Digital Health

Roland Eils' unit at the BIH consists of three research groups: Artificial Intelligence (Roland Eils), Computational Oncology (Naveed Ishaque), and Health Data (Jürgen Eils and Harald Wagener). The unit is part of the BIH Center for Digital Health, chaired by Roland Eils as founding director of the Center. Roland Eils is also heading the Hub for Innovations in Digital Health, HiDiH, a joint collaboration of his BIH unit and the Health Data Science Unit at the Medical Faculty of Heidelberg University. In addition, Roland Eils is an active member of the Medical Informatics Initiative, where he has founded and coordinated HiGHmed. HiGHmed brings together 10 university medical centers for developing interoperable solutions and infrastructures for processing and sharing of clinical and translational research data.

Artificial Intelligence - ailslab

Roland Eils has assembled a small but highly innovative team of students and scientists venturing into different aspects of digital health. The ailslab focusses on innovative methods from the wider field of artificial intelligence for pioneering digital health applications. At the heart of this lab is the integration of huge and deep datasets from both healthcare and research for tackling pressing issues in health and disease. The ambition is to deepen our understanding of disease mechanisms and to improve diagnosis and treatment of cardiovascular and cancer patients among others. Current projects focus on cardiovascular risk modelling, omni-genetic phenotype models, and building computational frameworks with model-to-data approaches for opening medical data for research purposes. Please visit https://www.hidih.org/research/ailslab for further details.

