--- title: Publications --- - [franziska.mueller@bih-charite.de](mailto:franziska.mueller@bih-charite.de) - [news](https://www.hidih.org/news?hsLang=en) - [gesundhyte.de](https://www.hidih.org/magazine-gesundhyte.de?hsLang=en) - [publications](https://www.hidih.org/publications) - [contact](https://www.hidih.org/contact?hsLang=en) [![BIH-003\_Logo\_HiDiH\_01\_600px\_200124](https://www.hidih.org/hubfs/CD/Logos/BIH-003_Logo_HiDiH_01_600px_200124.png "BIH-003_Logo_HiDiH_01_600px_200124")](https://www.hidih.org/?hsLang=en) - [Research Groups](https://www.hidih.org/research) - [Artificial Intelligence (B)](https://www.hidih.org/research/ailslab) - [Cancer Bioinformatics (B)](https://www.hidih.org/research/computational-oncology) - [Health Data (B/HD)](https://www.hidih.org/research/health-data) - [Intelligent Imaging (B)](https://www.hidih.org/research/intelligent-imaging) - [Medical Omics (B)](https://www.hidih.org/research/medicalomics) - [Systems Medicine (HD)](https://www.hidih.org/research/systems-medicine-hd) - BIH Visiting Professors - [From Singapore](https://www.hidih.org/international/singapore) - [From UK](https://www.hidih.org/international/uk-london) - Projects - Cancer - [EU-CIP](https://www.hidih.org/eu-cip) - [CANDLE](https://www.hidih.org/candle) - [PM4Onco](https://www.hidih.org/projects/pm4onco) - [SAGE](https://www.hidih.org/projects/sage) - Centers - [CRC/TR 412 MASLD](https://www.hidih.org/tr412) - [DZKJ](https://www.hidih.org/projects/dzkj) - [DZPG](https://www.hidih.org/projects/dzpg) - [ECPDC](https://www.hidih.org/projects/ecpdc) - [maia](https://www.hidih.org/projects/maia) - Cloud & IT - Infrastructures - [de.KDC](https://www.hidih.org/projects/dekcd) - [de.NBI/ELIXIR](https://www.hidih.org/projects/denbi-elixir) - [EOSC-Life](https://www.hidih.org/projects/eosc-life) - [Gaia-X](https://www.hidih.org/projects/gaia-x) - COVID-19 & SARS-CoV-2 - [COVID-19 & SARS-CoV-2](https://www.hidih.org/projects/covid-19-sars-cov-2) - [PATH2XNAT](https://www.hidih.org/projects/path2xnat) - Datamanagement - [environMENTAL](https://www.hidih.org/projects/environmental) - [FACE](https://www.hidih.org/projects/face) - European Health Data Space - [Data4Good](https://www.hidih.org/data4good) - [i2X](https://www.hidih.org/i2x) - [myHealth@myHands](https://www.hidih.org/myhealthmyhands) - [HEALTH-X dataLOFT](https://www.hidih.org/projects/health-xdataloft) - Medical Informatics Initiative - [ACRIBiS](https://www.hidih.org/projects/acribis) - [CAEHR](https://www.hidih.org/projects/caehr) - [CALM-QE](https://www.hidih.org/calm-qe) - [HiGHmed](https://www.hidih.org/projects/highmed) - [MII-Gaia](https://www.hidih.org/mii-gaia) - [PM4Onco](https://www.hidih.org/projects/pm4onco) - Omics - [EASI-Genomics](https://www.hidih.org/projects/easi-genomics) - [ESPACE](https://www.hidih.org/projects/espace) - Management - [Office Management](https://www.hidih.org/about-us/office-management) - [Center & Project Management](https://www.hidih.org/management/project-management) - Events - [SBHD](https://www.hidih.org/events_sbhd) - Education & Career - [Career](https://www.hidih.org/career) - [Education](https://www.hidih.org/education) ![AdobeStock\_©-razihusin\_179789354\_2000px\_200131](https://www.hidih.org/hs-fs/hubfs/CD/Modulbilder/Hero%20Banner/AdobeStock_%C2%A9-razihusin_179789354_2000px_200131.jpg?width=2000&name=AdobeStock_%C2%A9-razihusin_179789354_2000px_200131.jpg "AdobeStock_©-razihusin_179789354_2000px_200131") # Publications **Please check [http://www.researcherid.com/rid/B-6121-2009](http://www.researcherid.com/rid/B-6121-2009) for a full publication list of Roland Eils**   2025 Bolduan, F., Muller-Botticher, N., Debnath, O., Eichhorn, I., Giesecke, Y., Wetzel, A., Sahay, S., Zemojtel, T., Jaeger, M., Ungethuem, U., Roderburg, C., Kunze, C. A., Lehmann, A., Horst, D., Tacke, F., Eils, R., Wiedenmann, B., Sigal, M., & Ishaque, N. (2025). Small intestinal neuroendocrine tumors lack early genomic drivers, acquire DNA repair defects and harbor hallmarks of low REST expression. Sci Rep, 15(1), 17969. doi:10.1038/s41598-025-01912-4 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Berlin, Germany; Co-author Huang, X., Gu, L., Sun, J., & Eils, R. (2025). Bridging the gaps: Overcoming challenges of implementing AI in healthcare. Med, 6(4), 100666. doi:10.1016/j.medj.2025.100666 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Senior author Messingschlager, M., Mackowiak, S. D., Voelker, M. T., Bieg, M., Loske, J., Chua, R. L., Liebig, J., Lukassen, S., Thurmann, L., Seegebarth, A., Twardziok, S., Doncevic, D., Herrmann, C., Lorenz, S., Klages, S., Steinbeis, F., Witzenrath, M., Kurth, F., Conrad, C., Sander, L. E., Ishaque, N., Eils, R., Lehmann, I., Laudi, S., & Trump, S. (2025). DNA methylation changes during acute COVID-19 are associated with long-term transcriptional dysregulation in patients' airway epithelial cells. EMBO Mol Med, 17(5), 923–937. doi:10.1038/s44321-025-00215-5 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Berlin, Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; German Center for Lung Reseawrch (DZL), Giessen, Germany; Shared Senior author Muller-Bötticher, N., Sahay, S., Eils, R., & Ishaque, N. (2025). SpatialLeiden: spatially aware Leiden clustering. Genome Biol, 26(1), 24. doi:10.1186/s13059-025-03489-7 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Berlin, Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; Co-author Muller-Botticher, N., Tiesmeyer, S., Eils, R., & Ishaque, N. (2025). Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data. Small Methods, 9(5), e2401123. doi:10.1002/smtd.202401123 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Berlin, Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; Co-author Nonn, O., Debnath, O., Valdes, D. S., Sallinger, K., Secener, A. K., Fischer, C., Tiesmeyer, S., Nimo, J., Kuenzer, T., Ulrich, J., Maxian, T., Knofler, M., Karau, P., Bartolomaeus, H., Kroneis, T., Frolova, A., Neuper, L., Haase, N., Malt, A., Muller-Botticher, N., Kraker, K., Kedziora, S., Forstner, D., Eils, R., Schmidt-Ullrich, R., Haider, S., Verlohren, S., Stern, C., Sugulle, M., Jones, S., Thilaganathan, B., Kaitu'u-Lino, T. J., Tong, S., Huppertz, B., El-Heliebi, A., Staff, A. C., Coscia, F., Muller, D. N., Dechend, R., Gauster, M., Ishaque, N., & Herse, F. (2025). Senescent Syncytiotrophoblast Secretion During Early Onset Preeclampsia. Hypertension, 82(5), 787–799. doi:10.1161/HYPERTENSIONAHA.124.23362 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Co-author Sandmann, S., Hegselmann, S., Fujarski, M., Bickmann, L., Wild, B., Eils, R., & Varghese, J. (2025). Benchmark evaluation of DeepSeek large language models in clinical decision-making. Nat Med. doi:10.1038/s41591-025-03727-2 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Intelligent Medicine Institute, Fudan University, Shanghai, China   Shared Senior author Corresponding author Steinfeldt, J., Wild, B., Buergel, T., Pietzner, M., Upmeier Zu Belzen, J., Vauvelle, A., Hegselmann, S., Denaxas, S., Hemingway, H., Langenberg, C., Landmesser, U., Deanfield, J., & Eils, R. (2025). Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats. Nat Commun, 16(1), 585. doi:10.1038/s41467-025-55879-x Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; Shared Senior author Corresponding author Yuan, D., Jugas, R., Pokorna, P., Sterba, J., Slaby, O., Schmid, S., Siewert, C., Osberg, B., Capper, D., Halldorsson, S., Vik-Mo, E. O., Zeiner, P. S., Weber, K. J., Harter, P. N., Thomas, C., Albers, A., Rechsteiner, M., Reimann, R., Appelt, A., Schuller, U., Jabareen, N., Mackowiak, S., Ishaque, N., Eils, R., Lukassen, S., & Euskirchen, P. (2025). crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors. Nat Cancer. doi:10.1038/s43018-025-00976-5 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin,  Germany; Co-author 2024 Amit, I., Ardlie, K., Arzuaga, F., Awandare, G., Bader, G., Bernier, A., Carninci, P., Donnelly, S., Eils, R., Forrest, A. R. R., Greely, H. T., Guigo, R., Hacohen, N., Haniffa, M., Kirby, E. S., Knoppers, B. M., Kriegstein, A., Lein, E. S., Linnarsson, S., Majumder, P. P., Merad, M., Meyer, K., Mhlanga, M. M., Nolan, G., Ntusi, N. A. B., Pe'er, D., Prabhakar, S., Raven-Adams, M., Regev, A., Rozenblatt-Rosen, O., Saha, S., Saltzman, A., Shalek, A. K., Shin, J. W., Stunnenberg, H., Teichmann, S. A., Tickle, T., Villani, A. C., Wells, C., Wold, B., Yang, H., & Zhuang, X. (2024). The commitment of the human cell atlas to humanity. Nat Commun, 15(1), 10019. doi:10.1038/s41467-024-54306-x Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin, Germany; Co-author Ganna, A., Carracedo, A., Christiansen, C. F., Di Angelantonio, E., Dykstra, P. A., Dzhambov, A. M., Eils, R., Green, S., Schneider, K. L., Varga, T. V., Vuorinen, A. L., Zuccolo, L., Rod, N. H., & Hoeyer, K. (2024). The European Health Data Space can be a boost for research beyond borders. Nat Med, 30(11), 3053-3056. doi:10.1038/s41591-024-03246-6 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin, Germany; Co-author Heumos, L., Ehmele, P., Treis, T., Upmeier Zu Belzen, J., Roellin, E., May, L., Namsaraeva, A., Horlava, N., Shitov, V. A., Zhang, X., Zappia, L., Knoll, R., Lang, N. J., Hetzel, L., Virshup, I., Sikkema, L., Curion, F., Eils, R., Schiller, H. B., Hilgendorff, A., & Theis, F. J. (2024). An open-source framework for end-to-end analysis of electronic health record data. Nat Med, 30(11), 3369-3380. doi:10.1038/s41591-024-03214-0 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin, Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; Co-author Loske, J., Voller, M., Lukassen, S., Stahl, M., Thurmann, L., Seegebarth, A., Rohmel, J., Wisniewski, S., Messingschlager, M., Lorenz, S., Klages, S., Eils, R., Lehmann, I., Mall, M. A., Graeber, S. Y., & Trump, S. (2024). Pharmacological Improvement of CFTR Function Rescues Airway Epithelial Homeostasis and Host Defense in Children with Cystic Fibrosis. Am J Respir Crit Care Med. doi:10.1164/rccm.202310-1836OC Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin, Germany;     German Centre for Lung Research (DZL), Associated Partner Site, Berlin, Germany; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Berlin, Germany Co-author Peng, Z., Apfelbacher, C., Brandstetter, S., Eils, R., Kabesch, M., Lehmann, I., Trump, S., Wellmann, S., Genuneit, J., & NAMIBIO App Consortium (2024). Directed acyclic graph for epidemiological studies in childhood food allergy: Construction, user's guide, and application. Allergy. doi:10.1111/all.16025 Center for Digital Health, Berlin Institute of Health (BIH) at Charité-Universitatsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany; German Center of Child and Youth Health (DZKJ), Germany Co-author NAMIBIO App Consortium Citation (listed as consortium member/collaborator)   Polemiti, E., Hese, S., Schepanski, K., Yuan, J. C., Schumann, G., & EnvironMENTAL Consortium (2024). How does the macroenvironment influence brain and behaviour-a review of current status and future perspectives. Molecular Psychiatry. doi:10.1038/s41380-024-02557-x Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany EnvironMENTAL Consortium Citation  (listed as consortium member/collaborator) Radke, J., Meinhardt, J., Aschman, T., Chua, R. L., Farztdinov, V., Lukassen, S., Ten, F. W., Friebel, E., Ishaque, N., Franz, J., Huhle, V. H., Mothes, R., Peters, K., Thomas, C., Schneeberger, S., Schumann, E., Kawelke, L., Junger, J., Horst, V., Streit, S., von Manitius, R., Kortvelyessy, P., Vielhaber, S., Reinhold, D., Hauser, A. E., Osterloh, A., Enghard, P., Ihlow, J., Elezkurtaj, S., Horst, D., Kurth, F., Muller, M. A., Gassen, N. C., Melchert, J., Jechow, K., Timmermann, B., Fernandez-Zapata, C., Bottcher, C., Stenzel, W., Kruger, E., Landthaler, M., Wyler, E., Corman, V., Stadelmann, C., Ralser, M., Eils, R., Heppner, F. L., Mulleder, M., Conrad, C., & Radbruch, H. (2024). Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19. Nat Neurosci, 27(3), 409-420. doi:10.1038/s41593-024-01573-y Center of Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany Co-author Semler, S. C., Boeker, M., Eils, R., Krefting, D., Loeffler, M., Bussmann, J., Wissing, F., & Prokosch, H. U. (2024). The Medical Informatics Initiative at a glance-establishing a health research data infrastructure in Germany. Bundesgesundheitsblatt-Gesundheitsforschung-Gesundheitsschutz. doi:10.1007/s00103-024-03887-5 Health Data Science Unit, Medizinische Fakultät Heidelberg, Universität Heidelberg, Heidelberg, Deutschland Co-author   2023 Adam, L., Stanifer, M., Springer, F., Mathony, J., Brune, M., Di Ponzio, C., Eils, R., Boulant, S., Niopek, D., & Kallenberger, S. M. (2023). Transcriptomics-inferred dynamics of SARS-CoV-2 interactions with host epithelial cells. Sci Signal, 16(804), eabl8266. doi:10.1126/scisignal.abl8266 Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, 69120, Heidelberg, Germany;  Co-author Bosquillon de Jarcy, L., Akbil, B., Mhlekude, B., Leyens, J., Postmus, D., Harnisch, G., Jansen, J., Schmidt, M. L., Aigner, A., Pott, F., Chua, R. L., Krist, L., Gentile, R., Muhlemann, B., Jones, T. C., Niemeyer, D., Fricke, J., Keil, T., Pischon, T., Janke, J., Conrad, C., Iacobelli, S., Drosten, C., Corman, V. M., Ralser, M., Eils, R., Kurth, F., Sander, L., & Goffinet, C. (2023). 90K/LGALS3BP expression is upregulated in COVID-19 but may not restrict SARS-CoV-2 infection. Clin Exp Med, 23(7), 3689-3700. doi:10.1007/s10238-023-01077-2 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 , Berlin, Germany;  Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany;  Health Data Science Unit, Heidelberg University Hospital and BioQuant, 69120, Heidelberg, Germany Co-author     Kohler, S., Bosca, D., Karcher, F., Haarbrandt, B., Prinz, M., Marschollek, M., & Eils, R. (2023). Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model. J Biomed Inform, 144, 104437. doi:10.1016/j.jbi.2023.104437 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Digital Health Center, Kapelle-Ufer 2, 10117 Berlin, Germany;  Health Data Science Unit, Heidelberg University Hospital and BioQuant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany Senior author Corresponding author Magalhaes, V. G., Lukassen, S., Drechsler, M., Loske, J., Burkart, S. S., Wust, S., Jacobsen, E. M., Rohmel, J., Mall, M. A., Debatin, K. M., Eils, R., Autenrieth, S., Janda, A., Lehmann, I., & Binder, M. (2023). Immune-epithelial cell cross-talk enhances antiviral responsiveness to SARS-CoV-2 in children. EMBO Rep, 24(12), e57912. doi:10.15252/embr.202357912 Center for Digital Health, Berlin Institute of Health at the Charite- Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research, Associated Partner, Berlin, Germany; Health Data Science Unit, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany Co-author Messingschlager, M., Bartel-Steinbach, M., Mackowiak, S. D., Denkena, J., Bieg, M., Klos, M., Seegebarth, A., Straff, W., Suring, K., Ishaque, N., Eils, R., Lehmann, I., Lermen, D., & Trump, S. (2023). Genome-wide DNA methylation sequencing identifies epigenetic perturbations in the upper airways under long-term exposure to moderate levels of ambient air pollution. Environ Res, 233, 116413. doi:10.1016/j.envres.2023.116413 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany; German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, 69120, Heidelberg, Germany;  Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 14, 14195, Berlin, Germany Co-author Muller, A., Christmann, L. S., Kohler, S., Eils, R., & Prasser, F. (2023). Machine Learning for Medical Data Integration. Stud Health Technol Inform, 302, 691-695. doi:10.3233/SHTI230241 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany Co-author Polychronidou, M., Hou, J., Babu, M. M., Liberali, P., Amit, I., Deplancke, B., Lahav, G., Itzkovitz, S., Mann, M., Saez-Rodriguez, J., Theis, F., & Eils, R. (2023). Single-cell biology: what does the future hold? Mol Syst Biol, e11799. doi:10.15252/msb.202311799 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany  Senior author  Raab, R., Kuderle, A., Zakreuskaya, A., Stern, A. D., Klucken, J., Kaissis, G., Rueckert, D., Boll, S., Eils, R., Wagener, H., & Eskofier, B. M. (2023). Federated electronic health records for the European Health Data Space. Lancet Digit Health, 5(11), e840-e847. doi:10.1016/S2589-7500(23)00156-5 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany Co-author Schapranow, M. P., Borchert, F., Bougatf, N., Hund, H., & Eils, R. (2023). Software-Tool Support for Collaborative, Virtual, Multi-Site Molecular Tumor Boards. SN Comput Sci, 4(4), 358. doi:10.1007/s42979-023-01771-8 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany Senior author Schumann, G., Andreassen, O. A., Banaschewski, T., Calhoun, V. D., Clinton, N., Desrivieres, S., Brandlistuen, R. E., Feng, J. F., Hese, S., Hitchen, E., Hoffmann, P., Jia, T. Y., Jirsa, V., Marquand, A. F., Nees, F., Nöthen, M. M., Novarino, G., Polemiti, E., Ralser, M., Rapp, M., Schepanski, K., Schikowski, T., Slater, M., Sommer, P., Stahl, B. C., Thompson, P. M., Twardziok, S., van der Meer, D., Walter, H., Westlye, L., & EnvironMENTAL Consortium (2023). Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review. Jama Psychiatry, 80(10), 1066-1074. doi:10.1001/jamapsychiatry.2023.2996 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany EnvironMENTAL Consortium Citation (listed as consortium member/collaborator) Stricker, S., Ziegahn, N., Karsten, M., Boeckel, T., Stich-Boeckel, H., Maske, J., Rugo, E., Balazs, A., Millar Buchner, P., Dang-Heine, C., Schriever, V., Eils, R., Lehmann, I., Sander, L. E., Ralser, M., Corman, V. M., Mall, M. A., Sawitzki, B., & Roehmel, J. (2023). RECAST: Study protocol for an observational study for the understanding of the increased REsilience of Children compared to Adults in SARS-CoV-2 infecTion. BMJ Open, 13(4), e065221. doi:10.1136/bmjopen-2022-065221 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany; German Center for Lung Research, Giessen, Germany  Co-author Ten, F. W., Yuan, D., Jabareen, N., Phua, Y. J., Eils, R., Lukassen, S., & Conrad, C. (2023). resVAE ensemble: Unsupervised identification of gene sets in multi-modal single-cell sequencing data using deep ensembles. Front Cell Dev Biol, 11, 1091047. doi:10.3389/fcell.2023.1091047 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; Health Data Science Unit, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany Co-author Thurmann, L., Klos, M., Mackowiak, S. D., Bieg, M., Bauer, T., Ishaque, N., Messingschlager, M., Herrmann, C., Roder, S., Bauer, M., Schauble, S., Faessler, E., Hahn, U., Weichenhan, D., Mucke, O., Plass, C., Borte, M., von Mutius, E., Stangl, G. I., Lauener, R., Karvonen, A. M., Divaret-Chauveau, A., Riedler, J., Heinrich, J., Standl, M., von Berg, A., Schaaf, B., Herberth, G., Kabesch, M., Eils, R., Trump, S., & Lehmann, I. (2023). Global hypomethylation in childhood asthma identified by genome-wide DNA-methylation sequencing preferentially affects enhancer regions. Allergy, 78(6), 1489-1506. doi:10.1111/all.15658 Associated Member of the German Center for Lung Research, Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, German; German Center for Lung Research (DZL), Heidelberg, Germany  Shared senior author  Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., Lett, T., Yu, L., Nothen, M. M., Feng, J., Yu, C., Marquand, A., Schumann, G., & the environ, M. C. (2023). Effects of urban living environments on mental health in adults. Nat Med, 29(6), 1456–1467. doi:10.1038/s41591-023-02365-w Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany EnvironMENTAL Consortium Citation (listed as consortium member/collaborator)  Yeung, A. W. K., Torkamani, A., Butte, A. J., Glicksberg, B. S., Schuller, B., Rodriguez, B., Ting, D. S. W., Bates, D., Schaden, E., Peng, H., Willschke, H., van der Laak, J., Car, J., Rahimi, K., Celi, L. A., Banach, M., Kletecka-Pulker, M., Kimberger, O., Eils, R., Islam, S. M. S., Wong, S. T., Wong, T. Y., Gao, W., Brunak, S., & Atanasov, A. G. (2023). The promise of digital healthcare technologies. Front Public Health, 11, 1196596. doi:10.3389/fpubh.2023.1196596 Digital Health Center, Berlin Institute of Health (BIH), Charité – Universitätsmedizin Berlin, Berlin, Germany Co-author 2022 Balazs, A., Millar-Buechner, P., Muelleder, M., Farztdinov, V., Szyrwiel, L., Addante, A., Kuppe, A., Rubil, T., Drescher, M., Seidel, K., Stricker, S., Eils, R., Lehmann, I., Sawitzki, B., Roehmel, J., Ralser, M., & Mall, M. A. (2022). Age-Related Differences in Structure and Function of Nasal Epithelial Cultures From Healthy Children and Elderly People. Frontiers in Immunology, 13, 11. doi:10.3389/fimmu.2022.822437 Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany Co-author     Buergel, T., Steinfeldt, J., Ruyoga, G., Pietzner, M., Bizzarri, D., Vojinovic, D., Upmeier Zu Belzen, J., Loock, L., Kittner, P., Christmann, L., Hollmann, N., Strangalies, H., Braunger, J. M., Wild, B., Chiesa, S. T., Spranger, J., Klostermann, F., van den Akker, E. B., Trompet, S., Mooijaart, S. P., Sattar, N., Jukema, J. W., Lavrijssen, B., Kavousi, M., Ghanbari, M., Ikram, M. A., Slagboom, E., Kivimaki, M., Langenberg, C., Deanfield, J., Eils, R., & Landmesser, U. (2022). Metabolomic profiles predict individual multidisease outcomes. Nat Med, 28(11), 2309-2320. doi:10.1038/s41591-022-01980-3 Center for Digital Health, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Shared Senior author Corresponding author Georg, P., Astaburuaga-Garcia, R., Bonaguro, L., Brumhard, S., Michalick, L., Lippert, L. J., Kostevc, T., Gabel, C., Schneider, M., Streitz, M., Demichev, V., Gemund, I., Barone, M., Tober-Lau, P., Helbig, E. T., Hillus, D., Petrov, L., Stein, J., Dey, H. P., Paclik, D., Iwert, C., Mulleder, M., Aulakh, S. K., Djudjaj, S., Bulow, R. D., Mei, H. E., Schulz, A. R., Thiel, A., Hippenstiel, S., Saliba, A. E., Eils, R., Lehmann, I., Mall, M. A., Stricker, S., Rohmel, J., Corman, V. M., Beule, D., Wyler, E., Landthaler, M., Obermayer, B., von Stillfried, S., Boor, P., Demir, M., Wesselmann, H., Suttorp, N., Uhrig, A., Muller-Redetzky, H., Nattermann, J., Kuebler, W. M., Meisel, C., Ralser, M., Schultze, J. L., Aschenbrenner, A. C., Thibeault, C., Kurth, F., Sander, L. E., Bluthgen, N., Sawitzki, B., & Pa-Covid- Study Group (2022). Complement activation induces excessive T cell cytotoxicity in severe COVID-19. CELL, 185(3), 493-+. doi:10.1016/j.cel.2021.12.040 Center for Digital Health, Berlin Institute of Health (BIH), Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany Co-author Herrera, V. L. M., Walkey, A. J., Nguyen, M. Q., Gromisch, C. M., Mosaddhegi, J. Z., Gromisch, M. S., Jundi, B., Lukassen, S., Carstensen, S., Denis, R., Belkina, A. C., Baron, R. M., Pinilla-Vera, M., Mueller, M., Kimberly, W. T., Goldstein, J. N., Lehmann, I., Shih, A. R., Eils, R., Levy, B. D., & Ruiz-Opazo, N. (2022). A targetable 'rogue' neutrophil-subset, CD11b+DEspR+ immunotype, is associated with severity and mortality in acute respiratory distress syndrome (ARDS) and COVID-19-ARDS. Scientific Reports, 12(1), 24. doi:10.1038/s41598-022-09343-1 Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin; Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany Co-author Klein, P., Kallenberger, S. M., Roth, H., Roth, K., Ly-Hartig, T. B. N., Magg, V., Ales, J., Talemi, S. R., Qiang, Y., Wolf, S., Oleksiuk, O., Kurilov, R., Di Ventura, B., Bartenschlager, R., Eils, R., Rohr, K., Hamprecht, F. A., Hofer, T., Fackler, O. T., Stoecklin, G., & Ruggieri, A. (2022). Temporal control of the integrated stress response by a stochastic molecular switch. Science Advances, 8(12), 21. doi:10.1126/sciadv.abk2022 Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany Co-author Laplana, M., Bieg, M., Faltus, C., Melnik, S., Bogatyrova, O., Gu, Z. G., Muley, T., Meister, M., Dienemann, H., Herpel, E., Amos, C. I., Schlesner, M., Eils, R., Plass, C., & Risch, A. (2022). Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers. Epigenetics, 17(2), 117-132. doi:10.1080/15592294.2021.1878723 Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Berlin, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany Co-author Loske, J., Rohmel, J., Lukassen, S., Stricker, S., Magalhaes, V. G., Liebig, J., Chua, R. L., Thurmann, L., Messingschlager, M., Seegebarth, A., Timmermann, B., Klages, S., Ralser, M., Sawitzki, B., Sander, L. E., Corman, V. M., Conrad, C., Laudi, S., Binder, M., Trump, S., Eils, R., Mall, M. A., & Lehmann, I. (2022). Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children. Nat Biotechnol, 40(3), 319-324. doi:10.1038/s41587-021-01037-9 Center for Digital Health, Berlin Institute of Health at the Charité - Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), associated partner, Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany Shared Senior author Corresponding author Pietzner, M., Chua, R. L., Wheeler, E., Jechow, K., Willett, J. D. S., Radbruch, H., Trump, S., Heidecker, B., Zeberg, H., Heppner, F. L., Eils, R., Mall, M. A., Richards, J. B., Sander, L. E., Lehmann, I., Lukassen, S., Wareham, N. J., Conrad, C., & Langenberg, C. (2022). ELF5 is a potential respiratory epithelial cell-specific risk gene for severe COVID-19. Nat Commun, 13(1), 4484. doi:10.1038/s41467-022-31999-6 Center for Digital Health, Berlin Institute of Health (BIH) at Charité –Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany; German Center for Lung Research (DZL), associated partner site, Augustenburger Platz 1, 13353 Berlin, Germany Co-author Prokosch, H. U., Bahls, T., Bialke, M., Eils, J., Fegeler, C., Gruendner, J., Haarbrandt, B., Hampf, C., Hoffmann, W., Hund, H., Kampf, M., Kapsner, L. A., Kasprzak, P., Kohlbacher, O., Krefting, D., Mang, J. M., Marschollek, M., Mate, S., Muller, A., Prasser, F., Sass, J., Semler, S., Stenzhorn, H., Thun, S., Zenker, S., & Eils, R. (2022). The COVID-19 Data Exchange Platform of the German University Medicine. Stud Health Technol Inform, 294, 674-678. doi:10.3233/SHTI220554 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany Senior author Radke, J., Ishaque, N., Koll, R., Gu, Z., Schumann, E., Sieverling, L., Uhrig, S., Hubschmann, D., Toprak, U. H., Lopez, C., Hostench, X. P., Borgoni, S., Juraeva, D., Pritsch, F., Paramasivam, N., Balasubramanian, G. P., Schlesner, M., Sahay, S., Weniger, M., Pehl, D., Radbruch, H., Osterloh, A., Korfel, A., Misch, M., Onken, J., Faust, K., Vajkoczy, P., Moskopp, D., Wang, Y., Jodicke, A., Trumper, L., Anagnostopoulos, I., Lenze, D., Kuppers, R., Hummel, M., Schmitt, C. A., Wiestler, O. D., Wolf, S., Unterberg, A., Eils, R., Herold-Mende, C., Brors, B., ICGC MMML-Seq Consortium, Siebert, R., Wiemann, S., & Heppner, F. L. (2022). The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat Commun, 13(1), 2558. doi:10.1038/s41467-022-30050-y10.1038/s41467-022-30050-y Digital Health Center, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany; Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany Co-author ICGC MMML-Seq Consortium citation (listed as consortium member/collaborator) Schuth, S., Le Blanc, S., Krieger, T. G., Jabs, J., Schenk, M., Giese, N. A., Buchler, M. W., Eils, R., Conrad, C., & Strobel, O. (2022). Patient-specific modeling of stroma-mediated chemoresistance of pancreatic cancer using a three-dimensional organoid-fibroblast co-culture system. J Exp Clin Cancer Res, 41(1), 312. doi:10.1186/s13046-022-02519-7 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany Co-author Steinfeldt, J., Buergel, T., Loock, L., Kittner, P., Ruyoga, G., Zu Belzen, J. U., Sasse, S., Strangalies, H., Christmann, L., Hollmann, N., Wolf, B., Ference, B., Deanfield, J., Landmesser, U., & Eils, R. (2022). Neural network-based integration of polygenic and clinical information: development and validation of a prediction model for 10-year risk of major adverse cardiac events in the UK Biobank cohort. Lancet Digit Health, 4(2), e84-e94. doi:10.1016/S2589-7500(21)00249-1 Center for Digital Health, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany;  Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Shared Senior author  Corresponding author Sunami, Y., Chen, Y., Trojanowicz, B., Sommerer, M., Hammerle, M., Eils, R., & Kleeff, J. (2022). Single Cell Analysis of Cultivated Fibroblasts from Chronic Pancreatitis and Pancreatic Cancer Patients. Cells, 11(16). doi:10.3390/cells11162583 Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, 69120 Heidelberg, Germany Shared Senior author Tiesmeyer, S., Sahay, S., Muller-Botticher, N., Eils, R., Mackowiak, S. D., & Ishaque, N. (2022). SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data. Frontiers in Genetics, 13, 7. doi:10.3389/fgene.2022.785877 Digital Health Center, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany Co-author Trefzer, T. B., Schneider, M. A., Jechow, K., Chua, R. L., Muley, T., Winter, H., Kriegsmann, M., Meister, M., Eils, R., & Conrad, C. (2022). Intratumoural heterogeneity and immune modulation in lung adenocarcinoma in female smokers and never smokers. Cancer research. doi:10.1158/0008-5472.Can-21-3836 Digital Health Center, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany Shared Senior author      2021 Aslam, M., Kandasamy, N., Ullah, A., Paramasivam, N., Ozturk, M. A., Naureen, S., Arshad, A., Badshah, M., Khan, K., Wajid, M., Abbasi, R., Ilyas, M., Eils, R., Schlesner, M., Wade, R. C., Ahmad, N., & von Engelhardt, J. (2021). Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson's disease. Npj Genomic Medicine, 6(1), 10. doi:10.1038/s41525-020-00163-8 Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Bioquant, Medical Faculty, University of Heidelberg, Heidelberg, Germany Co-author     Bieg, M., Moskalev, E. A., Will, R., Hebele, S., Schwarzbach, M., Schmeck, S., Hohenberger, P., Jakob, J., Kasper, B., Gaiser, T., Strobel, P., Wardelmann, E., Kontny, U., Braunschweig, T., Sirbu, H., Grutzmann, R., Meidenbauer, N., Ishaque, N., Eils, R., Wiemann, S., Hartmann, A., Agaimy, A., Fritchie, K., Giannini, C., & Haller, F. (2021). Gene Expression in Solitary Fibrous Tumors (SFTs) Correlates with Anatomic Localization and NAB2-STAT6 Gene Fusion Variants. American Journal of Pathology, 191(4), 602-617. doi:10.1016/j.ajpath.2020.12.015 Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany;  Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany Co-author Borchert, F., Mock, A., Tomczak, A., Hugel, J., Alkarkoukly, S., Knurr, A., Volckmar, A. L., Stenzinger, A., Schirmacher, P., Debus, J., Jager, D., Longerich, T., Frohling, S., Eils, R., Bougatf, N., Sax, U., & Schapranow, M. P. (2021). Knowledge bases and software support for variant interpretation in precision oncology. Briefings in Bioinformatics, 22(6), 17. doi:10.1093/bib/bbab134 Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Center for Digital Health, Berlin Institute of Health and Charité Universitötsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany Co-author Dentro, S. C., Leshchiner, I., Haase, K., Tarabichi, M., Wintersinger, J., Deshwar, A. G., Yu, K., Rubanova, Y., Macintyre, G., Demeulemeester, J., Vazquez-Garcia, I., Kleinheinz, K., Livitz, D. G., Malikic, S., Donmez, N., Sengupta, S., Anur, P., Jolly, C., Cmero, M., Rosebrock, D., Schumacher, S. E., Fan, Y., Fittall, M., Drews, R. M., Yao, X., Watkins, T. B. K., Lee, J., Schlesner, M., Zhu, H., Adams, D. J., McGranahan, N., Swanton, C., Getz, G., Boutros, P. C., Imielinski, M., Beroukhim, R., Sahinalp, S. C., Ji, Y., Peifer, M., Martincorena, I., Markowetz, F., Mustonen, V., Yuan, K., Gerstung, M., Spellman, P. T., Wang, W., Morris, Q. D., Wedge, D. C., Van Loo, P. on behalf of the  PCAWG Evolution Heterogeneity Working and the PCAWG Consortium (2021). Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell, 184(8), 2239-2254 e2239. doi:10.1016/j.cell.2021.03.009 PCAWG Consortium citation (listed as consortium member/collaborator) Derrien, J., Guerin-Charbonnel, C., Gaborit, V., Campion, L., Devic, M., Douillard, E., Roi, N., Avet-Loiseau, H., Decaux, O., Facon, T., Mallm, J. P., Eils, R., Munshi, N. C., Moreau, P., Herrmann, C., Magrangeas, F., & Minvielle, S. (2021). The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability. Genome Medicine, 13(1), 21. doi:10.1186/s13073-021-00938-3 Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, Berlin, 10178, Germany; Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt- Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany; Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, 69120, Germany Co-author Espinet, E., Gu, Z. G., Imbusch, C. D., Giese, N. A., Buscher, M., Safavi, M., Weisenburger, S., Klein, C., Vogel, V., Falcone, M., Insua-Rodriguez, J., Reitberger, M., Thiel, V., Kossi, S. O., Muckenhuber, A., Sarai, K., Lee, A. Y. L., Backx, E., Zarei, S., Gaida, M. M., Rodriguez-Paredes, M., Donato, E., Yen, H. Y., Eils, R., Schlesner, M., Pfarr, N., Hackert, T., Plass, C., Brors, B., Steiger, K., Weichenhan, D., Arda, H. E., Rooman, I., Kopp, J. L., Strobel, O., Weichert, W., Sprick, M. R., & Trumpp, A. (2021). Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer Discovery, 11(3), 638-659. doi:10.1158/2159-8290.Cd-20-1202 Digital Health Centre, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, University Hospital and University of Heidelberg, Heidelberg, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany Co-author Gassen, N. C., Papies, J., Bajaj, T., Emanuel, J., Dethloff, F., Chua, R. L., Trimpert, J., Heinemann, N., Niemeyer, C., Weege, F., Honzke, K., Aschman, T., Heinz, D. E., Weckmann, K., Ebert, T., Zellner, A., Lennarz, M., Wyler, E., Schroeder, S., Richter, A., Niemeyer, D., Hoffmann, K., Meyer, T. F., Heppner, F. L., Corman, V. M., Landthaler, M., Hocke, A. C., Morkel, M., Osterrieder, N., Conrad, C., Eils, R., Radbruch, H., Giavalisco, P., Drosten, C., & Muller, M. A. (2021). SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals. Nat Commun, 12(1), 15. doi:10.1038/s41467-021-24007-w Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany; Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Co-author Haller, F., Schlieben, L. D., Ferrazzi, F., Michal, M., Stohr, R., Moskalev, E. A., Bieg, M., Bovee, J., Strobel, P., Ishaque, N., Grutzmann, R., Meidenbauer, N., Eils, R., Wiemann, S., Hartmann, A., Michal, M., & Agaimy, A. (2021). Lipomatous Solitary Fibrous Tumors Harbor Rare NAB2-STAT6 Fusion Variants and Show Up-Regulation of the Gene PPARG, Encoding for a Regulator of Adipocyte Differentiation. American Journal of Pathology, 191(7), 1314-1324. doi:10.1016/j.ajpath.2021.03.012 Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany Co-author Hensel, N., Gu, Z. G., Sagar, Wieland, D., Jechow, K., Kemming, J., Llewellyn-Lacey, S., Gosticle, E., Sogukpinar, O., Emmerich, F., Price, D. A., Bengsch, B., Boettler, T., Neumann-Haefelin, C., Eils, R., Conrad, C., Bartenschlager, R., Grun, D., Ishaque, N., Thimme, R., & Hofmann, M. (2021). Memory-like HCV-specific CD8(+) T cells retain a molecular scar after cure of chronic HCV infection. Nature Immunology, 22(2), 229-U246. doi:10.1038/s41590-020-00817-w Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany; Health Data Science Unit, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany Co-author Herrera, V. L. M., Walkey, A. J., Nguyen, M. Q., Gromisch, C. M., Mosaddhegi, J. Z., Gromisch, M. S., Jundi, B., Lukassen, S., Carstensen, S., Denis, R., Belkina, A. C., Baron, R. M., Pinilla-Vera, M., Muller, M., Kimberly, W. T., Goldstein, J. N., Lehmann, I., Shih, A. R., Eils, R., Levy, B. D., & Ruiz-Opazo, N. (2021). Increased Neutrophil-Subset Associated With Severity/Mortality In ARDS And COVID19-ARDS Expresses The Dual Endothelin-1/VEGFsignal-Peptide Receptor (DEspR): An Actionable Therapeutic Target. Res Sq. doi:10.21203/rs.3.rs-846250/v1 Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany Co-author  Hoffmann, M. D., Mathony, J., Zu Belzen, J. U., Harteveld, Z., Aschenbrenner, S., Stengl, C., Grimm, D., Correia, B. E., Eils, R., & Niopek, D. (2021). Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein. Nucleic acids research, 49(5), 11. doi:10.1093/nar/gkaa1198 Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany; Health Data Science Unit, BioQuant and Medical Faculty of Heidelberg University, Heidelberg 69120, Germany Shared Senior author  Corresponding author     Hubschmann, D., Jopp-Saile, L., Andresen, C., Kramer, S., Gu, Z. G., Heilig, C. E., Kreutzfeldt, S., Teleanu, V., Frohling, S., Eils, R., & Schlesner, M. (2021). Analysis of mutational signatures with yet another package for signature analysis. Genes Chromosomes & Cancer, 60(5), 314-331. doi:10.1002/gcc.22918 Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany Co-author Hubschmann, D., Kleinheinz, K., Wagener, R., Bernhart, S. H., Lopez, C., Toprak, U. H., Sungalee, S., Ishaque, N., Kretzmer, H., Kreuz, M., Waszak, S. M., Paramasivam, N., Ammerpohl, O., Aukema, S. M., Beekman, R., Bergmann, A. K., Bieg, M., Binder, H., Borkhardt, A., Borst, C., Brors, B., Bruns, P., Pau, E. C. D., Claviez, A., Doose, G., Haake, A., Karsch, D., Haas, S., Hansmann, M. L., Hoell, J. I., Hovestadt, V., Huang, B. D., Hummel, M., Jager-Schmidt, C., Kerssemakers, J. N. A., Korbel, J. O., Kube, D., Lawerenz, C., Lenze, D., Martens, J. H. A., Ott, G., Radlwimmer, B., Reisinger, E., Richter, J., Rico, D., Rosenstiel, P., Rosenwald, A., Schillhabel, M., Stilgenbauer, S., Stadler, P. F., Martin-Subero, J. I., Szczepanowski, M., Warsow, G., Weniger, M. A., Zapatka, M., Valencia, A., Stunnenberg, H. G., Lichter, P., Moller, P., Loeffler, M., Eils, R., Klapper, W., Hoffmann, S., Trumper, L., Kuppers, R., Schlesner, M., Siebert, R., Consortium, I. M.-S., Consortium, I. D.-M., & Consortium, B. (2021). Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia, 35(7), 2002-2016. doi:10.1038/s41375-021-01251-z Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany Co-author Krieger, T. G., Le Blanc, S., Jabs, J., Ten, F. W., Ishaque, N., Jechow, K., Debnath, O., Leonhardt, C. S., Giri, A., Eils, R., Strobel, O., & Conrad, C. (2021). Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy. Nat Commun, 12(1), 13. doi:10.1038/s41467-021-26059-4 Digital Health Center, Berlin Institute of Health (BIH)/Charité-Universitätsmedizin Berlin, Berlin, Germany;  Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany Shared Senior author Corresponding author Landmesser, U., Lehmann, I., & Eils, R. (2021). Hyperinflammation as underlying mechanism predisposing patients with cardiovascular diseases for severe COVID-19. European Heart Journal, 42(18), 1720-1721. doi:10.1093/eurheartj/ehab191 Berlin Institute of Health, Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Digital Health Center, Kapelle-Ufer 2, 12555 Berlin, Germany Senior author     Lee, S., Yu, Y., Trimpert, J., Benthani, F., Mairhofer, M., Richter-Pechanska, P., Wyler, E., Belenki, D., Kaltenbrunner, S., Pammer, M., Kausche, L., Firsching, T. C., Dietert, K., Schotsaert, M., Martinez-Romero, C., Singh, G., Kunz, S., Niemeyer, D., Ghanem, R., Salzer, H. J. F., Paar, C., Mulleder, M., Uccellini, M., Michaelis, E. G., Khan, A., Lau, A., Schonlein, M., Habringer, A., Tomasits, J., Adler, J. M., Kimeswenger, S., Gruber, A. D., Hoetzenecker, W., Steinkellner, H., Purfurst, B., Motz, R., Di Pierro, F., Lamprecht, B., Osterrieder, N., Landthaler, M., Drosten, C., Garcia-Sastre, A., Langer, R., Ralser, M., Eils, R., Reimann, M., Fan, D. N. Y., & Schmitt, C. A. (2021). Virus-induced senescence is a driver and therapeutic target in COVID-19. NATURE, 599(7884), 283-+. doi:10.1038/s41586-021-03995-1 Center for Digital Health, Charité - Universitätsmedizin and Berlin Institute of Health (BIH), Berlin, Germany Co-author Lukassen, S., & Eils, R. (2021). Conserved host-pathogen interactions identify novel treatment options in betacoronavirus infections. Signal Transduction and Targeted Therapy, 6(1), 3. doi:10.1038/s41392-021-00480-z Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Senior author Corresponding author Mayer, G., Muller, W., Schork, K., Uszkoreit, J., Weidemann, A., Wittig, U., Rey, M., Quast, C., Felden, J., Glockner, F. O., Lange, M., Arend, D., Beier, S., Junker, A., Scholz, U., Schuler, D., Kestler, H. A., Wibberg, D., Puhler, A., Twardziok, S., Eils, J., Eils, R., Hoffmann, S., Eisenacher, M., & Turewicz, M. (2021). Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. Briefings in Bioinformatics, 22(5), 14. doi:10.1093/bib/bbab010 Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany,  Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin; Heidelberg University Hospital and BioQuant, Health Data Science Unit, Heidelberg, Germany Co-author Meinhardt, J., Radke, J., Dittmayer, C., Franz, J., Thomas, C., Mothes, R., Laue, M., Schneider, J., Brunink, S., Greuel, S., Lehmann, M., Hassan, O., Aschman, T., Schumann, E., Chua, R. L., Conrad, C., Eils, R., Stenzel, W., Windgassen, M., Rossler, L., Goebel, H. H., Gelderblom, H. R., Martin, H., Nitsche, A., Schulz-Schaeffer, W. J., Hakroush, S., Winkler, M. S., Tampe, B., Scheibe, F., Kortvelyessy, P., Reinhold, D., Siegmund, B., Kuhl, A. A., Elezkurtaj, S., Horst, D., Oesterhelweg, L., Tsokos, M., Ingold-Heppner, B., Stadelmann, C., Drosten, C., Corman, V. M., Radbruch, H., & Heppner, F. L. (2021). Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19. Nature Neuroscience, 24(2), 168-175. doi:10.1038/s41593-020-00758-5 Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Health Data Science Unit, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany Co-author Muus, C., Luecken, M. D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E. D., Subramanian, A., Smillie, C., Jagadeesh, K. A., Duong, E. T., Fiskin, E., Torlai Triglia, E., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A. L., Chung, H., Montoro, D. T., Adams, T., Aliee, H., Allon, S. J., Andrusivova, Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L. T., Callori, S., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T. M., Cuoco, M. S., Cuomo, A. S. E., Deprez, M., Duclos, G., Fine, D., Fischer, D. S., Ghazanfar, S., Gillich, A., Giotti, B., Gould, J., Guo, M., Gutierrez, A. J., Habermann, A. C., Harvey, T., He, P., Hou, X., Hu, L., Hu, Y., Jaiswal, A., Ji, L., Jiang, P., Kapellos, T. S., Kuo, C. S., Larsson, L., Leney-Greene, M. A., Lim, K., Litviňuková, M., Ludwig, L. S., Lukassen, S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Leroy, S., Mayr, C. H., Mbano, I. M., McAdams, A. M., Nabhan, A. N., Nyquist, S. K., Penland, L., Poirion, O. B., Poli, S., Qi, C., Queen, R., Reichart, D., Rosas, I., Schupp, J. C., Shea, C. V., Shi, X., Sinha, R., Sit, R. V., Slowikowski, K., Slyper, M., Smith, N. P., Sountoulidis, A., Strunz, M., Sullivan, T. B., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K. J., Tucker, N. R., Vernon, K. A., Wadsworth, M. H., Waldman, J., Wang, X., Xu, K., Yan, W., Zhao, W., Ziegler, C. G. K., Deutsch, G. H., Dutra, J., Gaulton, K. J., Holden-Wiltse, J., Huyck, H. L., Mariani, T. J., Misra, R. S., Poole, C., Preissl, S., Pryhuber, G. S., Rogers, L., Sun, X., Wang, A., Whitsett, J. A., Xu, Y., Alladina, J., Banovich, N. E., Barbry, P., Beane, J. E., Bhattacharyya, R. P., Black, K. E., Brazma, A., Campbell, J. D., Cho, J. L., Collin, J., Conrad, C., de Jong, K., Desai, T., Ding, D. Z., Eickelberg, O., Eils, R., Ellinor, P. T., Faiz, A., Falk, C. S., Farzan, M., Gellman, A., Getz, G., Glass, I. A., Greka, A., Haniffa, M., Hariri, L. P., Hennon, M. W., Horvath, P., Hübner, N., Hung, D. T., Huyck, H. L., Janssen, W. J., Juric, D., Kaminski, N., Koenigshoff, M., Koppelman, G. H., Krasnow, M. A., Kropski, J. A., Kuhnemund, M., Lafyatis, R., Lako, M., Lander, E. S., Lee, H., Lenburg, M. E., Marquette, C.-H., Metzger, R. J., Linnarsson, S., Liu, G., Lo, Y. M. D., Lundeberg, J., Marioni, J. C., Mazzilli, S. A., Medoff, B. D., Meyer, K. B., Miao, Z., Misharin, A. V., Nawijn, M. C., Nikolić, M. Z., Noseda, M., Ordovas-Montanes, J., Oudit, G. Y., Pe’er, D., Powell, J. E., Quake, S. R., Rajagopal, J., Tata, P. R., Rawlins, E. L., Regev, A., Reid, M. E., Reyfman, P. A., Rieger-Christ, K. M., Rojas, M., Rozenblatt-Rosen, O., Saeb-Parsy, K., Samakovlis, C., Sanes, J. R., Schiller, H. B., Schultze, J. L., Schwarz, R. F., Segre, A. V., Seibold, M. A., Seidman, C. E., Seidman, J. G., Shalek, A. K., Shepherd, D. P., Sinha, R., Spence, J. R., Spira, A., Sun, X., Sundström, E., Teichmann, S. A., Theis, F. J., Tsankov, A. M., Vallier, L., van den Berge, M., Van Zyl, T. A., Villani, A.-C., Weins, A., Xavier, R. J., Yildirim, A. Ö., Zaragosi, L.-E., Zerti, D., Zhang, H., Zhang, K., Zhang, X., The, N. L. C., & The Human Cell Atlas Lung Biological, N. (2021). Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine, 27(3), 546-559. doi:10.1038/s41591-020-01227-z Berlin Institute of Health (BIH), Center for Digital Health, Berlin, Germany; Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Human Cell Atlas Lung Biological Network citation (listed as consortium member/collaborator) Park, J., Choi, W., Tiesmeyer, S., Long, B., Borm, L. E., Garren, E., Nguyen, T. N., Tasic, B., Codeluppi, S., Graf, T., Schlesner, M., Stegle, O., Eils, R., & Ishaque, N. (2021). Cell segmentation-free inference of cell types from in situ transcriptomics data. Nat Commun, 12(1), 13. doi:10.1038/s41467-021-23807-4 Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Digital Health Center, Kapelle-Ufer 2, 10117, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany Shared Senior author Corresponding author Schmidt, C., Benda, S., Kraft, P., Wiedmann, F., Pleger, S., Buscher, A., Thomas, D., Wachter, R., Schmid, C., Eils, R., Katus, H. A., & Kallenberger, S. M. (2021). Prospective multicentric validation of a novel prediction model for paroxysmal atrial fibrillation. Clinical Research in Cardiology, 110(6), 868-876. doi:10.1007/s00392-020-01773-z Digital Health Center, Berlin Institute of Health (BIH) and Charité, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120, Heidelberg, Germany Co-author Schultz, B., Zaliani, A., Ebeling, C., Reinshagen, J., Bojkova, D., Lage-Rupprecht, V., Karki, R., Lukassen, S., Gadiya, Y., Ravindra, N. G., Das, S., Baksi, S., Domingo-Fernandez, D., Lentzen, M., Strivens, M., Raschka, T., Cinatl, J., DeLong, L. N., Gribbon, P., Geisslinger, G., Ciesek, S., van Dijk, D., Gardner, S., Kodamullil, A. T., Froehlich, H., Peitsch, M., Jacobs, M., Hoeng, J., Eils, R., Claussen, C., & Hofmann-Apitius, M. (2021). A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization. Scientific Reports, 11(1), 10. doi:10.1038/s41598-021-90296-2 Center for Digital Health, Berlin Institute of Health (BIH), Charité Universitätsmedizin Berlin, Berlin, Germany Co-author Schwarz, E., Alnaes, D., Andreassen, O. A., Cao, H., Chen, J. F., Degenhardt, F., Doncevic, D., Dwyer, D., Eils, R., Erdmann, J., Herrmann, C., Hofmann-Apitius, M., Kaufmann, T., Koutsouleris, N., Kodamullil, A. T., Khuntia, A., Mucha, S., Nothen, M. M., Paul, R., Pedersen, M. L., Quintero, A., Schunkert, H., Sharma, A., Tost, H., Westlye, L. T., Zhang, Y. C., & Meyer-Lindenberg, A. (2021). Identifying multimodal signatures underlying the somatic comorbidity of psychosis: the COMMITMENT roadmap. Molecular Psychiatry, 26(3), 722-724. doi:10.1038/s41380-020-00915-z Center for Digital Health, Berlin Institute of Health and Charité, Berlin, 10117, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, 69120, Germany Co-author Tosti, L., Hang, Y., Debnath, O., Tiesmeyer, S., Trefzer, T., Steiger, K., Ten, F. W., Lukassen, S., Ballke, S., Kuhl, A. A., Spieckermann, S., Bottino, R., Ishaque, N., Weichert, W., Kim, S. K., Eils, R., & Conrad, C. (2021). Single-Nucleus and In Situ RNA-Sequencing Reveal Cell Topographies in the Human Pancreas. Gastroenterology, 160(4), 1330-+. doi:10.1053/j.gastro.2020.11.010 Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; Health Data Science Unit, Medical Faculty and BioQuant, University of Heidelberg, Heidelberg, Germany.  Shared Senior author Corresponding author Trump, S., Lukassen, S., Anker, M. S., Chua, R. L., Liebig, J., Thurmann, L., Corman, V. M., Binder, M., Loske, J., Klasa, C., Krieger, T., Hennig, B. P., Messingschlager, M., Pott, F., Kazmierski, J., Twardziok, S., Albrecht, J. P., Eils, J., Hadzibegovic, S., Lena, A., Heidecker, B., Burgel, T., Steinfeldt, J., Goffinet, C., Kurth, F., Witzenrath, M., Volker, M. T., Muller, S. D., Liebert, U. G., Ishaque, N., Kaderali, L., Sander, L. E., Drosten, C., Laudi, S., Eils, R., Conrad, C., Landmesser, U., & Lehmann, I. (2021). Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nat Biotechnol, 39(6), 705-716. doi:10.1038/s41587-020-00796-1 Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany; Health Data Science Unit, Medical Faculty and BioQuant, University of Heidelberg, Heidelberg, Germany Shared Senior author Corresponding author Wang, Q., Wu, Y. H., Vorberg, T., Eils, R., & Herrmann, C. (2021). Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer. Frontiers in Genetics, 12, 11. doi:10.3389/fgene.2021.664654 Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany; Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany Co-author Wendisch, D., Dietrich, O., Mari, T., von Stillfried, S., Ibarra, I. L., Mittermaier, M., Mache, C., Chua, R. L., Knoll, R., Timm, S., Brumhard, S., Krammer, T., Zauber, H., Hiller, A. L., Pascual-Reguant, A., Mothes, R., Bülow, R. D., Schulze, J., Leipold, A. M., Djudjaj, S., Erhard, F., Geffers, R., Pott, F., Kazmierski, J., Radke, J., Pergantis, P., Baßler, K., Conrad, C., Aschenbrenner, A. C., Sawitzki, B., Landthaler, M., Wyler, E., Horst, D., Hippenstiel, S., Hocke, A., Heppner, F. L., Uhrig, A., Garcia, C., Machleidt, F., Herold, S., Elezkurtaj, S., Thibeault, C., Witzenrath, M., Cochain, C., Suttorp, N., Drosten, C., Goffinet, C., Kurth, F., Schultze, J. L., Radbruch, H., Ochs, M., Eils, R., Müller-Redetzky, H., Hauser, A. E., Luecken, M. D., Theis, F. J., Wolff, T., Boor, P., Selbach, M., Saliba, A. E., Sander, L. E., & (DeCOI), D. C.