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)

2019

Aslam, M., Ullah, A., Paramasivam, N., Kandasamy, N., Naureen, S., Badshah, M., Khan, K., Wajid, M., Abbasi, R., Eils, R., Brockmann, M.A., Schlesner, M., Ahmad, N., & von Engelhardt, J. (2019). Segregation and potential functional impact of a rare stop-gain PABPC4L variant in familial atypical Parkinsonism. Scientific Reports, 9(1), 13576. doi: 10.1038/s41598-019-50102-6

              BIH/Charité Berlin, Universitätsklinikum Heidelberg, middle author

Bubeck, F., Hoffmann, M.D., Harteveld, Z., Aschenbrenner, S., Bietz, A., Notbohm, J., Stengl, C., Mathony, J., Waldhauer, M.C., Dietz, L., Borner, K., Fakhiri, J., Schmelas, C., Grimm, D., Correia, B.E., Eils, R., & Niopek, D. (2019). Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9. Molecular Therapy, 27(4), 297-297.

Chan, C.W.Y., Gu, Z.G., Bieg, M., Eils, R., & Herrmann, C. (2019). Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC Medical Genomics, 12. doi: 10.1186/s12920-019-0525-4

              DKFZ Heidelberg, BIH/Charité Berlin, Universitätsklinikum Heidelberg

              Corresponding Author

Erkek, S., Johann, P.D., Finetti, M.A., Drosos, Y., Chou, H.C., Zapatka, M., Sturm, D., Jones, D.T.W., Korshunov, A., Rhyzova, M., Wolf, S., Mallm, J.P., Beck, K., Witt, O., Kulozik, A.E., Fruhwald, M.C., Northcott, P.A., Korbel, J.O., Lichter, P., Eils, R., Gajjar, A., Roberts, C.W.M., Williamson, D., Hasselblatt, M., Chavez, L., Pfister, S.M., & Kool, M. (2019). Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer Cell, 35(1), 95-+. doi: 10.1016/j.ccell.2018.11.014

              DKFZ Heidelberg, Division of Theoretical Bioinformatics (B080),

Gladilin, E., Ohse, S., Boerries, M., Busch, H., Xu, C., Schneider, M., Meister, M., & Eils, R. (2019). TGF beta-induced cytoskeletal remodeling mediates elevation of cell stiffness and invasiveness in NSCLC. Scientific Reports, 9. doi: 10.1038/s41598-019-43409-x

              BIH/Charité Berlin, Universitätsklinikum Heidelberg/ Corresponding author

Groschel, S., Hubschmann, D., Raimondi, F., Horak, P., Warsow, G., Frohlich, M., Klink, B., Gieldon, L., Hutter, B., Kleinheinz, K., Bonekamp, D., Marschal, O., Chudasama, P., Mika, J., Groth, M., Uhrig, S., Kramer, S., Heining, C., Heilig, C.E., Richter, D., Reisinger, E., Pfutze, K., Eils, R., Wolf, S., von Kalle, C., Brandts, C., Scholl, C., Weichert, W., Richter, S., Bauer, S., Penzel, R., Schrock, E., Stenzinger, A., Schlenk, R.F., Brors, B., Russell, R.B., Glimm, H., Schlesner, M., & Frohling, S. (2019). Defective homologous recombination DNA repair as therapeutic target in advanced chordoma. Nat Commun, 10(1), 1635. doi: 10.1038/s41467-019-09633-9

DKFZ Heidelberg

Haller, F., Bieg, M., Will, R., Korner, C., Weichenhan, D., Bott, A., Ishaque, N., Lutsik, P., Moskalev, E.A., Mueller, S.K., Bahr, M., Woerner, A., Kaiser, B., Scherl, C., Haderlein, M., Kleinheinz, K., Fietkau, R., Iro, H., Eils, R., Hartmann, A., Plass, C., Wiemann, S., & Agaimy, A. (2019). Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nature Communications, 10. doi: 10.1038/s41467-018-08069-x

              BIH/Charité Berlin, DKFZ-HIPO Heidelberg, Universitätsklinikum Heidelberg, TLRC Heidelberg

Senior author? à à FACTScience “middle author”

Haller, F., Skalova, A., Ihrler, S., Markl, B., Bieg, M., Moskalev, E.A., Erber, R., Blank, S., Winkelmann, C., Hebele, S., Baneckova, M., Wiemann, S., Mueller, S., Zenk, J., Eils, R., Iro, H., Hartmann, A., & Agaimy, A. (2019). Nuclear NR4A3 Immunostaining Is a Specific and Sensitive Novel Marker for Acinic Cell Carcinoma of the Salivary Glands. American Journal of Surgical Pathology, 43(9), 1264-1272. doi: 10.1097/pas.0000000000001279

              BIH/Charité Berlin

Hoffmann, M.D., Aschenbrenner, S., Grosse, S., Rapti, K., Domenger, C., Fakhiri, J., Mastel, M., Borner, K., Eils, R.*, Grimm, D., & Niopek, D. (2019). Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic Acids Research, 47(13). doi: 10.1093/nar/gkz271

              BIH/Charité Berlin, Universitätsklinikum Heidelberg/Corresponding author

Horak, P., Weischenfeldt, J., von Amsberg, G., Beyer, B., Schutte, A., Uhrig, S., Gieldon, L., Klink, B., Feuerbach, L., Hubschmann, D., Kreutzfeldt, S., Heining, C., Maier, S., Hutter, B., Penzel, R., Schlesner, M., Eils, R., Sauter, G., Stenzinger, A., Brors, B., Schrock, E., Glimm, H., Frohling, S., & Schlomm, T. (2019). Response to olaparib in a PALB2 germline mutated prostate cancer and genetic events associated with resistance. Cold Spring Harbor Molecular Case Studies, 5(2). doi: 10.1101/mcs.a003657

              Universitätsklinikum Heidelberg, BIH/Charité Berlin/

middle author

Klös, M., Thürmann, L., Bauer, M., Heinrich, J., Standl, M., von Berg, A., Schaaf, B., Weichenhan, D., Mucke, O., Plass, C., Roder, S., Herberth, G., Sack, U., Borte, M., Stangl, G.I., Eils, R., Trump, S., & Lehmann, I. (2019). Longitudinal trends of serum IgE and IL5RA expression throughout childhood are associated with asthma but not with persistent wheeze. Allergy, 74(10), 2002-2006. doi: 10.1111/all.13837

              BIH/Charité Berlin, Universitätsklinikum Heidelberg/

middle author

Liu, L.Q., Liu, C.Y., Quintero, A., Wu, L., Yuan, Y., Wang, M.Y., Cheng, M.N., Leng, L.Z., Xu, L.Q., Dong, G.Y., Li, R., Liu, Y., Wei, X.Y., Xu, J.S., Chen, X.W., Lu, H.R., Chen, D.S., Wang, Q.L., Zhou, Q., Lin, X.X., Li, G.B., Liu, S.P., Wang, Q., Wang, H.R., Fink, J.L., Gao, Z.L., Liu, X., Hou, Y., Zhu, S.D., Yang, H.M., Ye, Y.M., Lin, G., Chen, F., Herrmann, C., Eils, R.*, Shang, Z.C., & Xu, X. (2019). Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nature Communications, 10. doi: 10.1038/s41467-018-08205-7

              Universitätsklinikum Heidelberg, BIH/Charité Berlin/

Corresponding author

Lopez, C., Kleinheinz, K., Aukema, S.M., Rohde, M., Bernhart, S.H., Hubschmann, D., Wagener, R., Toprak, U.H., Raimondi, F., Kreuz, M., Waszak, S.M., Huang, Z.Q., Sieverling, L., Paramasivam, N., Seufert, J., Sungalee, S., Russell, R.B., Bausinger, J., Kretzmer, H., Ammerpohl, O., Bergmann, A.K., Binder, H., Borkhardt, A., Brors, B., Claviez, A., Doose, G., Feuerbach, L., Haake, A., Hansmann, M.L., Hoell, J., Hummel, M., Korbel, J.O., Lawerenz, C., Lenze, D., Radlwimmer, B., Richter, J., Rosenstiel, P., Rosenwald, A., Schilhabel, M.B., Stein, H., Stilgenbauer, S., Stadler, P.F., Szczepanowski, M., Weniger, M.A., Zapatka, M., Eils, R., Lichter, P., Loeffler, M., Moller, P., Trumper, L., Klapper, W., Hoffmann, S., Kuppers, R., Burkhardt, B., Schlesner, M., Siebert, R., Wagner, S., Richter, G., Eils, J., Kerssemakers, J., Jaeger-Schmidt, C., Scholz, I., Borst, C., Braulke, F., Dreyling, M., Eberth, S., Einsele, H., Frickhofen, N., Haas, S., Karsch, D., Klepl, N., Kneba, M., Lisfeld, J., Mantovani-Loffler, L., Ott, G., Stadler, C., Staib, P., Zenz, T., Kube, D., Kostezka, U., Binder, V., Leich, E., Nagel, I., Pischimariov, J., Schreiber, S., Vater, I., Hopp, L., Langenberger, D., Rosolowski, M., & Consortium, I.M.-S. (2019). Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nature Communications, 10. doi: 10.1038/s41467-019-08578-3

              DKFZ Heidelberg, BioQuant Heidelberg/

middle author

Paramasivam, N., Huebschmann, D., Toprak, U.H., Ishaque, N., Neidert, M., Schrimpf, D., Stichel, D., Reuss, D., Sievers, P., Reinhardt, A., Wefers, A.K., Jones, D.T.W., Gu, Z.G., Werner, J., Uhrig, S., Wirsching, H.G., Schick, M., Bewerunge-Hudler, M., Beck, K., Brehmer, S., Urbschat, S., Seiz-Rosenhagen, M., Hanggi, D., Herold-Mende, C., Ketter, R., Eils, R., Ram, Z., Pfister, S.M., Wick, W., Weller, M., Grossmann, R., von Deimling, A., Schlesner, M., & Sahm, F. (2019). Mutational patterns and regulatory networks in epigenetic subgroups of meningioma. Acta Neuropathologica, 138(2), 295-308. doi: 10.1007/s00401-019-02008-w

              DKFZ Heidelberg, BIH/Charité Berlin, BioQuant Heidelberg/

middle author

Prager, I., Liesche, C., van Ooijen, H., Urlaub, D., Verron, Q., Sandstrom, N., Fasbender, F., Claus, M., Eils, R., Beaudouin, J., Onfelt, B., & Watzl, C. (2019). NK cells switch from granzyme B to death receptor-mediated cytotoxicity during serial killing. Journal of Experimental Medicine, 216(9), 2113-2127. doi: 10.1084/jem.20181454

              DKFZ Heidelberg, BioQuant Heidelberg

Schmitt, K., Molfenter, B., Laureano, N.K., Tawk, B., Bieg, M., Hostench, X.P., Weichenhan, D., Ullrich, N.D., Shang, V., Richter, D., Stogbauer, F., Schroeder, L., Prunes, B.D., Visioli, F., Rados, P.V., Jou, A., Plath, M., Federspil, P.A., Thierauf, J., Doscher, J., Weissinger, S.E., Hoffmann, T.K., Wagner, S., Wittekindt, C., Ishaque, N., Eils, R., Klussmann, J.P., Holzinger, D., Plass, C., Abdollahi, A., Freier, K., Weichert, W., Zaoui, K., & Hess, J. (2019). Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer. International Journal of Cancer, 145(12), 3299-3310. doi: 10.1002/ijc.32481

              DKFZ Heidelberg, DKFZ-HIPO Heidelberg

Tirier, S.M., Park, J., Preusser, F., Amrhein, L., Gu, Z.G., Steiger, S., Mallm, J.P., Krieger, T., Waschow, M., Eismann, B., Gut, M., Gut, I.G., Rippe, K., Schlesner, M., Theis, F., Fuchs, C., Ball, C.R., Glimm, H., Eils, R.*, & Conrad, C. (2019). Pheno-seq - linking visual features and gene expression in 3D cell culture systems. Scientific Reports, 9. doi: 10.1038/s41598-019-48771-4

              BIH/Charité Berlin, BioQuant Heidelberg, DKFZ Heidelberg, DKFZ-HIPO Heidelberg, Health Data Science Unit Heidelberg

              Corresponding author

Upmeier zu Belzen, B., Bürgel, T., Holderbach, S., Bubeck, F., Adam, L., Gandor, C., Klein, M., Mathony, J., Pfuderer, P., 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(5), 225-235. doi: doi:10.1038/s42256-019-0049-9

BIH/Charité Berlin, Health Data Science Unit Heidelberg

Corresponding Author

2018

Ali, S., Amunts, K., Eils, R., Axer, M., Rohr, K., & Ieee. (2018). SCALE-BUNDLE SPLINE-BASED NON-RIGID REGISTRATION FOR HANDLING FISSURES 2018 Ieee 15th International Symposium on Biomedical Imaging (pp. 762-765).

              BioQuant Heidelberg, DKFZ Heidelberg

Ali, S., Axer, M., Amunts, K., Eils, R., Rohr, K., & Ieee. (2018). EVALUATING LOCAL FEATURES IN HIGH-RESOLUTION 3D-PLI DATA 2018 Ieee 15th International Symposium on Biomedical Imaging (pp. 729-733).

              BioQuant Heidelberg, DKFZ Heidelberg

Ali, S., Worz, S., Amunts, K., Eils, R., Axer, M., & Rohr, K. (2018). Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution. Neuroimage, 181, 235-251. doi: 10.1016/j.neuroimage.2018.06.084

              DKFZ Heidelberg,

Bubeck, F., Hoffmann, M.D., Harteveld, Z., Aschenbrenner, S., Bietz, A., Waldhauer, M.C., Borner, K., Fakhiri, J., Schmelas, C., Dietz, L., Grimm, D., Correia, B.E., Eils, R.*, & Niopek, D. (2018). Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nature Methods, 15(11), 924-+. doi: 10.1038/s41592-018-0178-9

              BioQuant Heidelberg, DKFZ Heidelberg, BIH/Charité Berlin, Health Data Science Unit Heidelberg/

Corresponding author

Chudasama, P., Mughal, S.S., Sanders, M.A., Hubschmann, D., Chung, I., Deeg, K.I., Wong, S.H., Rabe, S., Hlevnjak, M., Zapatka, M., Ernst, A., Kleinheinz, K., Schlesner, M., Sieverling, L., Klink, B., Schrock, E., Hoogenboezem, R.M., Kasper, B., Heilig, C.E., Egerer, G., Wolf, S., von Kalle, C., Eils, R., Stenzinger, A., Weichert, W., Glimm, H., Groschel, S., Kopp, H.G., Omlor, G., Lehner, B., Bauer, S., Schimmack, S., Ulrich, A., Mechtersheimer, G., Rippe, K., Brors, B., Hutter, B., Renner, M., Hohenberger, P., Scholl, C., & Frohling, S. (2018). Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nature Communications, 9. doi: 10.1038/s41467-017-02602-0

              DKFZ Heidelberg, BioQuant Heidelberg, DKFZ-HIPO Heidelberg

Dimitrov, B., Himmelreich, N., Ederveen, A.L.H., Luchtenborg, C., Okun, J.G., Breuer, M., Hutter, A.M., Carl, M., Guglielmi, L., Hellwig, A., Thiemann, K.C., Jost, M., Peters, V., Staufner, C., Hoffmann, G.F., Hackenberg, A., Paramasivam, N., Wiemann, S., Eils, R., Schlesner, M., Strahl, S., Brugger, B., Wuhrer, M., Korenke, G.C., & Thiel, C. (2018). Cutis laxa, exocrine pancreatic insufficiency and altered cellular metabolomics as additional symptoms in a new patient with ATP6AP1-CDG. Molecular Genetics and Metabolism, 123(3), 364-374. doi: 10.1016/j.ymgme.2018.01.008

              DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), BioQuant Heidelberg, Bioinformatics and Omics Data Analytics (B240)

Gerhauser, C., Favero, F., Risch, T., Simon, R., Feuerbach, L., Assenov, Y., Heckmann, D., Sidiropoulos, N., Waszak, S.M., Hubschmann, D., Urbanucci, A., Girma, E.G., Kuryshev, V., Klimczak, L.J., Saini, N., Stutz, A.M., Weichenhan, D., Bottcher, L.M., Toth, R., Hendriksen, J.D., Koop, C., Lutsik, P., Matzk, S., Warnatz, H.J., Amstislayskiy, V., Feuerstein, C., Raeder, B., Bogatyrova, O., Schmitz, E.M., Hube-Magg, C., Kluth, M., Huland, H., Graefen, M., Lawerenz, C., Henry, G.H., Yamaguchi, T.N., Malewska, A., Meiners, J., Schilling, D., Reisinger, E., Eils, R., Schlesner, M., Strand, D.W., Bristow, R.G., Boutros, P.C., von Kalle, C., Gordenin, D., Sultmann, H., Brors, B., Sauter, G., Plass, C., Yaspo, M.L., Korbel, J.O., Schlomm, T., & Weischenfeldt, J. (2018). Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell, 34(6), 996-+. doi: 10.1016/j.ccell.2018.10.016

              DKFZ Heidelberg, BioQuant Heidelberg, Departement for Bioinformatics anf Functional Genomics/

middle author

Glont, M., Nguyen, T.V.N., Graesslin, M., Halke, R., Ali, R., Schramm, J., Wimalaratne, S.M., Kothamachu, V.B., Rodriguez, N., Swat, M.J., Eils, J., Eils, R., Laibe, C., Malik-Sheriff, R.S., Chelliah, V., Novere, N., & Hermjakob, H. (2018). BioModels: expanding horizons to include more modelling approaches and formats. Nucleic Acids Research, 46(D1), D1248-D1253. doi: 10.1093/nar/gkx1023

              Departement for Bioinformatics anf Functional Genomics, BioQuant Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), DKFZ Heidelberg

Grobner, 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.H., Liu, Y.L., 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., & ICGC, I.P.-S.P. (2018). The landscape of genomic alterations across childhood cancers. Nature, 555(7696), 321-+. doi: 10.1038/nature25480

              DKFZ Heidelberg, Departement for Bioinformatics anf Functional Genomics/

middle author

Gu, Z.G., Eils, R., Schlesner, M., & Ishaque, N. (2018). EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC Genomics, 19. doi: 10.1186/s12864-018-4625-x

              Division of Theoretical Bioinformatics (B080), DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB),

Haarbrandt, B., Schreiweis, B., Rey, S., Sax, U., Scheithauer, S., Rienhoff, O., Knaup-Gregori, P., Bavendiek, U., Dieterich, C., Brors, B., Kraus, I., Thoms, C.M., Jager, D., Ellenrieder, V., Bergh, B., Yahyapour, R., Eils, R., Marschollek, M., & HiGHmed Consortium (2018). HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries. Methods of Information in Medicine, 57, E66-E81. doi: 10.3414/me18-02-0002

              BIH/Charité Berlin, Health Data Science Unit Heidelberg

              Middle Author

Hoffmann, M.D., Bubeck, F., Eils, R., & Niopek, D. (2018). Controlling Cells with Light and LOV. Advanced Biosystems, 2(9). doi: 10.1002/adbi.201800098

              DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), BIH/Charité Berlin, Health Data Science Unit Heidelberg

              Corresponding Author

Hwang, G.H., Park, J., Lim, K., Kim, S., Yu, J., Yu, E., Kim, S.T., Eils, R., Kim, J.S., & Bae, S. (2018). Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics, 19. doi: 10.1186/s12859-018-2585-4

              BIH/Charité Berlin, Health Data Science Unit Heidelberg/

middle author

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.G., 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. doi: 10.1038/s41467-018-07041-z

              DKFZ-HIPO Heidelberg, DKFZ Heidelberg, BioQuant Heidelberg

Jahreis, S., Trump, S., Bauer, M., Bauer, T., Thurmann, L., Feltens, R., Wang, Q., Gu, L., Grutzmann, K., Roder, S., Averbeck, M., Weichenhan, D., Plass, C., Sack, U., Borte, M., Dubourg, V., Schuurmann, G., Simon, J.C., von Bergen, M., Hackermuller, J., Eils, R., Lehmann, I., & Polte, T. (2018). Maternal phthalate exposure promotes allergic airway inflammation over 2 generations through epigenetic modifications. Journal of Allergy and Clinical Immunology, 141(2), 741-753. doi: 10.1016/j.jaci.2017.03.017

              DKFZ Heidelberg

Junge, K.M., Leppert, B., Jahreis, S., Wissenbach, D.K., Feltens, R., Grutzmann, K., Thurmann, L., Bauer, T., Ishaque, N., Schick, M., Bewerunge-Hudler, M., Roder, S., Bauer, M., Schulz, A., Borte, M., Landgraf, K., Korner, A., Kiess, W., von Bergen, M., Stangl, G.I., Trump, S., Eils, R., Polte, T., & Lehmann, I. (2018). MEST mediates the impact of prenatal bisphenol A exposure on long-term body weight development. Clinical Epigenetics, 10. doi: 10.1186/s13148-018-0478-z

              DKFZ Heidelberg, BIH/Charité Berlin, Health Data Science Unit Heidelberg/

middle author

Kumar, A., Bandapalli, O.R., Paramasivam, N., Giangiobbe, S., Diquigiovanni, C., Bonora, E., Eils, R., Schlesner, M., Hemminki, K., & Forsti, A. (2018). Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family. Scientific Reports, 8. doi: 10.1038/s41598-018-29952-z

              DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), BioQuant Heidelberg

Liesche, C., Sauer, P., Prager, I., Urlaub, D., Claus, M., Eils, R., Beaudouin, J., & Watzl, C. (2018). Single-Fluorescent Protein Reporters Allow Parallel Quantification of Natural Killer Cell-Mediated Granzyme and Caspase Activities in Single Target Cells. Frontiers in Immunology, 9. doi: 10.3389/fimmu.2018.01840

              DKFZ Heidelberg, BioQuant Heidelberg

Maier, L.J., Kallenberger, S.M., Jechow, K., Waschow, M., Eils, R.*, & Conrad, C. (2018). Unraveling mitotic protein networks by 3D multiplexed epitope drug screening. Molecular Systems Biology, 14(8). doi: 10.15252/msb.20188238

              BioQuant Heidelberg, DKFZ Heidelberg, BIH/Charité Berlin

              Corresponding author

Muckenhuber, A., Berger, A.K., Schlitter, A.M., Steiger, K., Konukiewitz, B., Trumpp, A., Eils, R., Werner, J., Friess, H., Esposito, I., Kloppel, G., Ceyhan, G.O., Jesinghaus, M., Denkert, C., Bahra, M., Stenzinger, A., Sprick, M.R., Jager, D., Springfeld, C., & Weichert, W. (2018). Pancreatic Ductal Adenocarcinoma Subtyping Using the Biomarkers Hepatocyte Nuclear Factor-1A and Cytokeratin-81 Correlates with Outcome and Treatment Response. Clinical Cancer Research, 24(2), 351-359. doi: 10.1158/1078-0432.ccr-17-2180

              DKFZ-HIPO Heidelberg, DKFZ Heidelberg, BioQuant Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB)/

middle author

Schlereth, K., Weichenhan, D., Bauer, T., Heumann, T., Giannakouri, E., Lipka, D., Jaeger, S., Schlesner, M., Aloy, P., Eils, R., Plass, C., & Augustin, H.G. (2018). The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium. Elife, 7. doi: 10.7554/eLife.34423

              DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), BioQuant Heidelberg

Schmelas, C.C., Gleixner, J., Schmidt, F., Eils, R., Di Ventura, B., & Grimm, D. (2018). Enhanced Genome Editing Using Split Staphylococcus Aureus Cas9 Delivered in Double-Stranded Adeno-Associated Viral Vectors.

Thürmann, L., Grutzmann, K., Klos, M., Bieg, M., Winter, M., Polte, T., Bauer, T., Schick, M., Bewerunge-Hudler, M., Roder, S., Bauer, M., Wissenbach, D.K., Sack, U., Weichenhan, D., Mucke, O., Plass, C., Borte, M., von Bergen, M., Lehmann, I., Eils, R.*, & Trump, S. (2018). Early-onset childhood atopic dermatitis is related to NLRP2 repression. Journal of Allergy and Clinical Immunology, 141(4), 1482-+. doi: 10.1016/j.jaci.2017.11.018

              DKFZ Heidelberg, DKFZ-HIPO Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), TLRC Heidelberg

Trump, S., Klos, M., Schmidt, M., Bauer, T., Ishaque, N., Thurmann, L., Bieg, M., Herrmann, C., Roder, S., Bauer, M., Weichenhan, D., Muecke, O., Plass, C., Borte, M., Von Mutius, E., Kabesch, M., Stangl, G.I., Lauener, R., Pekkanen, J., Dalphin, J., Riedler, J., Eils, R., & Lehmann, I. (2018). Development of early childhood asthma goes along with massive enhancer activation in blood cells. Allergy, 73, 314-314.

Warsow, G., Hubschmann, D., Kleinheinz, K., Nientiedt, C., Heller, M., Van Coile, L., Tolstov, Y., Trennheuser, L., Wieczorek, K., Pecqueux, C., Gasch, C., Kuru, T., Nyarangi-Dix, J., Hatiboglu, G., Teber, D., Perner, S., Stenzinger, A., Roth, W., Hadaschik, B., Pahernik, S., Jager, D., Grullich, C., Duensing, A., Eils, R., Schlesner, M., Sultmann, H., Hohenfellner, M., & Duensing, S. (2018). Genomic features of renal cell carcinoma with venous tumor thrombus. Scientific Reports, 8. doi: 10.1038/s41598-018-25544-z

              Division of Theoretical Bioinformatics (B080), DKFZ Heidelberg, Institute for Pharmacy and Molecular Biotechnology (IPMB), BioQuant Heidelberg

Waszak, S.M., Northcott, P.A., Buchhalter, I., Robinson, G.W., Sutter, C., Groebner, S., Grund, K.B., Brugieres, L., Jones, D.T.W., Pajtler, K.W., Morrissy, A.S., Kool, M., Sturm, D., Chavez, L., Ernst, A., Brabetz, S., Hain, M., Zichner, T., Segura-Wang, M., Weischenfeldt, J., Rausch, T., Mardin, B.R., Zhou, X., Baciu, C., Lawerenz, C., Chan, J.A., Varlet, P., Guerrini-Rousseau, L., Fults, D.W., Grajkowska, W., Hauser, P., Jabado, N., Ra, Y.S., Zitterbart, K., Shringarpure, S.S., De La Vega, F.M., Bustamante, C.D., Ng, H.K., Perry, A., MacDonald, T.J., Driever, P.H., Bendel, A.E., Bowers, D.C., McCowage, G., Chintagumpala, M.M., Cohn, R., Hassall, T., Fleischhack, G., Eggen, T., Wesenberg, F., Feychting, M., Lannering, B., Schuz, J., Johansen, C., Andersen, T.V., Roosli, M., Kuehni, C.E., Grotzer, M., Kjaerheim, K., Monoranu, C.M., Archer, T.C., Duke, E., Pomeroy, S.L., Shelagh, R., Frank, S., Sumerauer, D., Scheurlen, W., Ryzhova, M.V., Milde, T., Kratz, C.P., Samuel, D., Zhang, J.H., Solomon, D.A., Marra, M., Eils, R., Bartram, C.R., von Hoff, K., Rutkowski, S., Ramaswamy, V., Gilbertson, R.J., Korshunov, A., Taylor, M.D., Lichter, P., Malkin, D., Gajjar, A., Korbel, J.O., & Pfister, S.M. (2018). Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. Lancet Oncology, 19(6), 785-798. doi: 10.1016/s1470-2045(18)30242-0

Division of Theoretical Bioinformatics (B080), DKFZ Heidelberg

Middle author

Weichenhan, D., Wang, Q., Adey, A., Wolf, S., Shendure, J., Eils, R., & Plass, C. (2018). Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing. Methods in Molecular Biology, 1708, 105-122. doi: 10.1007/978-1-4939-7481-8_6

              Division of Theoretical Bioinformatics (B080), DKFZ Heidelberg

2017

Ahsendorf, T., Muller, F.J., Topkar, V., Gunawardena, J., & Eils, R. (2017). Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant. Plos One, 12(12). doi: 10.1371/journal.pone.0186324

Backes, M., Berrang, P., Bieg, M., Eils, R., Herrmann, C., Humbert, M., Lehmann, I., & Ieee. (2017). Identifying Personal DNA Methylation Profiles by Genotype Inference 2017 Ieee Symposium on Security and Privacy (pp. 957-976).

Dieter, S.M., Heining, C., Agaimy, A., Huebschmann, D., Bonekamp, D., Hutter, B., Ehrenberg, K.R., Frohlich, M., Schlesner, M., Scholl, C., Schlemmer, H.P., Wolf, S., Mavratzas, A., Jung, C.S., Groschel, S., von Kalle, C., Eils, R., Brors, B., Penzel, R., Kriegsmann, M., Reuss, D.E., Schirmacher, P., Stenzinger, A., Federspil, P.A., Weichert, W., Glimm, H., & Frohling, S. (2017). Mutant KIT as imatinib-sensitive target in metastatic sinonasal carcinoma. Annals of Oncology, 28(1), 142-148. doi: 10.1093/annonc/mdw446

Dikow, N., Granzow, M., Graul-Neumann, L.M., Karch, S., Hinderhofer, K., Paramasivam, N., Behl, L.J., Kaufmann, L., Fischer, C., Evers, C., Schlesner, M., Eils, R., Borck, G., Zweier, C., Bartram, C.R., Carey, J.C., & Moog, U. (2017). DDX3X mutations in two girls with a phenotype overlapping Toriello-Carey syndrome. American Journal of Medical Genetics Part A, 173(5), 1369-1373. doi: 10.1002/ajmg.a.38164

Evers, C., Staufner, C., Granzow, M., Paramasivam, N., Hinderhofer, K., Kaufmann, L., Fischer, C., Thiel, C., Opladen, T., Kotzaeridou, U., Wiemann, S., Schlesner, M., Eils, R., Kolker, S., Bartram, C.R., Hoffmann, G.F., & Moog, U. (2017). Impact of clinical exomes in neurodevelopmental and neurometabolic disorders. Molecular Genetics and Metabolism, 121(4), 297-307. doi: 10.1016/j.ymgme.2017.06.014

Evers, C., Seitz, A., Assmann, B., Opladen, T., Karch, S., Hinderhofer, K., Granzow, M., Paramasivam, N., Eils, R., Diessl, N., Bartram, C.R., & Moog, U. (2017). Diagnosis of CoPAN by whole exome sequencing: Waking up a sleeping tiger's eye. American Journal of Medical Genetics Part A, 173(7), 1878-1886. doi: 10.1002/ajmg.a.38252

Fricke, F., Beaudouin, J., Malkusch, S., Eils, R., & Heilemann, M. (2017). Quantitative Single-Molecule Localization Microscopy (qSMLM) of Membrane Proteins Based on Kinetic Analysis of Fluorophore Blinking Cycles. Methods in Molecular Biology, 1663, 115-126. doi: 10.1007/978-1-4939-7265-4_10