- 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.^§ (2020). Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nature Biotechnology doi: 10.1038/s41587-020-00796-1
- Chua, R.L.*, Lukassen, S.*,Trump, S.*, Hennig, B.P.*, Wendisch, D.*, Pott, F., Debnath, O., Thürmann, L., Kurth, F., Völker, M.T., Kazmierski, J., Timmermann, B., Twardziok, S., Schneider, S., Machleidt, F., Müller-Redetzky, H., Maier, M., Krannich, A., Schmidt, S., Balzer, F., Liebig, J., Loske, J., Suttorp, N., Eils, J., Ishaque, N., Liebert, U.G., von Kalle, C., Hocke, A., Witzenrath, M., Goffinet, C., Drosten, C., Laudi, S.^§,Lehmann, I., Conrad, C.^§, Sander, L.-E.^§& Eils, R.^§ (2020). COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis. Nature Biotechnology doi: 10.1038/s41587-020-0602-4
- 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), doi: 10.15252/embj.20105114
- Upmeier zu Belzen, J., Bürgel, T., Holderbach, S., Bubeck, F., Adam, L., Gandor, C., Klein, M., Mathony, J., Pfuderer, P. L., Platz, L., Przybilla, M., Schwendemann, M., Heid, D., Hoffmann, M. D., Jendrusch, M., Schmelas, C., Waldhauer, M., Lehmann, I., Niopek, D.^§ & Eils, R.^§ (2019). Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. Nature Machine Intelligence 1, 225-235. doi: 10.1038/s42256-019-0049-9
- Zapatka, M.*, Borozan, I.*, Brewer, D.S.*, Iskar, M.*, Grundhoff, A., Alawi, M., Desai, N., Cooper, C.S., Eils, R., Ferretti, V. & Lichter, P.^§ (2020). The landscape of viral association in human cancers. Nature Genetics, doi: 10.1101/465757
- Liu, L.*, Liu, C.*, Quintero, A.*, Wu, L*., Yuan, Y.*, Wang, M., Cheng, M., Leng, L., Xu, L., Dong, G., Li, R., Liu, Y., Wei, X., Xu, J., Chen, X., Lu, H., Chen, D., Wang, Q., Zhou, Q., Lin, X., Li, G., Liu, S., Wang, Q., Wang, H., Fink, J.L., Gao, Z., Liu, X., Hou, Y., Zhu, S., Yang, H., Ye, Y., Lin, G., Chen, F., Herrmann, C., Eils, R.^§, Shang, Z.^§ & Xu, X.^§ (2019). Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nature Communications, 10(1), 470. doi: 10.1038/s41467-018-08205-7
- Northcott, P. A.*, Buchhalter, I.*, Morrissy, A. S.*, Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., Warnatz, H. J., Sidiropoulos, N., Phillips, A. H., Schumacher, S., Kleinheinz, K., Waszak, S. M., Erkek, S., Jones, D. T. W., Worst, B. C., Kool, M., Zapatka, M., Jäger, N., Chavez, L., Hutter, B., Bieg, M., Paramasivam, N., Heinold, M., Gu, Z., Ishaque, N., Jäger-Schmidt, C., Imbusch, C. D., Jugold, A., Hübschmann, D., Risch, T., Amstislavskiy, V., Gonzalez, F. G. R., Weber, U. D., Wolf, S., Robinson, G. W., Zhou, X., Wu, G., Finkelstein, D., Liu, Y., Cavalli, F. M. G., Luu, B., Ramaswamy, V., Wu, X., Koster, J., Ryzhova, M., Cho, Y. J., Pomeroy, S. L., Herold-Mende, C., Schuhmann, M., Ebinger, M., Liau, L. M., Mora, J., McLendon, R. E., Jabado, N., Kumabe, T., Chuah, E., Ma, Y., Moore, R. A., Mungall, A. J., Mungall, K. L., Thiessen, N., Tse, K., Wong, T., Jones, S. J. M., Witt, O., Milde, T., Von Deimling, A., Capper, D., Korshunov, A., Yaspo, M. L., Kriwacki, R., Gajjar, A., Zhang, J., Beroukhim, R., Fraenkel, E., Korbel, J. O., Brors, B., Schlesner, M., Eils, R.^§, Marra, M. A.^§, Pfister, S. M.^§, Taylor, M. D.^§ & Lichter, P.^§ (2017). The whole-genome landscape of medulloblastoma subtypes. Nature. 2017 Jul 19;547(7663):311-317. doi: 10.1038/nature22973
- Bauer, T.*, Trump, S.*, Ishaque, N.*, Thurmann, L.*, Gu, L.*, Bauer, M.*, Bieg, M., Gu, Z.G., Weichenhan, D., Mallm, J.P., Roder, S., Herberth, G., Takada, E., Mucke, O., Winter, M., Junge, K.M., Grutzmann, K., Rolle-Kampczyk, U., Wang, Q., Lawerenz, C., Borte, M., Polte, T., Schlesner, M., Schanne, M., Wiemann, S., Georg, C., Stunnenberg, H.G., Plass, C., Rippe, K., Mizuguchi, J., Herrmann, C.*, Eils, R.^§ & Lehmann, I.^§ (2016). Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Molecular Systems Biology, 12(3). doi: 10.15252/msb.20156520
- Jäger, N., Schlesner, M., Jones, David T.W., Raffel, S., Mallm, J.-P., Junge, Kristin M., Weichenhan, D., Bauer, T., Ishaque, N., Kool, M., Northcott, Paul A., Korshunov, A., Drews, Ruben M., Koster, J., Versteeg, R., Richter, J., Hummel, M., Mack, Stephen C., Taylor, Michael D., Witt, H., Swartman, B., Schulte-Bockholt, D., Sultan, M., Yaspo, M.-L., Lehrach, H., Hutter, B., Brors, B., Wolf, S., Plass, C., Siebert, R., Trumpp, A., Rippe, K., Lehmann, I., Lichter, P., Pfister, Stefan M. & Eils, R.^§ (2013). Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer. Cell, 155(3), 567-581. doi: 10.1016/j.cell.2013.09.042
*these authors contributed equally. ^§corresponding author
For a full publication list, please click here.

Computational Oncology

Naveed Ishaque recently started his own research group in the BIH unit of Roland Eils with research focus on applying computational approaches to understanding the basis of molecular biological heterogeneity in -omics data of human disease. They employ artificial intelligence and data science methods, not only to address the underlying causes of this heterogeneity, but also the interactions between different molecular -omics layers. The team has a strong specialization in the application area of oncology, but is also very interested in immunology and neurodegenerative diseases.

A better understanding of global and local patterns in biological data allows for better differentiation of the mechanistics behind biological and molecular processes from technical noise. As such, the team establishes close ties with experimental collaborators who are able to provide large-scale and high-dimensional datasets profiled using state-of-the-art and exotic profiling techniques, including recent technological advances that are able to resolve single cell, spatial, temporal and genetic heterogeneity.

