sphingosine Kinase 1 Regulates Inflammation and Contributes to Acute Lung Injury in Pneumococcal Pneumonia via the Sphingosine-1-Phosphate Receptor 2." Critical Care Medicine.

Hopp, L., Loeffler-Wirth, H., Nersisyan, L., Arakelyan, A. and Binder, H. (2018). "Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome." Frontiers in Immunology 9: 1620.

Kaplonek, P., Khan, N., Reppe, K., Schumann, B., Emmadi, M., Lisboa, M. P., Xu, F.-F., Calow, A. D. J., Parameswarappa, S. G., Witzenrath, M., Pereira, C. L. and Seeberger, P. H. (2018). "Improving vaccines against Streptococcus pneumoniae using synthetic glycans." Proceedings of the National Academy of Sciences of the United States of America 115(52): 13353-13358.

Marin-Sanguino, A., Vera, J. and Alves, R. (2018). "Editorial: Foundations of Theoretical Approaches in Systems Biology." Frontiers in Genetics 9: 290.

Regier, Y., Komma, K., Weigel, M., Pulliainen, A. T., Goettig, S., Hein, T. and Kempf, V. A. J. (2018). "Microbiome Analysis Reveals the Presence of Bartonella spp. and Acinetobacter spp. in Deer Keds (Lipoptena cervi)." Frontiers in Microbiology 9: 3100.

Ruiz-Moreno, J. S., Hamann, L., Jin, L., Sander, L. E., Puzianowska-Kuznicka, M., Cambier, J., Witzenrath, M., Schumann, R. R., Suttorp, N. and Opitz, B. (2018). "The cGAS/STING Pathway Detects Streptococcus pneumoniae but Appears Dispensable for Antipneumococcal Defense in Mice and Humans." Infection and Immunity 86(3).

Ruiz-Moreno, J. S., Hamann, L., Shah, J. A., Verbon, A., Mockenhaupt, F. P., Puzianowska-Kuznicka, M., Naujoks, J., Sander, L. E., Witzenrath, M., Cambier, J. C., Suttorp, N., Schumann, R. R., Jin, L., Hawn, T. R., Opitz, B. and Group, C. S. (2018). "The common HAQ STING variant impairs cGAS-dependent antibacterial responses and is associated with susceptibility to Legionnaires' disease in humans." PLoS pathogens 14(1): e1006829.

Santos, G., Lai, X., Eberhardt, M. and Vera, J. (2018). "Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling." Frontiers in Cellular and Infection Microbiology 8.

Schumann, B., Reppe, K., Kaplonek, P., Wahlbrink, A., Anish, C., Witzenrath, M., Pereira, C. L. and Seeberger, P. H. (2018). "Development of an Efficacious, Semisynthetic Glycoconjugate Vaccine Candidate against Streptococcus pneumoniae Serotype 1." ACS central science 4(3): 357-361.

Vera, J. and Santos, G. (2018). "Can Gamification Contribute to Computer Modeling-Driven Biomedical Research?" Frontiers in Physiology 9: 908.

Wienhold, S.-M., Macrì, M., Nouailles, G., Dietert, K., Gurtner, C., Gruber, A. D., Heimesaat, M. M., Lienau, J., Schumacher, F., Kleuser, B., Opitz, B., Suttorp, N., Witzenrath, M. and Müller-Redetzky, H. C. (2018). "Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice." Critical Care (London, England) 22(1): 282.


Arakelyan, A., Nersisyan, L., Poghosyan, D., Khondkaryan, L., Hakobyan, A., Löffler-Wirth, H., Melanitou, E. and Binder, H. (2017). "Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles." PloS One 12(11): e0187572.

Cantone, M., Santos, G., Wentker, P., Lai, X. and Vera, J. (2017). "Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection." Frontiers in Physiology 8: 645.