-O. I. (2021). SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis. CELL, 184(26), 6243-6261.e6227. doi:10.1016/j.cell.2021.11.033 Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany Co-author Wulff, A., Baier, C., Ballout, S., Tute, E., Sommer, K. K., Kaase, M., Sargeant, A., Drenkhahn, C., Schlüter, D., Marschollek, M., & Scheithauer, S. (2021). Transformation of microbiology data into a standardised data representation using OpenEHR. Sci Rep, 11(1), 10556. doi:10.1038/s41598-021-89796-y  Infection Control Study Group citation (listed as consortium member/collaborator) Zowada, M. K., Tirier, S. M., Dieter, S. M., Krieger, T. G., Oberlack, A., Chua, R. L., Huerta, M., Ten, F. W., Laaber, K., Park, J., Jechow, K., Muller, T., Kalxdorf, M., Kriegsmann, M., Kriegsmann, K., Herbst, F., Krijgsveld, J., Schneider, M., Eils, R., Glimm, H., Conrad, C., & Ball, C. R. (2021). Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer. Cancers, 13(5), 32. doi:10.3390/cancers13051097 Digital Health Center, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Division of Theoretical Bioinformatics, DKFZ Heidelberg, 69120 Heidelberg, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany Co-author   **2020**   Antwi, E. B., Olins, A., Teif, V. B., Bieg, M., Bauer, T., Gu, Z. G., Brors, B., Eils, R., Olins, D., & Ishaque, N. (2020). Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biology Open, 9(2), 11. doi:10.1242/bio.044222  Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany Co-author Aschenbrenner, S., Kallenberger, S. M., Hoffmann, M. D., Huck, A., Eils, R., & Niopek, D. (2020). Coupling Cas9 to artificial inhibitory domains enhances CRISPR-Cas9 target specificity. Science Advances, 6(6), 11. doi:10.1126/sciadv.aay0187 Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg 69120, Germany  Co-author  Corresponding author   Bailey, M. H., Meyerson, W. U., Dursi, L. J., Wang, L. B., Dong, G., Liang, W. W., Weerasinghe, A., Li, S., Li, Y., Kelso, S., Saksena, G., Ellrott, K., Wendl, M. C., Wheeler, D. A., Getz, G., Simpson, J. T., Gerstein, M. B., & Ding, L. (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun, 11(1), 4748. doi:10.1038/s41467-020-18151-y  PCAWG Consortium citation (listed as consortium member/collaborator)  PCAWG novel somatic mutation calling methods working group (listed as consortium member/collaborator)   Cmero, M., Yuan, K., Ong, C. S., Schröder, J., Corcoran, N. M., Papenfuss, T., Hovens, C. M., Markowetz, F., & Macintyre, G. (2020). Inferring structural variant cancer cell fraction. Nat Commun, 11(1), 730. doi:10.1038/s41467-020-14351-8  PCAWG Consortium citation   Cramer, D., Mazur, J., Espinosa, O., Schlesner, M., Hubschmann, D., Eils, R., & Staub, E. (2020). Genetic Interactions and Tissue Specificity Modulate the Association of Mutations with Drug Response. Molecular Cancer Therapeutics, 19(3), 927-936. doi:10.1158/1535-7163.Mct-19-0045 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Health Data Science Unit, Bioquant, Medical Faculty, Heidelberg University, Heidelberg, Germany; Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany Co-author   Eismann, B., Krieger, T. G., Beneke, J., Bulkescher, R., Adam, L., Erfle, H., Herrmann, C., Eils, R., & Conrad, C. (2020). Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes. JOURNAL OF CELL SCIENCE, 133(11), 11. doi:10.1242/jcs.245043  Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany;  Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany; Digital Health Center, Berlin Institute of Health (BIH)/Charité-Universitätsmedizin Berlin, Berlin 13353, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University, Heidelberg 69120, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, Heidelberg 69120, Germany Co-author  Corresponding author   Feng, B. H., Shen, Y., Hostench, X. P., Bieg, M., Plath, M., Ishaque, N., Eils, R., Freier, K., Weichert, W., Zaoui, K., & Hess, J. (2020). Integrative Analysis of Multi-omics Data Identified EGFR and PTGS2 as Key Nodes in a Gene Regulatory Network Related to Immune Phenotypes in Head and Neck Cancer. CLINICAL CANCER RESEARCH, 26(14), 3616-3628. doi:10.1158/1078-0432.Ccr-19-3997 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany; Center for Digital Health, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany Co-author Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K. X., Tarabichi, M., Deshwar, A., Wintersinger, J., Kleinheinz, K., Vazquez-Garcia, I., Haase, K., Jerman, L., Sengupta, S., Macintyre, G., Malikic, S., Donmez, N., Livitz, D. G., Cmero, M., Demeulemeester, J., Schumacher, S., Fan, Y., Yao, X. T., Lee, J., Schlesner, M., Boutros, P. C., Bowtell, D. D., Zhu, H. T., Getz, G., Imielinski, M., Beroukhim, R., Sahinalp, S. C., Ji, Y., Peifer, M., Markowetz, F., Mustonen, V., Yuan, K., Wang, W. Y., Morris, Q. D., Spellman, P. T., Wedge, D. C., Van Loo, P., Deshwar, A. G., Adams, D. J., Campbell, P. J., Cao, S. L., Christie, E. L., Cun, Y. P., Dawson, K. J., Drews, R. M., Eils, R., Fittall, M., Garsed, D. W., Ha, G., Lee-Six, H., Martincorena, I., Oesper, L., Peto, M., Raphael, B. J., Salcedo, A., Shi, R. A., Shin, S. J., Spiro, O., Stein, L. D., Vembu, S., Wheeler, D. A., Yang, T. P., Work, P. E. H., & Consortium, P. (2020). The evolutionary history of 2,658 cancers. NATURE, 578(7793), 122-+. doi:10.1038/s41586-019-1907-7 German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg University, Heidelberg, Germany PCAWG Consortium citation (listed as consortium member/collaborator) Haller, F., Moskalev, E. A., Kuck, S., Bieg, M., Winkelmann, C., Muller, S. K., Ihrler, S., Markl, B., Eils, R., Wiemann, S., Iro, H., Hartmann, A., & Agaimy, A. (2020). Nuclear NR4A2 (Nurr1) Immunostaining is a Novel Marker for Acinic Cell Carcinoma of the Salivary Glands Lacking the Classic NR4A3 (NOR-1) Upregulation. American Journal of Surgical Pathology, 44(9), 1290-1292. doi:10.1097/pas.0000000000001483 Center for Digital Health, Berlin Institute of Health and Charité-University Medicine Berlin, Berlin Co-author      Kaipa, J. M., Starkuviene, V., Erfle, H., Eils, R., & Gladilin, E. (2020). Transcriptome profiling reveals Silibinin dose-dependent response network in non-small lung cancer cells. Peerj, 8, 26. doi:10.7717/peerj.10373 Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany Co-author Krieger, T. G., Tirier, S. M., Park, J., Jechow, K., Eisemann, T., Peterziel, H., Angel, P., Eils, R., & Conrad, C. (2020). Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics. Neuro-Oncology, 22(8), 1138-1149. doi:10.1093/neuonc/noaa091 Digital Health Center, Berlin Institute of Health and Charité, Berlin, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany; Health Data Science Unit, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany Co-author Corresponding author Li, C. H., Prokopec, S. D., Sun, R. X., Yousif, F., Schmitz, N., & Boutros, P. C. (2020). Sex differences in oncogenic mutational processes. Nat Commun, 11(1), 4330. doi:10.1038/s41467-020-17359-2 PCAWG Consortium citation Luiken, S., Fraas, A., Bieg, M., Sugiyanto, R., Goeppert, B., Singer, S., Ploeger, C., Warsow, G., Marquardt, J. U., Sticht, C., De La Torre, C., Pusch, S., Mehrabi, A., Gretz, N., Schlesner, M., Eils, R., Schirmacher, P., Longerich, T., & Roessler, S. (2020). NOTCH target gene HES5 mediates oncogenic and tumor suppressive functions in hepatocarcinogenesis. Oncogene, 39(15), 3128-3144. doi:10.1038/s41388-020-1198-3 Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Berlin, Germany; Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany Co-author Lukassen, S., Chua, R. L., Trefzer, T., Kahn, N. C., Schneider, M. A., Muley, T., Winter, H., Meister, M., Veith, C., Boots, A. W., Hennig, B. P., Kreuter, M., Conrad, C., & Eils, R. (2020). SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. Embo Journal, 39(10), 15. doi:10.15252/embj.20105114 Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Center for Digital Health, Berlin Institute of Health (BIH), Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany Shared Senior author Corresponding author Lukassen, S., Ten, F. W., Adam, L., Eils, R., & Conrad, C. (2020). Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders. Nature Machine Intelligence, 2(12), 19. doi:10.1038/s42256-020-00269-9 Charité—Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany Shared Senior author Corresponding author Mascia, C., Frexia, F., Uva, P., Zanetti, G., Pireddu, L., Giacomelli, G., Jaeger-Schmidt, C., Tomczak, A., Schumacher, S., Kraecher, F., Eils, R., Ljosland Bakke, S., & Leslie, H. (2020). The openEHR Genomics Project. Stud Health Technol Inform, 270, 443-447. doi:10.3233/shti200199 HiGHmed Consortium citation Mathony, J., Harteveld, Z., Schmelas, C., zu Belzen, J. U., Aschenbrenner, S., Sun, W., Hoffmann, M. D., Stengl, C., Scheck, A., Georgeon, S., Rosset, S., Wang, Y. L., Grimm, D., Eils, R., Correia, B. E., & Niopek, D. (2020). Computational design of anti-CRISPR proteins with improved inhibition potency. Nature Chemical Biology, 16(7), 725-+. doi:10.1038/s41589-020-0518-9 Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany; Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany Co-author Quintero, A., Hubschmann, D., Kurzawa, N., Steinhauser, S., Rentzsch, P., Kramer, S., Andresen, C., Park, J., Eils, R., Schlesner, M., & Herrmann, C. (2020). ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets. Biology Methods & Protocols, 5(1), 7. doi:10.1093/biomethods/bpaa022 Health Data Science Unit, Medical Faculty and BioQuant, University Heidelberg, Heidelberg, Germany; Center for Digital Health, Berlin Institute of Health (BIH) and Charite´ – Universitätsmedizin Berlin, Germany Co-author     Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A., & Morris, Q. (2020). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun, 11(1), 731. doi:10.1038/s41467-020-14352-7 PCAWG Consortium citation Sieverling, L., Hong, C., Koser, S. D., Ginsbach, P., Kleinheinz, K., Hutter, B., Braun, D. M., Cortes-Ciriano, I., Xi, R. B., Kabbe, R., Park, P. J., Eils, R., Schlesner, M., Brors, B., Rippe, K., Jones, D. T. W., Feuerbach, L., Grp, P. S. V. W., & Consortium, P. (2020). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun, 11(1), 13. doi:10.1038/s41467-019-13824-9 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany;  Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany Co-author Smits, M., Zoldan, K., Ishaque, N., Gu, Z. G., Jechow, K., Wieland, D., Conrad, C., Eils, R., Fauvelle, C., Baumert, T. F., Emmerich, F., Bengsch, B., Neumann-Haefelin, C., Hofmann, M., Thimme, R., & Boettler, T. (2020). Follicular T helper cells shape the HCV-specific CD4(+) T cell repertoire after virus elimination. Journal of Clinical Investigation, 130(2), 998-1009. doi:10.1172/jci129642 Digital Health Center, Berlin Institute of Health (BIH) and Charité Universitätsmedizin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany Co-author Corresponding author Tucker, N. R., Chaffin, M., Bedi, K. C., Jr., Papangeli, I., Akkad, A. D., Arduini, A., Hayat, S., Eraslan, G., Muus, C., Bhattacharyya, R. P., Stegmann, C. M., Margulies, K. B., & Ellinor, P. T. (2020). Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis. Circulation, 142(7), 708-710. doi:10.1161/circulationaha.120.047911 Human Cell Atlas Lung Biological Network Consortium citation Whalley, J. P., Buchhalter, I., Rheinbay, E., Raine, K. M., Stobbe, M. D., Kleinheinz, K., Werner, J., Beltran, S., Gut, M., Hubschmann, D., Hutter, B., Livitz, D., Perry, M. D., Rosenberg, M., Saksena, G., Trotta, J. R., Eils, R., Gerhard, D. S., Campbell, P. J., Schlesner, M., & Gut, I. G. (2020). Framework for quality assessment of whole genome cancer sequences. Nat Commun, 11(1), 8. doi:10.1038/s41467-020-18688-y Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany Co-author Wu, Y. H., Fletcher, M., Gu, Z. G., Wang, Q., Costa, B., Bertoni, A., Man, K. H., Schlotter, M., Felsberg, J., Mangei, J., Barbus, M., Gaupel, A. C., Wang, W., Weiss, T., Eils, R., Weller, M., Liu, H. K., Reifenberger, G., Korshunov, A., Angel, P., Lichter, P., Herrmann, C., & Radlwimmer, B. (2020). Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nat Commun, 11(1), 19. doi:10.1038/s41467-020-20225-w Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany Co-author Yakneen, S., Waszak, S. M., Gertz, M., Korbel, J. O., Aminou, B., Bartolome, J., Boroevich, K. A., Boyce, R., Brooks, A. N., Buchanan, A., Buchhalter, I., Butler, A. P., Byrne, N. J., Cafferkey, A., Campbell, P. J., Chen, Z. H., Cho, S., Choi, W., Clapham, P., Davis-Dusenbery, B. N., De La Vega, F. M., Demeulemeester, J., Dow, M. T., Dursi, L. J., Eils, J., Eils, R., Ellrott, K., Farcas, C., Favero, F., Fayzullaev, N., Ferretti, V., Flicek, P., Fonseca, N. A., Gelpi, J. L., Getz, G., Gibson, B., Grossman, R. L., Harismendy, O., Heath, A. P., Heinold, M. C., Hess, J. M., Hofmann, O., Hong, J. H., Hudson, T. J., Hutter, B., Hutter, C. M., Hubschmann, D., Imoto, S., Ivkovic, S., Jeon, S. H., Jiao, W., Jung, J., Kabbe, R., Kahles, A., Kerssemakers, J. N. A., Kim, H. L., Kim, H., Kim, J., Kim, Y., Kleinheinz, K., Koscher, M., Koures, A., Kovacevic, M., Lawerenz, C., Leshchiner, I., Liu, J., Livitz, D., Mihaiescu, G. L., Mijalkovic, S., Lazic, A. M., Miyano, S., Miyoshi, N., Nahal-Bose, H. K., Nakagawa, H., Nastic, M., Newhouse, S. J., Nicholson, J., O'Connor, B. D., Ocana, D., Ohi, K., Ohno-Machado, L., Omberg, L., Ouellette, B. F. F., Paramasivam, N., Perry, M. D., Pihl, T. D., Prinz, M., Puiggros, M., Radovic, P., Raine, K. M., Rheinbay, E., Rosenberg, M., Royo, R., Ratsch, G., Saksena, G., Schlesner, M., Shorser, S. I., Short, C., Sofia, H. J., Spring, J., Stein, L. D., Struck, A. J., Tiao, G., Tijanic, N., Torrents, D., Van Loo, P., Vazquez, M., Vicente, D., Wala, J. A., Wang, Z. N., Weischenfeldt, J., Werner, J., Williams, A., Woo, Y., Wright, A. J., Xiang, Q., Yang, L. M., Yuen, D., Yung, C. K., Zhang, J. J., Grp, P. T. W., & Consortium, P. (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol, 38(3), 288-+. doi:10.1038/s41587-019-0360-3 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Germany; Heidelberg University, Heidelberg, Germany; New BIH Digital Health Center, Berlin Institute of Health (BIH) and Charité – Universitätsmedizin Berlin, Berlin, Germany PCAWG Consortium citation (listed as consortium member/collaborator) Zapatka, M., Borozan, I., Brewer, D. S., Iskar, M., Grundhoff, A., Alawi, M., Desai, N., Sultmann, H., Moch, H., Cooper, C. S., Eils, R., Ferretti, V., Lichter, P., Pathogens, P., & Consortium, P. (2020). The landscape of viral associations in human cancers. Nat Genet, 52(3), 320-+. doi:10.1038/s41588-019-0558-9 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University and BioQuant Center, Heidelberg, Germany; Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany Co-author PCAWG Consortium citation (listed as consortium member/collaborator)   \*these authors contributed equally §corresponding author ## A clear and bold heading ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 01 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 02 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 03 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 04 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 04 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 04 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 04 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ![placeholder\_200x200](https://static.hubspot.com/final/img/content/email-template-images/placeholder_200x200.png "placeholder_200x200") ### Service 04 **Service description goes here.** Lorem ipsum dolor sit amet, in falli deterruisset pri, utroque ponderum pertinax an vis.  ### Latest News [![](https://www.hidih.org/hubfs/image.png)](https://www.hidih.org/news/dekcd-industry-forum?hsLang=en) #### [de.KCD Industry Forum](https://www.hidih.org/news/dekcd-industry-forum?hsLang=en) As part of the de.KCD/de.NBI network the Center of Digital Health organizes this year’s de.KCD Industry Forum on June 18, 2026 at the Einstein Center Digital Future in Berlin. de.KCD creates a forum [![](https://www.hidih.org/hubfs/SBHD_2026_Banner.png)](https://www.hidih.org/news/sbhd-2026?hsLang=en) #### [SBHD 2026](https://www.hidih.org/news/sbhd-2026?hsLang=en) Our colleagues from Northestern University in Boston are organising the 18th INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY OF HUMAN DISEASE – SBHD 2026 in Boston from June 08-10. 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