Giessler, K.M., Kleinheinz, K., Huebschmann, D., Balasubramanian, G.P., Dubash, T.D., Dieter, S.M., Siegl, C., Herbst, F., Weber, S., Hoffmann, C.M., Fronza, R., Buchhalter, I., Paramasivam, N., Eils, R., Schmidt, M., von Kalle, C., Schneider, M., Ulrich, A., Scholl, C., Frohling, S., Weichert, W., Brors, B., Schlesner, M., Ball, C.R., & Glimm, H. (2017). Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer. Journal of Experimental Medicine, 214(7), 2073-2087. doi: 10.1084/jem.20162017

Gonzalez-Avalos, P., Murnseer, M., Deeg, J., Bachmann, A., Spatz, J., Dooley, S., Eils, R., & Gladilin, E. (2017). Quantification of substrate and cellular strains in stretchable 3D cell cultures: an experimental and computational framework. Journal of Microscopy, 266(2), 115-125. doi: 10.1111/jmi.12520

Horak, P., Klink, B., Heining, C., Groschel, S., Hutter, B., Frohlich, M., Uhrig, S., Hubschmann, D., Schlesner, M., Eils, R., Richter, D., Pfutze, K., Georg, C., Meissburger, B., Wolf, S., Schulz, A., Penzel, R., Herpel, E., Kirchner, M., Lier, A., Endris, V., Singer, S., Schirmacher, P., Weichert, W., Stenzinger, A., Schlenk, R.F., Schrock, E., Brors, B., von Kalle, C., Glimm, H., & Frohling, S. (2017). Precision oncology based on omics data: The NCT Heidelberg experience. International Journal of Cancer, 141(5), 877-886. doi: 10.1002/ijc.30828

Jabs, J., Zickgraf, F.M., Park, J., Wagner, S., Jiang, X.Q., Jechow, K., Kleinheinz, K., Toprak, U.H., Schneider, M.A., Meister, M., Spaich, S., Sutterlin, M., Schlesner, M., Trumpp, A., Sprick, M., Eils, R.*, & Conrad, C. (2017). Screening drug effects in patient-derived cancer cells links organoid responses to genome alterations. Molecular Systems Biology, 13(11). doi: 10.15252/msb.20177697

Jahreis, S., Trump, S., Bauer, M., Bauer, T., Thurmann, L., Feltens, R., Wang, Q., Gu, L., Grutzmann, K., Roder, S., Averbeck, M., Weichenhan, D., Plass, C., Sack, U., Borte, M., Dubourg, V., Schuurmann, G., Simon, J.C., von Bergen, M., Hackermuller, J., Eils, R.*, Lehmann, I., & Polte, T. (2018). Maternal phthalate exposure promotes allergic airway inflammation over 2 generations through epigenetic modifications. Journal of Allergy and Clinical Immunology, 141(2), 741-753. doi: 10.1016/j.jaci.2017.03.017

Kallenberger, S.M., Unger, A.L., Legewie, S., Lymperopoulos, K., Klingmuller, U., Eils, R.*, & Herten, D.P. (2017). Correlated receptor transport processes buffer single-cell heterogeneity. Plos Computational Biology, 13(9). doi: 10.1371/journal.pcbi.1005779

Liesche, C., Urlaub, D., Prager, I., Sauer, P., Claus, M., Eils, R., Beaudouin, J., & Watzl, C. (2017). Spatio-temporal granzyme B and caspase-8 activity in tumor cells during serial killing by Natural Killer cells. European Journal of Immunology, 47, 238-238.

Messica, Y., Laser-Azogui, A., Volberg, T., Elisha, Y., Lysakovskaia, K., Eils, R., Gladilin, E., Geiger, B., & Beck, R. (2017). The role of Vimentin in Regulating Cell Invasive Migration in Dense Cultures of Breast Carcinoma Cells. Nano Letters, 17(11), 6941-6948. doi: 10.1021/acs.nanolett.7b03358

Northcott, P.A., Buchhalter, I., Morrissy, A.S., Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Grobner, 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., Jager, N., Chavez, L., Hutter, B., Bieg, M., Paramasivam, N., Heinold, M., Gu, Z.G., Ishaque, N., Jager-Schmidt, C., Imbusch, C.D., Jugold, A., Hubschmann, 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.L., Cavalli, F.M.G., Luu, B., Ramaswamy, V., Wu, X.C., Koster, J., Ryzhova, M., Cho, Y.J., Pomeroy, S.L., Herold-Mende, C., Schuhmann, M., Ebinger, M., Liau, L.M., Mora, J., McLendon, 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.H., 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, 547(7663), 311-+. doi: 10.1038/nature22973

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg  J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er  D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants (2017) The Human Cell Atlas. Elife. 2017 Dec 5;6.

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, 261, 53-62. doi: 10.1016/j.jbiotec.2017.08.006

Winter, M., Thurmann, L., Gu, Z.G., Schueuermann, G., Herberth, G., Hinz, D., von Bergen, M., Harms, H., Olek, S., Roder, S., Borte, M., Eils, R., Lehmann, I., & Trump, S. (2017). The benzene metabolite 1,4-benzoquinone reduces regulatory T-cell function: A potential mechanism for tobacco smoke-associated atopic dermatitis. Journal of Allergy and Clinical Immunology, 140(2), 603-+. doi: 10.1016/j.jaci.2017.01.034

Wollmann, T., Erfle, H., Eils, R., Rohr, K., & Gunkel, M. (2017). Workflows for microscopy image analysis and cellular phenotyping. Journal of Biotechnology, 261, 70-75. doi: 10.1016/j.jbiotec.2017.07.019

Sahm, F., Toprak, U.H., Hubschmann, D., Kleinheinz, K., Buchhalter, I., Sill, M., Stichel, D., Schick, M., Bewerunge-Hudler, M., Schrimpf, D., Zadeh, G., Aldape, K., Herold-Mende, C., Beck, K., Staszewski, O., Prinz, M., Ben Harosh, C., Eils, R., Sturm, D., Jones, D.T.W., Pfister, S.M., Paulus, W., Ram, Z., Schlesner, M., Grossman, R., & von Deimling, A. (2017). Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature. Acta Neuropathologica, 134(1), 155-158. doi: 10.1007/s00401-017-1715-9

Schmelas, C.C., Gleixner, J., Heid, D., Schmidt, F., Eils, R., Di Ventura, B., & Grimm, D. (2017). Enhanced genome editing using split Staphylococcus aureus Cas9 delivered in self-complementary AAV vectors. Human Gene Therapy, 28(12), A62-A63.

Senis, E., Mockenhaupt, S., Rupp, D., Bauer, T., Paramasivam, N., Knapp, B., Gronych, J., Grosse, S., Windisch, M.P., Schmidt, F., Theis, F.J., Eils, R., Lichter, P., Schlesner, M., Bartenschlager, R., & Grimm, D. (2017). TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus. Nucleic Acids Research, 45(1). doi: 10.1093/nar/gkw805

Teif, V.B., Mallm, J.P., Sharma, T., Welch, D.B.M., Rippe, K., Eils, R., Langowski, J., Olins, A.L., & Olins, D.E. (2017). Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus, 8(2), 188-204. doi: 10.1080/19491034.2017.1295201

Trump, S., Klos, M., Gu, L., Bauer, T., Ishaque, N., Thurmann, L., Bieg, M., Bauer, M., Gu, Z., Borte, M., Mallm, J.P., Roder, S., Herrmann, C., Rippe, K., Lehmann, I., & Eils, R. (2017). Asthma Development In Early Childhood Is Associated With Enhancer Reprogramming. American Journal of Respiratory and Critical Care Medicine, 195.

Yamamoto, Y., Saito, A., Tateishi, A., Shimojo, H., Kanno, H., Tsuchiya, S., Ito, K., Cosatto, E., Graf, H.P., Moraleda, R.R., Eils, R., & Grabe, N. (2017). Quantitative diagnosis of breast tumors by morphometric classification of microenvironmental myoepithelial cells using a machine learning approach. Scientific Reports, 7. doi: 10.1038/srep46732

2016

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

Bender, S., Gronych, J., Warnatz, H.J., Hutter, B., Grobner, S., Ryzhova, M., Pfaff, E., Hovestadt, V., Weinberg, F., Halbach, S., Kool, M., Northcott, P.A., Sturm, D., Bjerke, L., Zichner, T., Stutz, A.M., Schramm, K., Huang, B., Buchhalter, I., Heinold, M., Risch, T., Worst, B.C., van Tilburg, C.M., Weber, U.D., Zapatka, M., Raeder, B., Milford, D., Heiland, S., von Kalle, C., Previti, C., Lawerenz, C., Kulozik, A.E., Unterberg, A., Witt, O., von Deimling, A., Capper, D., Truffaux, N., Grill, J., Jabado, N., Sehested, A.M., Sumerauer, D., Hmida-Ben Brahim, D., Trabelsi, S., Ng, H.K., Zagzag, D., Allen, J.C., Karajannis, M.A., Gottardo, N.G., Jones, C., Korbel, J., Schmidt, S., Wolf, S., Reifenberger, G., Felsberg, J., Brors, B., Herold-Mende, C., Lehrach, H., Brummer, T., Korshunov, A., Eils, R., Yaspo, M.L., Pfister, S.M., Lichter, P., Jones, D.T.W., & Int Canc Genome, C. (2016). Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nature Medicine, 22(11), 1314-1320. doi: 10.1038/nm.4204

Dieckmann, A.K., Babin, V., Harari, Y., Eils, R., Konig, R., Luke, B., & Kupiec, M. (2016). Role of the ESCRT Complexes in Telomere Biology. Mbio, 7(6). doi: 10.1128/mBio.01793-16

Forsti, A., Kumar, A., Paramasivam, N., Schlesner, M., Catalano, C., Dymerska, D., Lubinski, J., Eils, R., & Hemminki, K. (2016). Pedigree based DNA sequencing pipeline for germline genomes of cancer families. Hereditary Cancer in Clinical Practice, 14. doi: 10.1186/s13053-016-0058-1

Gu, Z.G., Eils, R., & Schlesner, M. (2016). gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC Bioinformatics, 17. doi: 10.1186/s12859-016-1051-4

Gu, Z.G., Eils, R., & Schlesner, M. (2016). HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. Bioinformatics, 32(15), 2372-2374. doi: 10.1093/bioinformatics/btw161

Gu, Z.G., Eils, R., & Schlesner, M. (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18), 2847-2849. doi: 10.1093/bioinformatics/btw313

Hezaveh, K., Kloetgen, A., Bernhart, S.H., Das Mahapatra, K., Lenze, D., Richter, J., Haake, A., Bergmann, A.K., Brors, B., Burkhardt, B., Claviez, A., Drexler, H.G., Eils, R., Haas, S., Hoffmann, S., Karsch, D., Klapper, W., Kleinheinz, K., Korbel, J., Kretzmer, H., Kreuz, M., Kuppers, R., Lawerenz, C., Leich, E., Loeffler, M., Mantovani-Loeffler, L., Lopez, C., McHardy, A.C., Moller, P., Rohde, M., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schlesner, M., Scholz, I., Stadler, P.F., Stilgenbauer, S., Sungalee, S., Szczepanowski, M., Trumper, L., Weniger, M.A., Siebert, R., Borkhardt, A., Hummel, M., Hoell, J.I., & Project, I.M.-S. (2016). Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica, 101(11), 1380-1389. doi: 10.3324/haematol.2016.143891

Hoefflin, R., Lahrmann, B., Warsow, G., Hubschmann, D., Spath, C., Walter, B., Chen, X., Hofer, L., Macher-Goeppinger, S., Tolstov, Y., Korzeniewski, N., Duensing, A., Grullich, C., Jager, D., Perner, S., Schonberg, G., Nyarangi-Dix, J., Isaac, S., Hatiboglu, G., Teber, D., Hadaschik, B., Pahernik, S., Roth, W., Eils, R., Schlesner, M., Sultmann, H., Hohenfellner, M., Grabe, N., & Duensing, S. (2016). Spatial niche formation but not malignant progression is a driving force for intratumoural heterogeneity. Nature Communications, 7. doi: 10.1038/ncomms11845

Johann, P.D., Erkek, S., Zapatka, M., Kerl, K., Buchhalter, I., Hovestadt, V., Jones, D.T.W., Sturm, D., Hermann, C., Wang, M.S., Korshunov, A., Rhyzova, M., Grobner, S., Brabetz, S., Chavez, L., Bens, S., Groschel, S., Kratochwil, F., Wittmann, A., Sieber, L., Georg, C., Wolf, S., Beck, K., Oyen, F., Capper, D., van Sluis, P., Volckmann, R., Koster, J., Versteeg, R., von Deimling, A., Milde, T., Witt, O., Kulozik, A.E., Ebinger, M., Shalaby, T., Grotzer, M., Sumerauer, D., Zamecnik, J., Mora, J., Jabado, N., Taylor, M.D., Huang, A., Aronica, E., Bertoni, A., Radlwimmer, B., Pietsch, T., Schuller, U., Schneppenheim, R., Northcott, P.A., Korbel, J.O., Siebert, R., Fruhwald, M.C., Lichter, P., Eils, R., Gajjar, A., Hasselblatt, M., Pfister, S.M., & Kool, M. (2016). Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes. Cancer Cell, 29(3), 379-393. doi: 10.1016/j.ccell.2016.02.001

Junge, K.M., Bauer, T., Geissler, S., Hirche, F., Thurmann, L., Bauer, M., Trump, S., Bieg, M., Weichenhan, D., Gu, L., Mallm, J.P., Ishaque, N., Muecke, O., Roder, S., Herberth, G., Diez, U., Borte, M., Rippe, K., Plass, C., Hermann, C., Stangl, G.I., Eils, R.*,  & Lehmann, I. (2016). Increased vitamin D levels at birth and in early infancy increase offspring allergy risk-evidence for involvement of epigenetic mechanisms. Journal of Allergy and Clinical Immunology, 137(2), 610-613. doi: 10.1016/j.jaci.2015.06.040

Kosaloglu, Z., Zornig, I., Halama, N., Kaiser, I., Buchhalter, I., Grabe, N., Eils, R., Schlesner, M., Califano, A., & Jager, D. (2016). Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases. Oncoimmunology, 5(11). doi: 10.1080/2162402x.2016.1213931

Lin, C.Y., Erkek, S., Tong, Y.A., Yin, L.L., Federation, A.J., Zapatka, M., Haldipur, P., Kawauchi, D., Risch, T., Warnatz, H.J., Worst, B.C., Ju, B.S., Orr, B.A., Zeid, R., Polaski, D.R., Segura-Wang, M., Waszak, S.M., Jones, D.T.W., Kool, M., Hovestadt, V., Buchhalter, I., Sieber, L., Johann, P., Chavez, L., Groschel, S., Ryzhova, M., Korshunov, A., Chen, W.B., Chizhikov, V.V., Millen, K.J., Amstislavskiy, V., Lehrach, H., Yaspo, M.L., Eils, R., Lichter, P., Korbel, J.O., Pfister, S.M., Bradner, J.E., & Northcott, P.A. (2016). Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature, 530(7588), 57-+. doi: 10.1038/nature16546

Niopek, D., Wehler, P., Roensch, J., Eils, R.*, & Di Ventura, B. (2016). Optogenetic control of nuclear protein export. Nature Communications, 7. doi: 10.1038/ncomms10624

