Publications

Please check 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