Emmadi, M., Khan, N., Lykke, L., Reppe, K., G Parameswarappa, S., Lisboa, M. P., Wienhold, S.-M., Witzenrath, M., Pereira, C. L. and Seeberger, P. H. (2017). "A Streptococcus pneumoniae Type 2 Oligosaccharide Glycoconjugate Elicits Opsonic Antibodies and Is Protective in an Animal Model of Invasive Pneumococcal Disease." Journal of the American Chemical Society 139(41): 14783-14791.

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Jensen, A. V., Faurholt-Jepsen, D., Egelund, G. B., Andersen, S. B., Petersen, P. T., Benfield, T., Witzenrath, M., Rohde, G., Ravn, P., German Community-Acquired Pneumonia Competence, N. and German Community-Acquired Pneumonia Competence, N. (2017). "Undiagnosed Diabetes Mellitus in Community-Acquired Pneumonia: A Prospective Cohort Study." Clinical Infectious Diseases 65(12): 2091-2098.

Jentho, E., Bodden, M., Schulz, C., Jung, A.-L., Seidel, K., Schmeck, B. and Bertrams, W. (2017). "microRNA-125a-3p is regulated by MyD88 in Legionella pneumophila infection and targets NTAN1." PloS One 12(4): e0176204.

Jung, A. L., Herkt, C. E., Schulz, C., Bolte, K., Seidel, K., Scheller, N., Sittka-Stark, A., Bertrams, W. and Schmeck, B. (2017). "Legionella pneumophila infection activates bystander cells differentially by bacterial and host cell vesicles." Scientific Reports 7(1): 6301.

Jung, A. L., Hoffmann, K., Herkt, C. E., Schulz, C., Bertrams, W. and Schmeck, B. (2017). "Legionella pneumophila Outer Membrane Vesicles: Isolation and Analysis of Their Pro-inflammatory Potential on Macrophages." Journal of Visualized Experiments: JoVE(120).

Lisboa, M. P., Khan, N., Martin, C., Xu, F.-F., Reppe, K., Geissner, A., Govindan, S., Witzenrath, M., Pereira, C. L. and Seeberger, P. H. (2017). "Semisynthetic glycoconjugate vaccine candidate againstStreptococcus pneumoniaeserotype 5." Proceedings of the National Academy of Sciences of the United States of America 114(42): 11063-11068.

Schulz, C., Lai, X., Bertrams, W., Jung, A. L., Sittka-Stark, A., Herkt, C. E., Janga, H., Zscheppang, K., Stielow, C., Schulte, L., Hippenstiel, S., Vera, J. and Schmeck, B. (2017). "THP-1-derived macrophages render lung epithelial cells hypo-responsive to Legionella pneumophila - a systems biology study." Scientific Reports 7(1): 11988.

Schumann, B., Hahm, H. S., Parameswarappa, S. G., Reppe, K., Wahlbrink, A., Govindan, S., Kaplonek, P., Pirofski, L.-A., Witzenrath, M., Anish, C., Pereira, C. L. and Seeberger, P. H. (2017). "A semisynthetic Streptococcus pneumoniae serotype 8 glycoconjugate vaccine." Science Translational Medicine 9(380).

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Wentker, P., Eberhardt, M., Dreyer, F. S., Bertrams, W., Cantone, M., Griss, K., Schmeck, B. and Vera, J. (2017). "An Interactive Macrophage Signal Transduction Map Facilitates Comparative Analyses of High-Throughput Data." Journal of Immunology (Baltimore, Md.: 1950) 198(5): 2191-2201.


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Du Bois, I., Marsico, A., Bertrams, W., Schweiger, M.R., Caffrey, B.E., Sittka-Stark, A., Eberhardt, M., Vera, J., Vingron, M., Schmeck, B.T., 2016. Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2. J. Infect. Dis. 214, 454–463.

Eberhardt, M., Lai, X., Tomar, N., Gupta, S., Schmeck, B., Steinkasserer, A., Schuler, G., Vera, J., 2016. Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive. Methods Mol. Biol. 1386, 135–179.

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