Noll, E.M., Eisen, C., Stenzinger, A., Espinet, E., Muckenhuber, A., Klein, C., Vogel, V., Klaus, B., Nadler, W., Rosli, C., Lutz, C., Kulke, M., Engelhardt, J., Zickgraf, F.M., Espinosa, O., Schlesner, M., Jiang, X.Q., Kopp-Schneider, A., Neuhaus, P., Bahra, M., Sinn, B.V., Eils, R., Giese, N.A., Hackert, T., Strobel, O., Werner, J., Buchler, M.W., Weichert, W., Trumpp, A., & Sprick, M.R. (2016). CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma. Nature Medicine, 22(3), 278-287. doi: 10.1038/nm.4038

Poos, A.M., Maicher, A., Dieckmann, A.K., Oswald, M., Eils, R., Kupiec, M., Luke, B., & Konig, R. (2016). Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast. Nucleic Acids Research, 44(10). doi: 10.1093/nar/gkw111

Sharma, A.K., Eils, R., & Konig, R. (2016). Copy Number Alterations in Enzyme-Coding and Cancer-Causing Genes Reprogram Tumor Metabolism. Cancer Research, 76(14), 4058-4067. doi: 10.1158/0008-5472.can-15-2350

Shostak, A., Ruppert, B., Ha, N., Bruns, P., Toprak, U.H., Eils, R., Schlesner, M., Diernfellner, A., Brunner, M., & Project, I.M.-S. (2016). MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation. Nature Communications, 7. doi: 10.1038/ncomms11807

Steinhauser, S., Kurzawa, N., Eils, R., & Herrmann, C. (2016). A comprehensive comparison of tools for differential ChIP-seq analysis. Briefings in Bioinformatics, 17(6), 953-966. doi: 10.1093/bib/bbv110

Sturm, D., Orr, B.A., Toprak, U.H., Hovestadt, V., Jones, D.T.W., Capper, D., Sill, M., Buchhalter, I., Northcott, P.A., Leis, I., Ryzhova, M., Koelsche, C., Pfaff, E., Allen, S.J., Balasubramanian, G., Worst, B.C., Pajtler, K.W., Brabetz, S., Johann, P.D., Sahm, F., Reimand, J., Mackay, A., Carvalho, D.M., Remke, M., Phillips, J.J., Perry, A., Cowdrey, C., Drissi, R., Fouladi, M., Giangaspero, F., Lastowska, M., Grajkowska, W., Scheurlen, W., Pietsch, T., Hagel, C., Gojo, J., Loetsch, D., Berger, W., Slavc, I., Haberler, C., Jouvet, A., Holm, S., Hofer, S., Prinz, M., Keohane, C., Fried, I., Mawrin, C., Scheie, D., Mobley, B.C., Schniederjan, M.J., Santi, M., Buccoliero, A.M., Dahiya, S., Kramm, C.M., von Bueren, A.O., von Hoff, K., Rutkowski, S., Herold-Mende, C., Fruehwald, M.C., Milde, T., Hasselblatt, M., Wesseling, P., Rossler, J., Schuller, U., Ebinger, M., Schittenhelm, J., Frank, S., Grobholz, R., Vajtai, I., Hans, V., Schneppenheim, R., Zitterbart, K., Collins, V.P., Aronica, E., Varlet, P., Puget, S., Dufour, C., Grill, J., Figarella-Branger, D., Wolter, M., Schuhmann, M.U., Shalaby, T., Grotzer, M., van Meter, T., Monoranu, C.M., Felsberg, J., Reifenberger, G., Snuderl, M., Forrester, L.A., Koster, J., Versteeg, R., Volckmann, R., van Sluis, P., Wolf, S., Mikkelsen, T., Gajjar, A., Aldape, K., Moore, A.S., Taylor, M.D., Jones, C., Jabado, N., Karajannis, M.A., Eils, R., Schlesner, M., Lichter, P., von Deimling, A., Pfister, S.M., Ellison, D.W., Korshunov, A., & Kool, M. (2016). New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell, 164(5), 1060-1072. doi: 10.1016/j.cell.2016.01.015

Trump, S., Bieg, M., Gu, Z.G., Thurmann, L., Bauer, T., Bauer, M., Ishaque, N., Roder, S., Gu, L., Herberth, G., Lawerenz, C., Borte, M., Schlesner, M., Plass, C., Diessl, N., Eszlinger, M., Mucke, O., Elvers, H.D., Wissenbach, D.K., von Bergen, M., Herrmann, C., Weichenhan, D., Wright, R.J., Lehmann, I., & Eils, R.* (2016). Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation. Scientific Reports, 6. doi: 10.1038/srep28616

Wehler, P., Niopek, D., Eils, R., & Di Ventura, B. (2016). Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS). Current Protocols in Chemical Biology, 8(2), 131-145. doi: 10.1002/cpch.4

2015

Alioto, T.S., Buchhalter, I., Derdak, S., Hutter, B., Eldridge, M.D., Hovig, E., Heisler, L.E., Beck, T.A., Simpson, J.T., Tonon, L., Sertier, A.S., Patch, A.M., Jager, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C., Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Grobner, S., Korshunov, A., Tarpey, P.S., Butler, A.P., Hinton, J., Jones, D., Menzies, A., Raine, K., Shepherd, R., Stebbings, L., Teague, J.W., Ribeca, P., Giner, F.C., Beltran, S., Raineri, E., Dabad, M., Heath, S.C., Gut, M., Denroche, R.E., Harding, N.J., Yamaguchi, T.N., Fujimoto, A., Nakagawa, H., Quesada, C., Valdes-Mas, R., Nakken, S., Vodak, D., Bower, L., Lynch, A.G., Anderson, C.L., Waddell, N., Pearson, J.V., Grimmond, S.M., Peto, M., Spellman, P., He, M.H., Kandoth, C., Lee, S., Zhang, J., Letourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D.A., Lopez-Otin, C., Campo, E., Campbell, P.J., Boutros, P.C., Puente, X.S., Gerhard, D.S., Pfister, S.M., McPherson, J.D., Hudson, T.J., Schlesner, M., Lichter, P., Eils, R.*, Jones, D.T.W., & Gut, I.G. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications, 6. doi: 10.1038/ncomms10001

Betts, M.J., Lu, Q.H., Jiang, Y.Y., Drusko, A., Wichmann, O., Utz, M., Valtierra-Gutierrez, I.A., Schlesner, M., Jaeger, N., Jones, D.T., Pfister, S., Lichter, P., Eils, R., Siebert, R., Bork, P., Apic, G., Gavin, A.C., & Russell, R.B. (2015). Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. Nucleic Acids Research, 43(2). doi: 10.1093/nar/gku1094

Eils, R., Ritzerfeld, J., & Wiechert, W. (2015). Editorial: Synthetic biology - ready for application. Biotechnology Journal, 10(2), 229-230. doi: 10.1002/biot.201500025

Evers, C., Paramasivam, N., Hinderhofer, K., Fischer, C., Granzow, M., Schmidt-Bacher, A., Eils, R., Steinbeisser, H., Schlesner, M., & Moog, U. (2015). SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract. European Journal of Human Genetics, 23(12), 1627-1633. doi: 10.1038/ejhg.2015.46

Fricke, F., Beaudouin, J., Eils, R., & Heilemann, M. (2015). One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy. Scientific Reports, 5. doi: 10.1038/srep14072

Gladilin, E., & Eils, R.* (2015). On the role of spatial phase and phase correlation in vision, illusion, and cognition. Frontiers in Computational Neuroscience, 9. doi: 10.3389/fncom.2015.00045

Granzow, M., Paramasivam, N., Hinderhofer, K., Fischer, C., Chotewutmontri, S., Kaufmann, L., Evers, C., Kotzaeridou, U., Rohrschneider, K., Schlesner, M., Sturm, M., Pinkert, S Eils, R., Bartram, C.R., Bauer, P., & Moog, U. (2015). Loss of function of PGAP1 as a cause of severe encephalopathy identified by Whole Exome Sequencing: Lessons of the bioinformatics pipeline. Molecular and Cellular Probes, 29(5), 323-329. doi: 10.1016/j.mcp.2015.05.012

Gu, L., Frommel, S.C., Oakes, C.C., Simon, R., Grupp, K., Gerig, C.Y., Bar, D., Robinson, M.D., Baer, C., Weiss, M., Gu, Z.G., Schapira, M., Kuner, R., Sultmann, H., Provenzano, M., Yaspo, M.L., Brors, B., Korbel, J., Schlomm, T., Sauter, G., Eils, R.*, Plass, C., Santoro, R., & Prostate, I.P.E.O. (2015). BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature Genetics, 47(1), 22-+. doi: 10.1038/ng.3165

Harder, N., Batra, R., Diessl, N., Gogolin, S., Eils, R., Westermann, F., Konig, R., & Rohr, K. (2015). Large-scale tracking and classification for automatic analysis of cell migration and proliferation, and experimental optimization of high-throughput screens of neuroblastoma cells. Cytometry Part A, 87A(6), 524-540. doi: 10.1002/cyto.a.22632

Jaiswal, A., Godinez, W.J., Eils, R., Lehmann, M.J., & Rohr, K. (2015). Tracking Virus Particles in Fluorescence Microscopy Images Using Multi-Scale Detection and Multi-Frame Association. Ieee Transactions on Image Processing, 24(11), 4122-4136. doi: 10.1109/tip.2015.2458174

Kretzmer, H., Bernhart, S.H., Wang, W., Haake, A., Weniger, M.A., Bergmann, A.K., Betts, M.J., Carrillo-de-Santa-Pau, E., Doose, G., Gutwein, J., Richter, J., Hovestadt, V., Huang, B.D., Rico, D., Juhling, F., Kolarova, J., Lu, Q.H., Otto, C., Wagener, R., Arnolds, J., Burkhardt, B., Claviez, A., Drexler, H.G., Eberth, S., Eils, R., Flicek, P., Haas, S., Hummel, M., Karsch, D., Kerstens, H.H.D., Klapper, W., Kreuz, M., Lawerenz, C., Lenze, D., Loeffler, M., Lopez, C., MacLeod, R.A.F., Martens, J.H.A., Kulis, M., Martin-Subero, J.I., Moller, P., Nagel, I., Picelli, S., Vater, I., Rohde, M., Rosenstiel, P., Rosolowski, M., Russell, R.B., Schilhabel, M., Schlesner, M., Stadler, P.F., Szczepanowski, M., Trumper, L., Stunnenberg, H.G., Kuppers, R., Lichter, P., Siebert, R., Hoffmann, S., Radlwimmer, B., Project, I.M.-S., & Project, B. (2015). DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature Genetics, 47(11), 1316-+. doi: 10.1038/ng.3413

Liesche, C., Grussmayer, K.S., Ludwig, M., Worz, S., Rohr, K., Herten, D.P., Beaudouin, J., & Eils, R.* (2015). Automated Analysis of Single-Molecule Photobleaching Data by Statistical Modeling of Spot Populations. Biophysical Journal, 109(11), 2352-2362. doi: 10.1016/j.bpj.2015.10.035

Nolte, N., Kurzawa, N., Eils, R., & Herrmann, C. (2015). MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences. Nucleic Acids Research, 43(W1), W547-W551. doi: 10.1093/nar/gkv417

Oberthuer, A., Juraeva, D., Hero, B., Volland, R., Sterz, C., Schmidt, R., Faldum, A., Kahlert, Y., Engesser, A., Asgharzadeh, S., Seeger, R., Ohira, M., Nakagawara, A., Scaruffi, P., Tonini, G.P., Janoueix-Lerosey, I., Delattre, O., Schleiermacher, G., Vandesompele, J., Speleman, F., Noguera, R., Piqueras, M., Benard, J., Valent, A., Avigad, S., Yaniv, I., Grundy, R.G., Ortmann, M., Shao, C.X., Schwab, M., Eils, R., Simon, T., Theissen, J., Berthold, F., Westermann, F., Brors, B., & Fischer, M. (2015). Revised Risk Estimation and Treatment Stratification of Low- and Intermediate-Risk Neuroblastoma Patients by Integrating Clinical and Molecular Prognostic Markers. Clinical Cancer Research, 21(8), 1904-1915. doi: 10.1158/1078-0432.ccr-14-0817

Pietkiewicz, S., Eils, R., Krammer, P.H., Giese, N., & Lavrik, I.N. (2015). Combinatorial treatment of CD95L and gemcitabine in pancreatic cancer cells induces apoptotic and RIP1-mediated necroptotic cell death network. Experimental Cell Research, 339(1), 1-9. doi: 10.1016/j.yexcr.2015.10.005

Schlesner, M., & Eils, R.* (2015). Hypermutation takes the driver's seat. Genome Medicine, 7. doi: 10.1186/s13073-015-0159-x

Schuol, S., Schickhardt, C., Wiemann, S., Bartram, C.R., Tanner, K., Eils, R., Meder, B., Richter, D., Glimm, H., von Kalle, C., & Winkler, E.C. (2015). So rare we need to hunt for them: reframing the ethical debate on incidental findings. Genome Medicine, 7. doi: 10.1186/s13073-015-0198-3

Tektonidis, M., Kim, I.H., Chen, Y.C.M., Eils, R., Spector, D.L., & Rohr, K. (2015). Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data. Medical Image Analysis, 19(1), 1-14. doi: 10.1016/j.media.2014.07.006

Vater, I., Montesinos-Rongen, M., Schlesners, M., Haakel, A., Purschke, F., Sprute, R., Mettenmeyer, N., Nazzal, I., Nagel, I., Gutwein, J., Richter, J., Buchhalter, I., Russell, R.B., Wiestler, O.D., Eils, R., Deckert, M., & Siebert, R. (2015). The mutational pattern of primary lymphoma of the central nervous system determined by whole-exome sequencing. Leukemia, 29(3), 677-685. doi: 10.1038/leu.2014.264

Waldhauer, M.C., Schmitz, S.N., Ahlmann-Eltze, C., Gleixner, J.G., Schmelas, C.C., Huhn, A.G., Bunne, C., Buscher, M., Horn, M., Klughammer, N., Kreft, J., Schafer, E., Bayer, P.A., Kramer, S.G., Neugebauer, J., Wehler, P., Mayer, M.P, Eils, R.*, & Di Ventura, B. (2015). Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation. Molecular Biosystems, 11(12), 3231-3243. doi: 10.1039/c5mb00341e

Wegert, J., Ishaque, N., Vardapour, R., Georg, C., Gu, Z.G., Bieg, M., Ziegler, B., Bausenwein, S., Nourkami, N., Ludwig, N., Keller, A., Grimm, C., Kneitz, S., Williams, R.D., Chagtai, T., Pritchard-Jones, K., van Sluis, P., Volckmann, R., Koster, J., Versteeg, R., Acha, T., O'Sullivan, M.J., Bode, P.K., Niggli, F., Tytgat, G.A., van Tinteren, H., van den Heuvel-Eibrink, M.M., Meese, E., Vokuhl, C., Leuschner, I., Graf, N., Eils, R., Pfister, S.M., Kool, M., & Gessler, M. (2015). Mutations in the SIX1/2 Pathway and the DROSHA/DGCR8 miRNA Microprocessor Complex Underlie High-Risk Blastemal Type Wilms Tumors. Cancer Cell, 27(2), 298-311. doi: 10.1016/j.ccell.2015.01.002

Werner, S., Brors, B., Eick, J., Marques, E., Pogenberg, V., Parret, A., Kemming, D., Wood, A.W., Edgren, H., Neubauer, H., Streichert, T., Riethdorf, S., Bedi, U., Baccelli, I., Jucker, M., Eils, R., Fehm, T., Trumpp, A., Johnsen, S.A., Klefstrom, J., Wilmanns, M., Muller, V., Pantel, K., & Wikman, H. (2015). Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid-Induced 2. Cancer Discovery, 5(5), 506-519. doi: 10.1158/2159-8290.cd-14-1042