Please visit https://www.hidih.org/research/computational-oncology for further details on ongoing projects in cancer multiomics and precision oncology, Immunology and allergies, or spatially resolved transcriptomics.

- Nina Hensel*, Zuguang Gu*, Sagar*, Dominik Wieland, Katharina Jechow, Janine Kemming, Sian Llewellyn-Lacey, Emma Gostick, Oezlem Sogukpinar, Florian Emmerich, David A. Price, Bertram Bengsch, Tobias Boettler, Christoph Neumann-Haefelin, Roland Eils, Christian Conrad, Ralf Bartenschlager, Dominic Grün, Naveed Ishaque^§, Robert Thimme^§ & Maike Hofmann^§ (2021). Memory-like HCV-specific CD8+ T cells retain a molecular scar after cure of chronic HCV infection. Nature Immunology https://doi.org/10.1038/s41590-020-00817-w
- 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.^§ (2020). Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nature Biotechnology doi: 10.1038/s41587-020-00796-1
- Ahmed Sadik*, Luis F Somarribas Patterson*, Selcen Öztürk*, Soumya R Mohapatra, Verena Panitz, Philipp F Secker, Pauline Pfänder, Stefanie Loth, Heba Salem, Mirja Tamara Prentzell, Bianca Berdel, Murat Iskar, Erik Faessler, Friederike Reuter, Isabelle Kirst, Verena Kalter, Kathrin I Foerster, Evelyn Jäger, Carina Ramallo Guevara, Mansour Sobeh, Thomas Hielscher, Gernot Poschet, Annekathrin Reinhardt, Jessica C Hassel, Marc Zapatka, Udo Hahn, Andreas von Deimling, Carsten Hopf, Rita Schlichting, Beate I Escher, Jürgen Burhenne, Walter E Haefeli, Naveed Ishaque, Alexander Böhme, Sascha Schäuble, Kathrin Thedieck, Saskia Trump^§, Martina Seiffert^§, Christiane A Opitz^§ (2020). IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression. Cell https://doi.org/10.1016/j.cell.2020.07.038
- Park, J.*, Choi, W.*, Tiesmeyer, S., Long, B., Borm, L.E., Garren, E., Nguyen, T.N., Codeluppi, S., Schlesner, M., Tasic, B., Eils, R.^§ & Ishaque, N.^§ (2019). Segmentation-free inference of cell types from in situ transcriptomics data. bioRxiv, doi: 10.1101/800748
- Mallm, J.-P.*, Iskar, M.*, Ishaque, N.*, Klett, L.C., Kugler, S.J., Muino, J.M., Teif, V.B., Poos, A.M., Großmann, S., Erdel, F., Tavernari, D., Koser, S.D., Schumacher, S., Brors, B., König, R., Remondini, D., Vingron, M., Stilgenbauer, S., Lichter, P., Zapatka, M., Mertens, D.^§ & Rippe, K.^§ (2019). Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology, 22;15(5):e8339. doi: 10.15252/msb.20188339
- Ishaque, N.*, Abba, M.L.*, Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Kleinheinz, K., Toprak, U.H., Hutter, B., Benner, A., Shavinskaya, A., Zhou, C., Gu, Z., Kerssemakers, J., Marx, A., Moniuszko, M., Kozlowski, M., Reszec, J., Niklinski, J., Eils, J., Schlesner, M., Eils, R., Brors, B. & Allgayer, H.^§ (2018). Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature Communications, 9(1), 4782. doi: 10.1038/s41467-018-07041-z
- Zuguang Gu, Roland Eils, Matthias Schlesner & Naveed Ishaque (2018). EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC Bioinformatics https://doi.org/10.1186/s12864-018-4625-x

Health Data

The Heath Data team, headed by Jürgen Eils, focusses on processes in medical informatics and bioinformatics. The team works on the automatization of computational workflows in biomedical research, provides data managing tools and infrastructures that support the fast transfer of new research results into healthcare. A fundamental challenge of a digital healthcare environment is the growing amount of sensitive patient data, e.g., created by smart wearables or whole genome sequencing data. Handling and processing of such huge data sets in daily routine diagnostics requires new infrastructures and IT solutions. Therefore, the team is also working on large-scale IT and cloud solutions, in particular the de.NBI cloud. The Health Data team is located in both Berlin and Heidelberg. Please visit https://www.hidih.org/research/health-data for further information.

- ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer Analysis of Whole Genomes, Nature, 578(7793), 82-93, doi: 10.1038/s41586-020-1969-6
- Yakneen, S.^§, Waszak, S.M., PCAWG Technical Working Group, Gertz, M., Korbel, J. O.^§, PCAWG Consortium (2020). Bulter enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, Epub ahead of print, doi: 10.1038/s41587-019-0360-3
- Ishaque, N.*, Abba, M.L.*, Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Kleinheinz, K., Toprak, U.H., Hutter, B., Benner, A., Shavinskaya, A., Zhou, C., Gu, Z., Kerssemakers, J., Marx, A., Moniuszko, M., Kozlowski, M., Reszec, J., Niklinski, J., Eils, J., Schlesner, M., Eils, R., Brors, B. & Allgayer, H.^§ (2018). Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature Communications, 9(1), 4782. doi: 10.1038/s41467-018-07041-z
- Gröbner, S.N.*, Worst, B.C.*, Weischenfeldt, J., Buchhalter, I., Kleinheinz, K., Rudneva, V.A., Johann, P.D., Balasubramanian, G.P., Segura-Wang, M., Brabetz, S., Bender, S., Hutter, B., Sturm, D., Pfaff, E., Hubschmann, D., Zipprich, G., Heinold, M., Eils, J., Lawerenz, C., Erkek, S., Lambo, S., Waszak, S., Blattmann, C., Borkhardt, A., Kuhlen, M., Eggert, A., Fulda, S., Gessler, M., Wegert, J., Kappler, R., Baumhoer, D., Burdach, S., Kirschner-Schwabe, R., Kontny, U., Kulozik, A.E., Lohmann, D., Hettmer, S., Eckert, C., Bielack, S., Nathrath, M., Niemeyer, C., Richter, G.H., Schulte, J., Siebert, R., Westermann, F., Molenaar, J.J., Vassal, G., Witt, H., Burkhardt, B., Kratz, C.P., Witt, O., van Tilburg, C.M., Kramm, C.M., Fleischhack, G., Dirksen, U., Rutkowski, S., Fruhwald, M., von Hoff, K., Wolf, S., Klingebiel, T., Koscielniak, E., Landgraf, P., Koster, J., Resnick, A.C., Zhang, J., Liu, Y., Zhou, X., Waanders, A.J., Zwijnenburg, D.A., Raman, P., Brors, B., Weber, U.D., Northcott, P.A., Pajtler, K.W., Kool, M., Piro, R.M., Korbel, J.O., Schlesner, M., Eils, R., Jones, D.T.W., Lichter, P., Chavez, L.^§, Zapatka, M.^§, Pfister, S.M.^§ (2018). The landscape of genomic alterations across childhood cancers. Nature, 559(7714), 321-327, doi: 10.1038/s41586-018-0167-2
- Reisinger, E.^§, Genthner, L., Kerssemakers, J., Kensche, P., Borufka, S., Jugold, A., Kling, A., Prinz, M., Scholz, I., Zipprich, G., Eils, R., Lawerenz, C., Eils, J. (2017). OTP: An automatized system for managing and processing NGS data. Journal of Biotechnology, 10(261), 53-62, doi: 10.1016/j.jbiotec.2017.08.006
*these authors contributed equally. ^§corresponding author

AG Eils - Team
Arbeitsgruppenleiter	Prof. Dr. Roland Eils	roland.eils@charite.de	Kapelle-Ufer 2	030450543084
Sekretariat	Bodogh, Sandra	sandra.bodogh@charite.de	Kapelle-Ufer 2	030450543088
Projektmanagement	Dr. Friedrich, Alexandra	alexandra.friedrich@charite.de	Kapelle-Ufer 2	030450543106
Projektmanagement	Dr. Hennig, Bianca	bianca.hennig@charite.de	Kapelle-Ufer 2	030450543104
Projektmanagement	Müller, Franziska	franziska.mueller@charite.de	Kapelle-Ufer 2	030450543085