Zepeda-Mendoza, C.J., Mukhopadhyay, S., Wong, E.S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M.A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A.M., & Spector, D.L. (2015). Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16. doi: 10.1186/s12864-015-2137-5

2014

Ahsendorf, T., Wong, F., Eils, R.*, & Gunawardena, J. (2014). A framework for modelling gene regulation which accommodates non-equilibrium mechanisms. Bmc Biology, 12. doi: 10.1186/s12915-014-0102-4

Beer, R., Herbst, K., Ignatiadis, N., Kats, I., Adlung, L., Meyer, H., Niopek, D., Christiansen, T., Georgi, F., Kurzawa, N., Meichsner, J., Rabe, S., Riedel, A., Sachs, J., Schessner, J., Schmidt, F., Walch, P., Niopek, K., Heinemann, T., Eils, R.*, & Di Ventura, B. (2014). Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange. Molecular Biosystems, 10(7), 1709-1718. doi: 10.1039/c3mb70594c

Bernardo-Faura, M., Massen, S., Falk, C.S., Brady, N.R., & Eils, R.* (2014). Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma. Plos Computational Biology, 10(9). doi: 10.1371/journal.pcbi.1003795

Cabezas-Wallscheid, N., Klimmeck, D., Hansson, J., Lipka, D.B., Reyes, A., Wang, Q., Weichenhan, D., Lier, A., von Paleske, L., Renders, S., Wunsche, P., Zeisberger, P., Brocks, D., Gu, L., Herrmann, C., Haas, S., Essers, M.A.G., Brors, B., Eils, R., Huber, W., Milsom, M.D., Plass, C., Krijgsveld, J., & Trumpp, A. (2014). Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis. Cell Stem Cell, 15(4), 507-522. doi: 10.1016/j.stem.2014.07.005

Eskova, A., Knapp, B., Matelska, D., Reusing, S., Arjonen, A., Lisauskas, T., Pepperkok, R., Russell, R., Eils, R., Ivaska, J., Kaderali, L., Erfle, H., & Starkuviene, V. (2014). An RNAi screen identifies KIF15 as a novel regulator of the endocytic trafficking of integrin. Journal of Cell Science, 127(11), 2433-2447. doi: 10.1242/jcs.137281

Gerola, S., Nittka, S., Kahler, G., Tao, S., Brenner, H., Binelli, G., Eils, R., Brors, B., & Neumaier, M. (2014). Genetic Variants in Apoptosis-Related Genes Associated with Colorectal Hyperplasia. Genes Chromosomes & Cancer, 53(9), 769-778. doi: 10.1002/gcc.22185

Gladilin, E., Gonzalez, P., & Eils, R.*(2014). Dissecting the contribution of actin and vimentin intermediate filaments to mechanical phenotype of suspended cells using high-throughput deformability measurements and computational modeling. Journal of Biomechanics, 47(11), 2598-2605. doi: 10.1016/j.jbiomech.2014.05.020

Gu, Z.G., Gu, L., Eils, R.*, Schlesner, M., & Brors, B. (2014). circlize implements and enhances circular visualization in R. Bioinformatics, 30(19), 2811-2812. doi: 10.1093/bioinformatics/btu393

Hovestadt, V., Jones, D.T.W., Picelli, S., Wang, W., Kool, M., Northcott, P.A., Sultan, M., Stachurski, K., Ryzhova, M., Warnatz, H.J., Ralser, M., Brun, S., Bunt, J., Jager, N., Kleinheinz, K., Erkek, S., Weber, U.D., Bartholomae, C.C., von Kalle, C., Lawerenz, C., Eils, J., Koster, J., Versteeg, R., Milde, T., Witt, O., Schmidt, S., Wolf, S., Pietsch, T., Rutkowski, S., Scheurlen, W., Taylor, M.D., Brors, B., Felsberg, J., Reifenberger, G., Borkhardt, A., Lehrach, H., Wechsler-Reya, R.J., Eils, R., Yaspo, M.L., Landgraf, P., Korshunov, A., Zapatka, M., Radlwimmer, B., Pfister, S.M., & Lichter, P. (2014). Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature, 510(7506), 537-+. doi: 10.1038/nature13268

Kallenberger, S.M., Beaudouin, J., Claus, J., Fischer, C., Sorger, P.K., Legewie, S., & Eils, R.* (2014). Intra- and Interdimeric Caspase-8 Self-Cleavage Controls Strength and Timing of CD95-Induced Apoptosis. Science Signaling, 7(316). doi: 10.1126/scisignal.2004738

Kool, M., Jones, D.T.W., Jager, N., Northcott, P.A., Pugh, T.J., Hovestadt, V., Piro, R.M., Esparza, L.A., Markant, S.L., Remke, M., Milde, T., Bourdeaut, F., Ryzhova, M., Sturm, D., Pfaff, E., Stark, S., Hutter, S., Seker-Cin, H., Johann, P., Bender, S., Schmidt, C., Rausch, T., Shih, D., Reimand, J., Sieber, L., Wittmann, A., Linke, L., Witt, H., Weber, U.D., Zapatka, M., Konig, R., Beroukhim, R., Bergthold, G., van Sluis, P., Volckmann, R., Koster, J., Versteeg, R., Schmidt, S., Wolf, S., Lawerenz, C., Bartholomae, C.C., von Kalle, C., Unterberg, A., Herold-Mende, C., Hofer, S., Kulozik, A.E., von Deimling, A., Scheurlen, W., Felsberg, J., Reifenberger, G., Hasselblatt, M., Crawford, J.R., Grant, G.A., Jabado, N., Perry, A., Cowdrey, C., Croul, S., Zadeh, G., Korbel, J.O., Doz, F., Delattre, O., Bader, G.D., McCabe, M.G., Collins, V.P., Kieran, M.W., Cho, Y.J., Pomeroy, S.L., Witt, O., Brors, B., Taylor, M.D., Schuller, U., Korshunov, A., Eils, R., Wechsler-Reya, R.J., Lichter, P., Pfister, S.M., & Project, I.P.T. (2014). Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition. Cancer Cell, 25(3), 393-405. doi: 10.1016/j.ccr.2014.02.004

Lipka, D.B., Wang, Q., Cabezas-Wallscheid, N., Klimmeck, D., Weichenhan, D., Herrmann, C., Lier, A., Brocks, D., von Paleske, L., Renders, S., Wunsche, P., Zeisberger, P., Gu, L., Haas, S., Essers, M.A., Brors, B., Eils, R., Trumpp, A., Milsom, M.D., & Plass, C. (2014). Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing. Cell Cycle, 13(22), 3476-3487. doi: 10.4161/15384101.2014.973334

Mack, S.C., Witt, H., Piro, R.M., Gu, L., Zuyderduyn, S., Stutz, A.M., Wang, X., Gallo, M., Garzia, L., Zayne, K., Zhang, X., Ramaswamy, V., Jager, N., Jones, D.T.W., Sill, M., Pugh, T.J., Ryzhova, M., Wani, K.M., Shih, D.J.H., Head, R., Remke, M., Bailey, S.D., Zichner, T., Faria, C.C., Barszczyk, M., Stark, S., Seker-Cin, H., Hutter, S., Johann, P., Bender, S., Hovestadt, V., Tzaridis, T., Dubuc, A.M., Northcott, P.A., Peacock, J., Bertrand, K.C., Agnihotri, S., Cavalli, F.M.G., Clarke, I., Nethery-Brokx, K., Creasy, C.L., Verma, S.K., Koster, J., Wu, X., Yao, Y., Milde, T., Sin-Chan, P., Zuccaro, J., Lau, L., Pereira, S., Castelo-Branco, P., Hirst, M., Marra, M.A., Roberts, S.S., Fults, D., Massimi, L., Cho, Y.J., Van Meter, T., Grajkowska, W., Lach, B., Kulozik, A.E., von Deimling, A., Witt, O., Scherer, S.W., Fan, X., Muraszko, K.M., Kool, M., Pomeroy, S.L., Gupta, N., Phillips, J., Huang, A., Tabori, U., Hawkins, C., Malkin, D., Kongkham, P.N., Weiss, W.A., Jabado, N., Rutka, J.T., Bouffet, E., Korbel, J.O., Lupien, M., Aldape, K.D., Bader, G.D., Eils, R., Lichter, P., Dirks, P.B., Pfister, S.M., Korshunov, A., & Taylor, M.D. (2014). Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature, 506(7489), 445-+. doi: 10.1038/nature13108

Niopek, D., Benzinger, D., Roensch, J., Draebing, T., Wehler, P., Eils, R.*, & Di Ventura, B. (2014). Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells. Nature Communications, 5. doi: 10.1038/ncomms5404

Northcott, P.A., Lee, C., Zichner, T., Stutz, A.M., Erkek, S., Kawauchi, D., Shih, D.J.H., Hovestadt, V., Zapatka, M., Sturm, D., Jones, D.T.W., Kool, M., Remke, M., Cavalli, F.M.G., Zuyderduyn, S., Bader, G.D., VandenBerg, S., Esparza, L.A., Ryzhova, M., Wang, W., Wittmann, A., Stark, S., Sieber, L., Seker-Cin, H., Linke, L., Kratochwil, F., Jager, N., Buchhalter, I., Imbusch, C.D., Zipprich, G., Raeder, B., Schmidt, S., Diessl, N., Wolf, S., Wiemann, S., Brors, B., Lawerenz, C., Eils, J., Warnatz, H.J., Risch, T., Yaspo, M.L., Weber, U.D., Bartholomae, C.C., von Kalle, C., Turanyi, E., Hauser, P., Sanden, E., Darabi, A., Siesjo, P., Sterba, J., Zitterbart, K., Sumerauer, D., van Sluis, P., Versteeg, R., Volckmann, R., Koster, J., Schuhmann, M.U., Ebinger, M., Grimes, H.L., Robinson, G.W., Gajjar, A., Mynarek, M., von Hoff, K., Rutkowski, S., Pietsch, T., Scheurlen, W., Felsberg, J., Reifenberger, G., Kulozik, A.E., von Deimling, A., Witt, O., Eils, R., Gilbertson, R.J., Korshunov, A., Taylor, M.D., Lichter, P., Korbel, J.O., Wechsler-Reya, R.J., & Pfister, S.M. (2014). Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature, 511(7510), 428-+. doi: 10.1038/nature13379

Piro, R.M., Wiesberg, S., Schramm, G., Rebel, N., Oswald, M., Eils, R., Reinelt, G., & Konig, R. (2014). Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. Bmc Systems Biology, 8. doi: 10.1186/1752-0509-8-56

Rohde, M., Richter, J., Schlesner, M., Betts, M.J., Claviez, A., Bonn, B.R., Zimmermann, M., Damm-Welk, C., Russell, R.B., Borkhardt, A., Eils, R., Hoell, J.I., Szczepanowski, M., Oschlies, I., Klapper, W., Burkhardt, B., Siebert, R., German, I.M.-S.-P., & Grp, N.-B.S. (2014). Recurrent RHOA Mutations in Pediatric Burkitt Lymphoma Treated According to the NHL-BFM Protocols. Genes Chromosomes & Cancer, 53(11), 911-916. doi: 10.1002/gcc.22202

Schacht, T., Oswald, M., Eils, R., Eichmuller, S.B., & Konig, R. (2014). Estimating the activity of transcription factors by the effect on their target genes. Bioinformatics, 30(17), I401-I407. doi: 10.1093/bioinformatics/btu446

Schumacher, M., Schuster, C., Rogon, Z.M., Bauer, T., Caushaj, N., Baars, S., Szabowski, S., Bauer, C., Schorpp-Kistner, M., Hess, J., Holland-Cunz, S., Wagner, E.F., Eils, R., Angel, P., & Hartenstein, B. (2014). Efficient Keratinocyte Differentiation Strictly Depends on JNK-Induced Soluble Factors in Fibroblasts. Journal of Investigative Dermatology, 134(5), 1332-1341. doi: 10.1038/jid.2013.535

Suratanee, A., Schaefer, M.H., Betts, M.J., Soons, Z., Mannsperger, H., Harder, N., Oswald, M., Gipp, M., Ramminger, E., Marcus, G., Manner, R., Rohr, K., Wanker, E., Russell, R.B., Andrade-Navarro, M.A., Eils, R., & Konig, R. (2014). Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. Plos Computational Biology, 10(9). doi: 10.1371/journal.pcbi.1003814

Tektonidis, M., Kim, I.H., Chen, Y.C., Eils, R., Spector, D.L., & Rohr, K. (2014). Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data. Medical Image Analysis, 19(1), 1-14. doi: 10.1016/j.media.2014.07.006

2013

Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Aparicio, S., Behjati, S., Biankin, A.V., Bignell, G.R., Bolli, N., Borg, A., Borresen-Dale, A.L., Boyault, S., Burkhardt, B., Butler, A.P., Caldas, C., Davies, H.R., Desmedt, C., Eils, R., Eyfjord, J.E., Foekens, J.A., Greaves, M., Hosoda, F., Hutter, B., Ilicic, T., Imbeaud, S., Imielinsk, M., Jager, N., Jones, D.T.W., Jones, D., Knappskog, S., Kool, M., Lakhani, S.R., Lopez-Otin, C., Martin, S., Munshi, N.C., Nakamura, H., Northcott, P.A., Pajic, M., Papaemmanuil, E., Paradiso, A., Pearson, J.V., Puente, X.S., Raine, K., Ramakrishna, M., Richardson, A.L., Richter, J., Rosenstiel, P., Schlesner, M., Schumacher, T.N., Span, P.N., Teague, J.W., Totoki, Y., Tutt, A.N.J., Valdes-Mas, R., van Buuren, M.M., van 't Veer, L., Vincent-Salomon, A., Waddell, N., Yates, L.R., Zucman-Rossi, J., Futreal, P.A., McDermott, U., Lichter, P., Meyerson, M., Grimmond, S.M., Siebert, R., Campo, E., Shibata, T., Pfister, S.M., Campbell, P.J., Stratton, M.R., Australian Pancreatic Canc, G., Consortium, I.B.C., Consortium, I.M.-S., & PedBrain, I. (2013). Signatures of mutational processes in human cancer. Nature, 500(7463), 415-+. doi: 10.1038/nature12477

Aschoff, M., Hotz-Wagenblatt, A., Glatting, K.H., Fischer, M., Eils, R.*, & Konig, R. (2013). SplicingCompass: differential splicing detection using RNA-Seq data. Bioinformatics, 29, 1141-1148. doi: 10.1093/bioinformatics/btt101

Beaudouin, J., Liesche, C., Aschenbrenner, S., Hoerner, M., & Eils, R.* (2013). Caspase-8 cleaves its substrates from the plasma membrane upon CD95-induced apoptosis. Cell Death and Differentiation, 20(4), 599-610. doi: 10.1038/cdd.2012.156

Briso, E.M., Guinea-Viniegra, J., Bakiri, L., Rogon, Z., Petzelbauer, P., Eils, R., Wolf, R., Rincón, M., Angel, P., & Wagner, E.F. (2013). Inflammation-mediated skin tumorigenesis induced by epidermal c-Fos. Genes & Development, 27(18), 1959-1973. doi: 10.1101/gad.223339.113

Frank, M., Prenzler, A., Eils, R., & Graf von der Schulenburg, J.-M. (2013). Genome sequencing: a systematic review of health economic evidence. Health Economics Review, 3(1), 29. doi: 10.1186/2191-1991-3-29

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

Jones, D.T.W., Hutter, B., Jaeger, N., Korshunov, A., Kool, M., Warnatz, H.-J., Zichner, T., Lambert, S.R., Ryzhova, M., Dong Anh Khuong, Q., Fontebasso, A.M., Stuetz, A.M., Hutter, S., Zuckermann, M., Sturm, D., Gronych, J., Lasitschka, B., Schmidt, S., Seker-Cin, H., Witt, H., Sultan, M., Ralser, M., Northcott, P.A., Hovestadt, V., Bender, S., Pfaff, E., Stark, S., Faury, D., Schwartzentruber, J., Majewski, J., Weber, U.D., Zapatka, M., Raeder, B., Schlesner, M., Worth, C.L., Bartholomae, C.C., von Kalle, C., Imbusch, C.D., Radomski, S., Lawerenz, C., van Sluis, P., Koster, J., Volckmann, R., Versteeg, R., Lehrach, H., Monoranu, C., Winkler, B., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A.E., Ebinger, M., Schuhmann, M.U., Cho, Y.-J., Pomeroy, S.L., von Deimling, A., Witt, O., Taylor, M.D., Wolf, S., Karajannis, M.A., Eberhart, C.G., Scheurlen, W., Hasselblatt, M., Ligon, K.L., Kieran, M.W., Korbel, J.O., Yaspo, M.-L., Brors, B., Felsberg, J., Reifenberger, G., Collins, V.P., Jabado, N., Eils, R.*, Lichter, P., Pfister, S.M., & Int Canc Genome, C. (2013). Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nature Genetics, 45(8), 927-U295. doi: 10.1038/ng.2682

Koch, Y., Wolf, T., Sorger, P.K., Eils, R., & Brors, B. (2013). Decision-Tree Based Model Analysis for Efficient Identification of Parameter Relations Leading to Different Signaling States. PLoS One, 8(12). doi: 10.1371/journal.pone.0082593

Maulik, U., Mukhopadhyay, A., Bhattacharyya, M., Kaderali, L., Brors, B., Bandyopadhyay, S., & Eils, R. (2013). Mining Quasi-Bicliques from HIV-1-Human Protein Interaction Network: A Multiobjective Biclustering Approach. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 10(2), 423-435. doi: 10.1109/tcbb.2012.139

Piro, R.M., Molineris, I., Di Cunto, F., Eils, R., & Koenig, R. (2013). Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. Bioinformatics, 29(4), 468-475. doi: 10.1093/bioinformatics/bts720

Renner, M., Wolf, T., Meyer, H., Hartmann, W., Penzel, R., Ulrich, A., Lehner, B., Hovestadt, V., Czwan, E., Egerer, G., Schmitt, T., Alldinger, I., Renker, E.K., Ehemann, V., Eils, R., Wardelmann, E., Buttner, R., Lichter, P., Brors, B., Schirmacher, P., & Mechtersheimer, G. (2013). Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas. Genome Biology, 14(12), 26. doi: 10.1186/gb-2013-14-12-r137

Reuss, D.E., Piro, R.M., Jones, D.T.W., Simon, M., Ketter, R., Kool, M., Becker, A., Sahm, F., Pusch, S., Meyer, J., Hagenlocher, C., Schweizer, L., Capper, D., Kickingereder, P., Mucha, J., Koelsche, C., Jaeger, N., Santarius, T., Tarpey, P.S., Stephens, P.J., Futreal, P.A., Wellenreuther, R., Kraus, J., Lenartz, D., Herold-Mende, C., Hartmann, C., Mawrin, C., Giese, N., Eils, R., Collins, V.P., Koenig, R., Wiestler, O.D., Pfister, S.M., & von Deimling, A. (2013). Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations. Acta Neuropathologica, 125(3), 351-358. doi: 10.1007/s00401-013-1093-x

Rieber, N., Zapatka, M., Lasitschka, B., Jones, D., Northcott, P., Hutter, B., Jager, N., Kool, M., Taylor, M., Lichter, P., Pfister, S., Wolf, S., Brors, B., & Eils, R.* (2013). Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies. PLoS One, 8(6), 11. doi: 10.1371/journal.pone.0066621

Wang, Q., Gu, L., Adey, A., Radlwimmer, B., Wang, W., Hovestadt, V., Baehr, M., Wolf, S., Shendure, J., Eils, R., Plass, C., & Weichenhan, D. (2013). Tagmentation-based whole-genome bisulfite sequencing. Nature Protocols, 8(10), 2022-2032. doi: 10.1038/nprot.2013.118

Weischenfeldt, J., Simon, R., Feuerbach, L., Schlangen, K., Weichenhan, D., Minner, S., Wuttig, D., Warnatz, H.-J., Stehr, H., Rausch, T., Jaeger, N., Gu, L., Bogatyrova, O., Stuetz, A.M., Claus, R., Eils, J., Eils, R., Gerhaeuser, C., Huang, P.-H., Hutter, B., Kabbe, R., Lawerenz, C., Radomski, S., Bartholomae, C.C., Faelth, M., Gade, S., Schmidt, M., Amschler, N., Hass, T., Galal, R., Gjoni, J., Kuner, R., Baer, C., Masser, S., von Kalle, C., Zichner, T., Benes, V., Raeder, B., Mader, M., Amstislavskiy, V., Avci, M., Lehrach, H., Parkhomchuk, D., Sultan, M., Burkhardt, L., Graefen, M., Huland, H., Kluth, M., Krohn, A., Sirma, H., Stumm, L., Steurer, S., Grupp, K., Sueltmann, H., Sauter, G., Plass, C., Brors, B., Yaspo, M.-L., Korbel, J.O., & Schlomm, T. (2013). Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer. Cancer Cell, 23(2), 159-170. doi: 10.1016/j.ccr.2013.01.002

Zhu, Y., Massen, S., Terenzio, M., Lang, V., Chen-Lindner, S., Eils, R., Novak, I., Dikic, I., Hamacher-Brady, A., & Brady, N.R. (2013). Modulation of Serines 17 and 24 in the LC3-interacting Region of Bnip3 Determines Pro-survival Mitophagy versus Apoptosis. Journal of Biological Chemistry, 288(2), 1099-1113. doi: 10.1074/jbc.M112.399345

2012

Batra, R., Harder, N., Gogolin, S., Diessl, N., Soons, Z., Jaeger-Schmidt, C., Lawerenz, C., Eils, R., Rohr, K., Westermann, F., & Koenig, R. (2012). Time-Lapse Imaging of Neuroblastoma Cells to Determine Cell Fate upon Gene Knockdown. PLoS One, 7(12). doi: 10.1371/journal.pone.0050988

Costa, B., Kean, M.J., Ast, V., Knight, J.D.R., Mett, A., Levy, Z., Ceccarelli, D.F., Badillo, B.G., Eils, R., Koenig, R., Gingras, A.-C., & Fainzilber, M. (2012). STK25 Protein Mediates TrkA and CCM2 Protein-dependent Death in Pediatric Tumor Cells of Neural Origin. Journal of Biological Chemistry, 287(35), 29285-29289. doi: 10.1074/jbc.C112.345397

Godinez, W.J., Lampe, M., Koch, P., Eils, R., Mueller, B., & Rohr, K. (2012). Identifying Virus-Cell Fusion in Two-Channel Fluorescence Microscopy Image Sequences Based on a Layered Probabilistic Approach. IEEE Transactions on Medical Imaging, 31(9), 1786-1808. doi: 10.1109/tmi.2012.2203142

Ivandic, B.T., Mastitsky, S.E., Schoensiegel, F., Bekeredjian, R., Eils, R., Frey, N., Katus, H.A., & Brors, B. (2012). Whole-genome analysis of gene expression associates the ubiquitin-proteasome system with the cardiomyopathy phenotype in disease-sensitized congenic mouse strains. Cardiovascular Research, 94(1), 87-95. doi: 10.1093/cvr/cvs080

Jones, D.T.W., Jaeger, N., Kool, M., Zichner, T., Hutter, B., Sultan, M., Cho, Y.-J., Pugh, T.J., Hovestadt, V., Stuetz, A.M., Rausch, T., Warnatz, H.-J., Ryzhova, M., Bender, S., Sturm, D., Pleier, S., Cin, H., Pfaff, E., Sieber, L., Wittmann, A., Remke, M., Witt, H., Hutter, S., Tzaridis, T., Weischenfeldt, J., Raeder, B., Avci, M., Amstislavskiy, V., Zapatka, M., Weber, U.D., Wang, Q., Lasitschka, B., Bartholomae, C.C., Schmidt, M., von Kalle, C., Ast, V., Lawerenz, C., Eils, J., Kabbe, R., Benes, V., van Sluis, P., Koster, J., Volckmann, R., Shih, D., Betts, M.J., Russell, R.B., Coco, S., Tonini, G.P., Schueller, U., Hans, V., Graf, N., Kim, Y.-J., Monoranu, C., Roggendorf, W., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A.E., von Deimling, A., Witt, O., Maass, E., Roessler, J., Ebinger, M., Schuhmann, M.U., Fruehwald, M.C., Hasselblatt, M., Jabado, N., Rutkowski, S., von Bueren, A.O., Williamson, D., Clifford, S.C., McCabe, M.G., Collins, V.P., Wolf, S., Wiemann, S., Lehrach, H., Brors, B., Scheurlen, W., Felsberg, J., Reifenberger, G., Northcott, P.A., Taylor, M.D., Meyerson, M., Pomeroy, S.L., Yaspo, M.-L., Korbel, J.O., Korshunov, A., Eils, R.*, Pfister, S.M., & Lichter, P. (2012). Dissecting the genomic complexity underlying medulloblastoma. Nature, 488(7409), 100-105. doi: 10.1038/nature11284

Lisauskas, T., Matula, P., Claas, C., Reusing, S., Wiemann, S., Erfle, H., Lehmann, L., Fischer, P., Eils, R., Rohr, K., Storrie, B., & Starkuviene, V. (2012). Live-Cell Assays to Identify Regulators of ER-to-Golgi Trafficking. Traffic, 13(3), 416-432. doi: 10.1111/j.1600-0854.2011.01318.x

Rausch, T., Jones, D.T.W., Zapatka, M., Stuetz, A.M., Zichner, T., Weischenfeldt, J., Jaeger, N., Remke, M., Shih, D., Northcott, P.A., Pfaff, E., Tica, J., Wang, Q., Massimi, L., Witt, H., Bender, S., Pleier, S., Cin, H., Hawkins, C., Beck, C., von Deimling, A., Hans, V., Brors, B., Eils, R., Scheurlen, W., Blake, J., Benes, V., Kulozik, A.E., Witt, O., Martin, D., Zhang, C., Porat, R., Merino, D.M., Wasserman, J., Jabado, N., Fontebasso, A., Bullinger, L., Ruecker, F.G., Doehner, K., Doehner, H., Koster, J., Molenaar, J.J., Versteeg, R., Kool, M., Tabori, U., Malkin, D., Korshunov, A., Taylor, M.D., Lichter, P., Pfister, S.M., & Korbel, J.O. (2012). Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations. Cell, 148(1-2), 59-71. doi: 10.1016/j.cell.2011.12.013

Reis, Y., Bernardo-Faura, M., Richter, D., Wolf, T., Brors, B., Hamacher-Brady, A., Eils, R., & Brady, N.R. (2012). Multi-Parametric Analysis and Modeling of Relationships between Mitochondrial Morphology and Apoptosis. PLoS One, 7(1), 19. doi: 10.1371/journal.pone.0028694

Renner, M., Czwan, E., Hartmann, W., Penzel, R., Brors, B., Eils, R., Wardelmann, E., Buettner, R., Lichter, P., Schirmacher, P., & Mechtersheimer, G. (2012). MicroRNA profiling of primary high-grade soft tissue sarcomas. Genes Chromosomes & Cancer, 51, 982-996. doi: 10.1002/gcc.21980

Richter, J., Schlesner, M., Hoffmann, S., Kreuz, M., Leich, E., Burkhardt, B., Rosolowski, M., Ammerpohl, O., Wagener, R., Bernhart, S.H., Lenze, D., Szczepanowski, M., Paulsen, M., Lipinski, S., Russell, R.B., Adam-Klages, S., Apic, G., Claviez, A., Hasenclever, D., Hovestadt, V., Hornig, N., Korbel, J.O., Kube, D., Langenberger, D., Lawerenz, C., Lisfeld, J., Meyer, K., Picelli, S., Pischimarov, J., Radlwimmer, B., Rausch, T., Rohde, M., Schilhabel, M., Scholtysik, R., Spang, R., Trautmann, H., Zenz, T., Borkhardt, A., Drexler, H.G., Moeller, P., MacLeod, R.A.F., Pott, C., Schreiber, S., Truemper, L., Loeffler, M., Stadler, P.F., Lichter, P., Eils, R., Kueppers, R., Hummel, M., Klapper, W., Rosenstiel, P., Rosenwald, A., Brors, B., Siebert, R., & Project, I.M.-S. (2012). Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature Genetics, 44(12), 1316-1320. doi: 10.1038/ng.2469

Schmidt-Glenewinkel, H., Reinz, E., Bulashevska, S., Beaudouin, J., Legewie, S., Alonso, A., & Eils, R. (2012). Multiparametric image analysis reveals role of Caveolin1 in endosomal progression rather than internalization of EGFR. FEBS Letters, 586(8), 1179-1189. doi: 10.1016/j.febslet.2012.02.041

Serva, A., Knapp, B., Tsai, Y.-T., Claas, C., Lisauskas, T., Matula, P., Harder, N., Kaderali, L., Rohr, K., Erfle, H., Eils, R., Braga, V., & Starkuviene, V. (2012). miR-17-5p Regulates Endocytic Trafficking through Targeting TBC1D2/Armus. PLoS One, 7(12). doi: 10.1371/journal.pone.0052555

2011

Avalos, P.G., Reichenzeller, M., Eils, R., & Gladilin, E. (2011). Probing compressibility of the nuclear interior in wild-type and lamin deficient cells using microscopic imaging and computational modeling. Journal of Biomechanics, 44(15), 2642-2648. doi: 10.1016/j.jbiomech.2011.08.014

Aydin, D., Filippov, M.A., Tschaepe, J.-A., Gretz, N., Prinz, M., Eils, R., Brors, B., & Mueller, U.C. (2011). Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex. BMC Genomics, 12. doi: 10.1186/1471-2164-12-160

Bauer, T., Eils, R.*, & Koenig, R. (2011). RIP: the regulatory interaction predictor-a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics, 27(16), 2239-2247. doi: 10.1093/bioinformatics/btr366

Chang, L., Godinez, W.J., Kim, I.-H., Tektonidis, M., de Lanerolle, P., Eils, R., Rohr, K., & Knipe, D.M. (2011). Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA. Proceedings of the National Academy of Sciences of the United States of America, 108(21), E136-E144. doi: 10.1073/pnas.1103411108

Godinez, W.J., Lampe, M., Eils, R., Mueller, B., Rohr, K., & IEEE. (2011). Tracking multiple particles in fluorescence microscopy images via probabilistic data association. 2011 8th Ieee International Symposium on Biomedical Imaging: From Nano To Macro, 1925-1928. doi: 10.1109/ISBI.2011.5872786

Hamacher-Brady, A., Stein, H.A., Turschner, S., Toegel, I., Mora, R., Jennewein, N., Efferth, T., Eils, R., & Brady, N.R. (2011). Artesunate Activates Mitochondrial Apoptosis in Breast Cancer Cells via Iron-catalyzed Lysosomal Reactive Oxygen Species Production. Journal of Biological Chemistry, 286(8), 6587-6601. doi: 10.1074/jbc.M110.210047

Hundeshagen, P., Hamacher-Brady, A., Eils, R., & Brady, N.R. (2011). Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy. BMC Biology, 9. doi: 10.1186/1741-7007-9-38

Kim, I.-H., Chen, Y.-C.M., Spector, D.L., Eils, R., & Rohr, K. (2011). Nonrigid Registration of 2-D and 3-D Dynamic Cell Nuclei Images for Improved Classification of Subcellular Particle Motion. IEE Transactions on Image Processing, 20(4), 1011-1022. doi: 10.1109/TIP.2010.2076377

Knapp, B., Rebhan, I., Kumar, A., Matula, P., Kiani, N.A., Binder, M., Erfle, H., Rohr, K., Eils, R., Bartenschlager, R., & Kaderali, L. (2011). Normalizing for individual cell population context in the analysis of high-content cellular screens. BMC Bioinformatics, 12. doi: 10.1186/1471-2105-12-485

Kober, A.M.M., Legewie, S., Pforr, C., Fricker, N., Eils, R., Krammer, P.H., & Lavrik, I.N. (2011). Caspase-8 activity has an essential role in CD95/Fas-mediated MAPK activation. Cell Death & Disease, 2. doi: 10.1038/cddis.2011.93

Kranz, A.L., Eils, R., & Konig, R. (2011). Enhancers regulate progression of development in mammalian cells. Nucleic Acids Research, 39(20), 8689-8702. doi: 10.1093/nar/gkr602

Lavrik, I.N., Neumann, L., Pforr, C., Beaudouin, J., Eils, R., & Krammer, P.H. (2011). DYNAMICS WITHIN THE CD95 DEATH-INDUCING SIGNALING COMPLEX DECIDE LIFE AND DEATH OF CELLS. In D. Wallach, A. Kovalenko & M. Feldman (Eds.), Advances in Tnf Family Research (Vol. 691, pp. 664-664).