Artificial Intelligence
Gruppenleiter Teilgruppe	Prof. Dr. Roland Eils	roland.eils@charite.de	Kapelle-Ufer 2	Gründungsdirektor Zentrum für Digitale Gesundheit	030450543084
Mitarbeiter	Bürgel, Thore	thore.buergel@charite.de	Kapelle-Ufer 2	Doktorand	030450543119
Mitarbeiter	Christmann, Lara-Sophie	lara-sophie.christmann@charite.de	Kapelle-Ufer 2	Informatikerin	030450543129
Mitarbeiter	Loock, Lukas	lukas.loock@charite.de	Kapelle-Ufer 2	Medizininformatiker	030450543124
Mitarbeiter	Upmeier zu Belzen, Julius Valten	julius.upmeier@charite.de	Kapelle-Ufer 2	Doktorand	030450543119
Mitarbeiter	Hollmann, Noah	noah.hollmann@charite.de	Kapelle-Ufer 2	Studentischer Mitarbeiter
Mitarbeiter	Kittner, Paul	paul.kittner@charite.de	Kapelle-Ufer 2	Studentischer Mitarbeiter
Mitarbeiter	Ruyoga, Greg	greg.ruyoga@charite.dee	Kapelle-Ufer 2	Studentischer Mitarbeiter
Mitarbeiter	Strangalies, Henrik	henrik.strangalies@charite.de	Kapelle-Ufer 2	Studentischer Mitarbeiter
Mitarbeiter	Wolf, Benedict	benedict.wolf@charite.de	Kapelle-Ufer 2	Studentischer Mitarbeiter

Health Data
Gruppenleiter Teilgruppe	Eils, Jürgen	juergen.eils@charite.de	Kapelle-Ufer 2	Gruppenleiter Health Data	030450543103
Mitarbeiter	Wagener, Harald	harald.wagener@bihealth.de	Kapelle-Ufer 2	Gruppenleiter Cloud	030450543087
Mitarbeiter	Braun, Martin	martin.braun@charite.de	Kapelle-Ufer 2	Cloudentwickler/ IT-Systemadministrator	030450543107
Mitarbeiter	Kohler, Severin	severin.kohler@charite.de	Kapelle-Ufer 2	Wissenschaftlicher Mitarbeiter
Mitarbeiter	Schneider, Stefan	stefan.schneider@charite.de	Kapelle-Ufer 2	It-Systemadministrator Cloud	030450543111
Mitarbeiter	Strubel, Philipp	philipp.strubel@charite.de	Kapelle-Ufer 2	Systemadministrator/ Fachinformatiker	030450543095
Mitarbeiter	Dr. Twardziok, Sven	sven.twardziok@charite.de	Kapelle-Ufer 2	Cloud-Entwickler	030450543105
Mitarbeiterin	Taron, Ulrike	ulrike.Taron@charite.de	Kapelle-Ufer 2	Data Manager OTP	030450543135

Computational Oncology
Gruppenleiter Teilgruppe	Ishaque, Naveed, PhD	naveed.ishaque@charite.de	Kapelle-Ufer 2	030450543096
Mitarbeiter	Mackowiak, Sebastian, Dr.	sebastian.Mackowiak@charite.de	Kapelle-Ufer 2	030450543090
Mitarbeiter	Debnath, Olivia	olivia.debnath@charite.de	Kapelle-Ufer 2	030450543116
Mitarbeiter	Sahay, Shashwat	shashwat.sahay@charite.de	Kapelle-Ufer 2	030450543118
Mitarbeiter	Tiesmeyer, Sebastian	sebastian.tiesmeyer@charite.de	Kapelle-Ufer 2	030450543117
Mitarbeiter	Weber, Christiane	christiane.weber@charite.de	Kapelle-Ufer 2	030450543131
Mitarbeiter	Graf, Tobias	tobias.graf@charite.de	Kapelle-Ufer 2

Phone:	+49 30 450 543 084
E-mail:	roland.eils@bihealth.de

Roland Eils

Artificial Intelligence - ailslab

Ausgewählte Publikationen Roland Eils, Artificial Intelligence

Computational Oncology

Selected Publications Naveed Ishaque, Computational Oncology

Health Data

Selected Publications Jürgen Eils/Harald Wagener, Health Data

Prof. Dr. Roland Eils