Mesecke, S., Urlaub, D., Busch, H., Eils, R.*, & Watzl, C. (2011). Integration of Activating and Inhibitory Receptor Signaling by Regulated Phosphorylation of Vav1 in Immune Cells. Science Signaling, 4. doi: 10.1126/scisignal.2001325

Oumeraci, T., Schmidt, B., Wolf, T., Zapatka, M., Pich, A., Brors, B., Eils, R., Fleischhacker, M., Schlegelberger, B., & von Neuhoff, N. (2011). Bronchoalveolar lavage fluid of lung cancer patients: Mapping the uncharted waters using proteomics technology. Lung Cancer, 72(1), 136-138. doi: 10.1016/j.lungcan.2011.01.015

Oyelade, J., Ewejobi, I., Brors, B., Eils, R., & Adebiyi, E. (2011). Computational identification of signalling pathways in Plasmodium falciparum. Infection Genetics and Evolution, 11(4), 755-764. doi: 10.1016/j.meegid.2010.11.006

Paulsen, M., Legewie, S., Eils, R., Karaulanov, E., & Niehrs, C. (2011). Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development. Proceedings of the National Academy of Sciences of the United States of America, 108(25), 10202-10207. doi: 10.1073/pnas.1100179108

Pforr, C., Neumann, L., Eils, R., Krammer, P.H., & Lavrik, I.N. (2011). Understanding Life and Death at CD95. In D. Wallach, A. Kovalenko & M. Feldman (Eds.), Advances in Tnf Family Research (Vol. 691, pp. 151-161).

Reiss, S., Rebhan, I., Backes, P., Romero-Brey, I., Erfle, H., Matula, P., Kaderali, L., Poenisch, M., Blankenburg, H., Hiet, M.-S., Longerich, T., Diehl, S., Ramirez, F., Balla, T., Rohr, K., Kaul, A., Buehler, S., Pepperkok, R., Lengauer, T., Albrecht, M., Eils, R., Schirmacher, P., Lohmann, V., & Bartenschlager, R. (2011). Recruitment and Activation of a Lipid Kinase by Hepatitis C Virus NS5A Is Essential for Integrity of the Membranous Replication Compartment. Cell Host & Microbe, 9(1), 32-45. doi: 10.1016/j.chom.2010.12.002

Wolf, T., Oumeraci, T., Gottlieb, J., Pich, A., Brors, B., Eils, R., Haverich, A., Schlegelberger, B., Welte, T., Zapatka, M., & von Neuhoff, N. (2011). Proteomic Bronchiolitis Obliterans Syndrome Risk Monitoring in Lung Transplant Recipients. Transplantation, 92(4), 477-485. doi: 10.1097/TP.0b013e318224c109

2010

Abbas, S., Beckmann, L., Chang-Claude, J., Hein, R., Kropp, S., Parthimos, M., Dunnebier, T., Hamann, U., Brors, B., Eils, R., Zapatka, M., Brauch, H., Justenhoven, C., Flesch-Janys, D., Braendle, W., Bruning, T., Pesch, B., Spickenheuer, A., Baisch, C., Ko, Y.D., & Su, M.-G.C.G. (2010). Polymorphisms in genes of the steroid receptor superfamily modify postmenopausal breast cancer risk associated with menopausal hormone therapy. International Journal of Cancer, 126(12), 2935-2946.

Abbas, S., Beckmann, L., Chang-Claude, J., Hein, R., Kropp, S., Parthimos, M., Dunnebier, T., Hamann, U., Brors, B., Eils, R., Zapatka, M., Brauch, H., Justenhoven, C., Flesch-Janys, D., Braendle, W., Bruning, T., Pesch, B., Spickenheuer, A., Baisch, C., Ko, Y.D., Dahmen, N., & Genetic, M.-G.C. (2010). Polymorphisms in the BRCA1 and ABCB1 genes modulate menopausal hormone therapy associated breast cancer risk in postmenopausal women. Breast Cancer Research and Treatment, 120(3), 727-736. doi: 10.1007/s10549-009-0489-8

Abbas, S., Baisch, C., Braendle, W., Brauch, H., Brors, B., Bruning, T., Chang-Claude, J., Dahmen, N., Dunnebier, T., Eils, R., Flesch-Janys, D., Hamann, U., Hein, R., Justenhoven, C., Ko, Y.D., Kropp, S., Pathimos, M., Pesch, B., Spickenheuer, A., Zapatka, M., & Genetic, M.-G.C. (2010). Postmenopausal estrogen monotherapy-associated breast cancer risk is modified by CYP17A1_-34_T > C polymorphism. Breast Cancer Research and Treatment, 120(3), 737-744. doi: 10.1007/s10549-009-0490-2

Baum, P., Schmid, R., Ittrich, C., Rust, W., Fundel-Clemens, K., Siewert, S., Baur, M., Mara, L., Gruenbaum, L., Heckel, A., Eils, R., Kontermann, R.E., Roth, G.J., Gantner, F., Schnapp, A., Park, J.E., Weith, A., Quast, K., & Mennerich, D. (2010). Phenocopy - A Strategy to Qualify Chemical Compounds during Hit-to-Lead and/or Lead Optimization. PLoS One, 5(12). doi: 10.1371/journal.pone.0014272

Bulashevska, S., Bulashevska, A., & Eils, R. (2010). Bayesian statistical modelling of human protein interaction network incorporating protein disorder information. BMC Bioinformatics, 11, 15. doi: 10.1186/1471-2105-11-46

Chang-Claude, J., Beckmann, L., Corson, C., Hein, R., Kropp, S., Parthimos, M., Duennebier, T., Hamann, U., Brors, B., Eils, R., Zapatka, M., Brauch, H., Justenhoven, C., Flesch-Janys, D., Braendle, W., Bruening, T., Pesch, B., Spickenheuer, A., Ko, Y.-D., Baisch, C., Dahmen, N., & Genetic, M.-G.C. (2010). Genetic polymorphisms in phase I and phase II enzymes and breast cancer risk associated with menopausal hormone therapy in postmenopausal women. Breast Cancer Research and Treatment, 119(2), 463-474. doi: 10.1007/s10549-009-0407-0

Fischer, M., Bauer, T., Oberthur, A., Hero, B., Theissen, J., Ehrich, M., Spitz, R., Eils, R., Westermann, F., Brors, B., Konig, R., & Berthold, F. (2010). Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q. Oncogene, 29(6), 865-875. doi: 10.1038/onc.2009.390

Fricker, N., Beaudouin, J., Richter, P., Eils, R., Krammer, P.H., & Lavrik, I.N. (2010). Model-based dissection of CD95 signaling dynamics reveals both a pro- and antiapoptotic role of c-FLIPL. Journal of Cell Biology, 190(3), 377-389. doi: 10.1083/jcb.201002060

Gladilin, E., Schulz, M., Kappel, C., & Eils, R. (2010). Contactless determination of nuclear compressibility using 3D image- and model-based analysis of drug-induced cellular deformation. Journal of Microscopy, 240(3), 216-226. doi: 10.1111/j.1365-2818.2010.03394.x

International Cancer Genome Consortium, Hudson, T.J., Anderson, W., Aretz, A., Barker, A.D., Bell, C., Bernabe, R.R., Bhan, M.K., Calvo, F., Eerola, I., Gerhard, D.S., Guttmacher, A., Guyer, M., Hemsley, F.M., Jennings, J.L., Kerr, D., Klatt, P., Kolar, P., Kusuda, J., Lane, D.P., Laplace, F., Lu, Y., Nettekoven, G., Ozenberger, B., Peterson, J., Rao, T.S., Remacle, J., Schafer, A.J., Shibata, T., Stratton, M.R., Vockley, J.G., Watanabe, K., Yang, H., Yuen, M.M.F., Knoppers, M., Bobrow, M., Cambon-Thomsen, A., Dressler, L.G., Dyke, S.O.M., Joly, Y., Kato, K., Kennedy, K.L., Nicolas, P., Parker, M.J., Rial-Sebbag, E., Romeo-Casabona, C.M., Shaw, K.M., Wallace, S., Wiesner, G.L., Zeps, N., Lichter, P., Biankin, A.V., Chabannon, C., Chin, L., Clement, B., de Alava, E., Degos, F., Ferguson, M.L., Geary, P., Hayes, D.N., Johns, A.L., Nakagawa, H., Penny, R., Piris, M.A., Sarin, R., Scarpa, A., van de Vijver, M., Futreal, P.A., Aburatani, H., Bayes, M., Bowtell, D.D.L., Campbell, P.J., Estivill, X., Grimmond, S.M., Gut, I., Hirst, M., Lopez-Otin, C., Majumder, P., Marra, M., Ning, Z., Puente, X.S., Ruan, Y., Stunnenberg, H.G., Swerdlow, H., Velculescu, V.E., Wilson, R.K., Xue, H.H., Yang, L., Spellman, P.T., Bader, G.D., Boutros, P.C., Flicek, P., Getz, G., Guigo, R., Guo, G., Haussler, D., Heath, S., Hubbard, T.J., Jiang, T., Jones, S.M., Li, Q., Lopez-Bigas, N., Luo, R., Pearson, J.V., Quesada, V., Raphael, B.J., Sander, C., Speed, T.P., Stuart, J.M., Teague, J.W., Totoki, Y., Tsunoda, T., Valencia, A., Wheeler, D.A., Wu, H., Zhao, S., Zhou, G., Stein, L.D., Lathrop, M., Ouellette, B.F.F., Thomas, G., Yoshida, T., Axton, M., Gunter, C., McPherson, J.D., Miller, L.J., Kasprzyk, A., Zhang, J., Haider, S.A., Wang, J., Yung, C.K., Cross, A., Liang, Y., Gnaneshan, S., Guberman, J., Hsu, J., Chalmers, D.R.C., Hasel, K.W., Kaan, T.S.H., Knoppers, B.M., Lowrance, W.W., Masui, T., Rodriguez, L.L., Vergely, C., Cloonan, N., Defazio, A., Eshleman, J.R., Etemadmoghadam, D., Gardiner, B.A., Kench, J.G., Sutherland, R.L., Tempero, M.A., Waddell, N.J., Wilson, P.J., Gallinger, S., Tsao, M.-S., Shaw, P.A., Petersen, G.M., Mukhopadhyay, D., DePinho, R.A., Thayer, S., Muthuswamy, L., Shazand, K., Beck, T., Sam, M., Timms, L., Ballin, V., Ji, J., Zhang, X., Chen, F., Hu, X., Yang, Q., Tian, G., Zhang, L., Xing, X., Li, X., Zhu, Z., Yu, Y., Yu, J., Tost, J., Brennan, P., Holcatova, I., Zaridze, D., Brazma, A., Egevad, L., Prokhortchouk, E., Banks, R.E., Uhlen, M., Viksna, J., Ponten, F., Skryabin, K., Birney, E., Borg, A., Borresen-Dale, A.-L., Caldas, C., Foekens, J.A., Martin, S., Reis-Filho, J.S., Richardson, A.L., Sotiriou, C., van't Veer, L., Birnbaum, D., Blanche, H., Boucher, P., Boyault, S., Masson-Jacquemier, J.D., Pauporte, I., Pivot, X., Vincent-Salomon, A., Tabone, E., Theillet, C., Treilleux, I., Bioulac-Sage, P., Decaens, T., Franco, D., Gut, M., Samuel, D., Zucman-Rossi, J., Eils, R., Brors, B., Korbel, J.O., Korshunov, A., Landgraf, P., Lehrach, H., Pfister, S., Radlwimmer, B., Reifenberger, G., Taylor, M.D., von Kalle, C., Majumder, P.P., Pederzoli, P., Lawlor, R.T., Delledonne, M., Bardelli, A., Gress, T., Klimstra, D., Zamboni, G., Nakamura, Y., Miyano, S., Fujimoto, A., Campo, E., de Sanjose, S., Montserrat, E., Gonzalez-Diaz, M., Jares, P., Himmelbaue, H., Bea, S., Aparicio, S., Easton, D.F., Collins, F.S., Compton, C.C., Lander, E.S., Burke, W., Green, A.R., Hamilton, S.R., Kallioniemi, O.P., Ley, T.J., Liu, E.T., Wainwright, B.J., & Int Canc Genome, C. (2010). International network of cancer genome projects. Nature, 464(7291), 993-998. doi: 10.1038/nature08987

Jakubowska, A., Gronwald, J., Menkiszak, J., Gorski, B., Huzarski, T., Byrski, T., Toloczko-Grabarek, A., Gilbert, M., Edler, L., Zapatka, M., Eils, R., Lubinski, J., Scott, R.J., & Hamann, U. (2010). BRCA1-associated breast and ovarian cancer risks in Poland: no association with commonly studied polymorphisms. Breast Cancer Research and Treatment, 119(1), 201-211. doi: 10.1007/s10549-009-0390-5

Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., Weitz, K.K., Eils, R., Koenig, R., Smith, R.D., & Palsson, B.O. (2010). Omic data from evolved E-coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology, 6. doi: 10.1038/msb.2010.47

Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., Konig, R., & Palsson, B.O. (2010). Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology, 28(12), 1279-U1291. doi: 10.1038/nbt.1711

Lohr, J.M., Faissner, R., Koczan, D., Bewerunge, P., Bassi, C., Brors, B., Eils, R., Frulloni, L., Funk, A., Halangk, W., Jesnowski, R., Kaderali, L., Kleeff, J., Kruger, B., Lerch, M.M., Losel, R., Magnani, M., Neumaier, M., Nittka, S., Sahin-Toth, M., Sanger, J., Serafini, S., Schnolzer, M., Thierse, H.J., Wandschneider, S., Zamboni, G., & Kloppel, G. (2010). Autoantibodies Against the Exocrine Pancreas in Autoimmune Pancreatitis: Gene and Protein Expression Profiling and Immunoassays Identify Pancreatic Enzymes as a Major Target of the Inflammatory Process. American Journal of Gastroenterology, 105(9), 2060-2071. doi: 10.1038/ajg.2010.141

Neumann, B., Walter, T., Heriche, J.K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wunsche, A., Satagopam, V., Schmitz, M.H.A., Chapuis, C., Gerlich, D.W., Schneider, R., Eils, R., Huber, W., Peters, J.M., Hyman, A.A., Durbin, R., Pepperkok, R., & Ellenberg, J. (2010). Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature, 464(7289), 721-727. doi: 10.1038/nature08869

Neumann, L., Pforr, C., Beaudouin, J., Pappa, A., Fricker, N., Krammer, P.H., Lavrik, I.N., & Eils, R. (2010). Dynamics within the CD95 death-inducing signaling complex decide life and death of cells. Molecular Systems Biology, 6, 352. doi: 10.1038/msb.2010.6

Oberthuer, A., Hero, B., Berthold, F., Juraeva, D., Faldum, A., Kahlert, Y., Asgharzadeh, S., Seeger, R., Scaruffi, P., Tonini, G.P., Janoueix-Lerosey, I., Delattre, O., Schleiermacher, G., Vandesompele, J., Vermeulen, J., Speleman, F., Noguera, R., Piqueras, M., Benard, J., Valent, A., Avigad, S., Yaniv, I., Weber, A., Christiansen, H., Grundy, R.G., Schardt, K., Schwab, M., Eils, R., Warnat, P., Kaderali, L., Simon, T., DeCarolis, B., Theissen, J., Westermann, F., Brors, B., & Fischer, M. (2010). Prognostic Impact of Gene Expression-Based Classification for Neuroblastoma. Journal of Clinical Oncology, 28(21), 3506-3515. doi: 10.1200/jco.2009.27.3367

Oberthuer, A., Hero, B., Juraeva, D., Faldum, A., Kahlert, Y., Asgharzadeh, S., Seeger, R., Scaruffi, P., Tonini, G.P., Janoueix-Lerosey, I., Delattre, O., Schleiermacher, G., Vandesompele, J., Vermeulen, J., Speleman, F., Noguera, R., Piqueras, M., Benard, J., Valent, A., Avigad, S., Yaniv, I., Weber, A., Christiansen, H., Grundy, R.G., Schardt, K., Schwab, M., Eils, R., Warnat, P., Kaderali, L., Simon, T., DeCarolis, B., Theissen, J., Westermann, F., Brors, B., Berthold, F., & Fischer, M. (2010). Gene expression-based classification improves risk estimation of neuroblastoma patients. Klinische Paediatrie, 222(3), 221.

Oberthuer, A., Juraeva, D., Li, L., Kahlert, Y., Westermann, F., Eils, R., Berthold, F., Shi, L., Wolfinger, R.D., Fischer, M., & Brors, B. (2010). Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics Journal, 10(4), 258-266. doi: 10.1038/tpj.2010.53

Plaimas, K., Eils, R., & Konig, R. (2010). Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Systems Biology, 4. doi: 10.1186/1752-0509-4-56

Riehl, A., Bauer, T., Brors, B., Busch, H., Mark, R., Nemeth, J., Gebhardt, C., Bierhaus, A., Nawroth, P., Eils, R., Konig, R., Angel, P., & Hess, J. (2010). Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation. BMC Genomics, 11. doi: 10.1186/1471-2164-11-537

Rohr, K., Godinez, W.J., Harder, N., Wörz, S., Mattes, J., Tvaruskó, W., & Eils, R. (2010). Tracking and Quantitative Analysis of Dynamic Movements of Cells and Particles. Cold Spring Harbor Protocols, 2010(6), pdb.top80. doi: 10.1101/pdb.top80

Schmid, R., Baum, P., Ittrich, C., Fundel-Clemens, K., Huber, W., Brors, B., Eils, R., Weith, A., Mennerich, D., & Quast, K. (2010). Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics, 11, 17. doi: 10.1186/1471-2164-11-349

Schramm, G., Surmann, E.M., Wiesberg, S., Oswald, M., Reinelt, G., Eils, R., & Konig, R. (2010). Analyzing the regulation of metabolic pathways in human breast cancer. Bmc Medical Genomics, 3. doi: 10.1186/1755-8794-3-39

Schramm, G., Wiesberg, S., Diessl, N., Kranz, A.-L., Sagulenko, V., Oswald, M., Reinelt, G., Westermann, F., Eils, R., & Koenig, R. (2010). PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways. Bioinformatics, 26(9), 1225-1231. doi: 10.1093/bioinformatics/btq113

Shi, L.M., Campbell, G., Jones, W.D., Campagne, F., Wen, Z.N., Walker, S.J., Su, Z.Q., Chu, T.M., Goodsaid, F.M., Pusztai, L., Shaughnessy, J.D., Oberthuer, A., Thomas, R.S., Paules, R.S., Fielden, M., Barlogie, B., Chen, W.J., Du, P., Fischer, M., Furlanello, C., Gallas, B.D., Ge, X.J., Megherbi, D.B., Symmans, W.F., Wang, M.D., Zhang, J., Bitter, H., Brors, B., Bushel, P.R., Bylesjo, M., Chen, M.J., Cheng, J., Chou, J., Davison, T.S., Delorenzi, M., Deng, Y.P., Devanarayan, V., Dix, D.J., Dopazo, J., Dorff, K.C., Elloumi, F., Fan, J.Q., Fan, S.C., Fan, X.H., Fang, H., Gonzaludo, N., Hess, K.R., Hong, H.X., Huan, J., Irizarry, R.A., Judson, R., Juraeva, D., Lababidi, S., Lambert, C.G., Li, L., Li, Y.N., Li, Z., Lin, S.M., Liu, G.Z., Lobenhofer, E.K., Luo, J., Luo, W., McCall, M.N., Nikolsky, Y., Pennello, G.A., Perkins, R.G., Philip, R., Popovici, V., Price, N.D., Qian, F., Scherer, A., Shi, T.L., Shi, W.W., Sung, J., Thierry-Mieg, D., Thierry-Mieg, J., Thodima, V., Trygg, J., Vishnuvajjala, L., Wang, S.J., Wu, J.P., Wu, Y.C., Xie, Q.A., Yousef, W.A., Zhang, L.A., Zhang, X.G., Zhong, S., Zhou, Y.M., Zhu, S., Arasappan, D., Bao, W.J., Lucas, A.B., Berthold, F., Brennan, R.J., Buness, A., Catalano, J.G., Chang, C., Chen, R., Cheng, Y.Y., Cui, J.A., Czika, W., Demichelis, F., Deng, X.T., Dosymbekov, D., Eils, R., Feng, Y., Fostel, J., Fulmer-Smentek, S., Fuscoe, J.C., Gatto, L., Ge, W.G., Goldstein, D.R., Guo, L., Halbert, D.N., Han, J., Harris, S.C., Hatzis, C., Herman, D., Huang, J.P., Jensen, R.V., Jiang, R., Johnson, C.D., Jurman, G., Kahlert, Y., Khuder, S.A., Kohl, M., Li, J.Y., Li, M.L., Li, Q.Z., Li, S., Li, Z.G., Liu, J., Liu, Y., Liu, Z.C., Meng, L., Madera, M., Martinez-Murillo, F., Medina, I., Meehan, J., Miclaus, K., Moffitt, R.A., Montaner, D., Mukherjee, P., Mulligan, G.J., Neville, P., Nikolskaya, T., Ning, B.T., Page, G.P., Parker, J., Parry, R.M., Peng, X.J., Peterson, R.L., Phan, J.H., Quanz, B., Ren, Y., Riccadonna, S., Roter, A.H., Samuelson, F.W., Schumacher, M.M., Shambaugh, J.D., Shi, Q.A., Shippy, R., Si, S.Z., Smalter, A., Sotiriou, C., Soukup, M., Staedtler, F., Steiner, G., Stokes, T.H., Sun, Q.L., Tan, P.Y., Tang, R., Tezak, Z., Thorn, B., Tsyganova, M., Turpaz, Y., Vega, S.C., Visintainer, R., von Frese, J., Wang, C., Wang, E., Wang, J.W., Wang, W., Westermann, F., Willey, J.C., Woods, M., Wu, S.J., Xiao, N.Q., Xu, J., Xu, L., Yang, L., Zeng, X.A., Zhang, J.L., Zhang, L., Zhang, M., Zhao, C., Puri, R.K., Scherf, U., Tong, W.D., Wolfinger, R.D., & Consortium, M. (2010). The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Pharmacogenomics Journal, S5-S16. doi: 10.1038/nbt.1665

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Spanagel, R., Bartsch, D., Brors, B., Dahmen, N., Deussing, J., Eils, R., Ende, G., Gallinat, J., Gebicke-Haerter, P., Heinz, A., Kiefer, F., Jager, W., Mann, K., Matthaus, F., Nothen, M., Rietschel, M., Sartorius, A., Schutz, G., Sommer, W.H., Sprengel, R., Walter, H., Wichmann, E., Wienker, T., Wurst, W., & Zimmer, A. (2010). An integrated genome research network for studying the genetics of alcohol addiction. Addiction Biology, 15(4), 369-379. doi: 10.1111/j.1369-1600.2010.00276.x

Suratanee, A., Rebhan, I., Matula, P., Kumar, A., Kaderali, L., Rohr, K., Bartenschlager, R., Eils, R., & Konig, R. (2010). Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. Bioinformatics, 26(18), i653-i658. doi: 10.1093/bioinformatics/btq398

Bandara, S., Schloder, J.P., Eils, R., Bock, H.G., & Meyer, T. (2009). Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model. PLoS Computational Biology, 5(11), 12. doi: 10.1371/journal.pcbi.1000558

Bulashevska, A., Stein, M., Jackson, D., & Eils, R. (2009). Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains. Computational Biology and Chemistry, 33(6), 457-460. doi: 10.1016/j.compbiolchem.2009.09.005

Fatumo, S., Plaimas, K., Mallm, J.P., Schramm, G., Adebiyi, E., Oswald, M., Eils, R., & Konig, R. (2009). Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infection Genetics and Evolution, 9(3), 351-358. doi: 10.1016/j.meegid.2008.01.007

Godinez, W.J., Lampe, M., Worz, S., Muller, B., Eils, R., & Rohr, K. (2009). Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences. Medical Image Analysis, 13, 325-342. doi: 10.1016/j.media.2008.12.004

Harder, N., Mora-Bermudez, F., Godinez, W.J., Wunsche, A., Eils, R., Ellenberg, J., & Rohr, K. (2009). Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time. Genome Research, 19(11), 2113-2124. doi: 10.1101/gr.092494.109

Harel, L., Costa, B., Tcherpakov, M., Zapatka, M., Oberthuer, A., Hansford, L.M., Vojvodic, M., Levy, Z., Chen, Z.Y., Lee, F.S., Avigad, S., Yaniv, I., Shi, L.M., Eils, R., Fischer, M., Brors, B., Kaplan, D.R., & Fainzilber, M. (2009). CCM2 Mediates Death Signaling by the TrkA Receptor Tyrosine Kinase. Neuron, 63(5), 585-591. doi: 10.1016/j.neuron.2009.08.020

Ivanchenko, S., Godinez, W.J., Lampe, M., Krausslich, H.G., Eils, R., Rohr, K., Brauchle, C., Muller, B., & Lamb, D.C. (2009). Dynamics of HIV-1 Assembly and Release. PLoS Pathogens, 5(11), 12. doi: 10.1371/journal.ppat.1000652

Lavrik, I.N., Eils, R., Fricker, N., Pforr, C., & Krammer, P.H. (2009). Understanding apoptosis by systems biology approaches. Molecular Biosystems, 5(10), 1105-1111. doi: 10.1039/b905129p

Matula, P., Kumar, A., Worz, I., Erfle, H., Bartenschlager, R., Eils, R., & Rohr, K. (2009). Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection. Cytometry A, 75(4), 309-318. doi: 10.1002/cyto.a.20662

Ridder, D.A., Bulashevska, S., Chaitanya, G.V., Babu, P.P., Brors, B., Eils, R., Schneider, A., & Schwaninger, M. (2009). Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis. Brain Research, 1272, 3-13. doi: 10.1016/j.brainres.2009.03.046

Rieber, N., Knapp, B., Eils, R., & Kaderali, L. (2009). RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens. Bioinformatics, 25(5), 678-679. doi: 10.1093/bioinformatics/btp014

Schmidt-Glenewinkel, H., Reinz, E., Eils, R., & Brady, N.R. (2009). Systems Biological Analysis of Epidermal Growth Factor Receptor Internalization Dynamics for Altered Receptor Levels. Journal of Biological Chemistry, 284(25), 17243-17252. doi: 10.1074/jbc.M809586200

Schnickmann, S., Camacho-Trullio, D., Bissinger, M., Eils, R., Angel, P., Schirmacher, P., Szabowski, A., & Breuhahn, K. (2009). AP-1-Controlled Hepatocyte Growth Factor Activation Promotes Keratinocyte Migration via CEACAM1 and Urokinase Plasminogen Activator/Urokinase Plasminogen Receptor. Journal of Investigative Dermatology, 129(5), 1140-1148. doi: 10.1038/jid.2008.350

Bar-Joseph, Z., Siegfried, Z., Brandeis, M., Brors, B., Lu, Y., Eils, R., Dynlacht, B.D., & Simon, I. (2008). Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proceedings of the National Academy of Sciences of the United States of America, 105(3), 955-960. doi: 10.1073/pnas.0704723105

Bulashevska, A., & Eils, R. (2008). Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered. Journal of Theoretical Biology, 254(4), 799-803. doi: 10.1016/j.jtbi.2008.05.040

Busch, H., Camacho-Trullio, D., Rogon, Z., Breuhahn, K., Angel, P., Eils, R., & Szabowski, A. (2008). Gene network dynamics controlling keratinocyte migration. Molecular Systems Biology, 4. doi: 10.1038/msb.2008.36

Chen, Y.C., Kappel, C., Beaudouin, J., Eils, R., & Spector, D.L. (2008). Live cell dynamics of promyelocytic leukemia nuclear bodies upon entry into and exit from mitosis. Mol Biol Cell, 19(7), 3147-3162. doi: 10.1091/mbc.E08-01-0035

Gladilin, E., Goetze, S., Mateos-Langerak, J., R, V.A.N.D., Eils, R., & Rohr, K. (2008). Shape normalization of 3D cell nuclei using elastic spherical mapping. Journal of Microscopy (Oxford), 231(Pt 1), 105-114. doi: 10.1111/j.1365-2818.2008.02021.x

Huesemann, Y., Geigl, J.B., Schubert, F., Musiani, P., Meyer, M., Burghart, E., Forni, G., Eils, R., Fehm, T., Riethmueller, G., & Klein, C.A. (2008). Systemic spread is an early step in breast cancer. Cancer Cell, 13(1), 58-68. doi: 10.1016/j.ccr.2007.12.003

Justenhoven, C., Hamann, U., Schubert, F., Zapatka, M., Pierl, C.B., Rabstein, S., Selinski, S., Mueller, T., Ickstadt, K., Gilbert, M., Ko, Y.D., Baisch, C., Pesch, B., Harth, V., Bolt, H.M., Vollmert, C., Illig, T., Eils, R., Dippon, J., & Brauch, H. (2008). Breast cancer: a candidate gene approach across the estrogen metabolic pathway. Breast Cancer Res Treat, 108(1), 137-149. doi: 10.1007/s10549-007-9586-8

Kim, J.T., & Eils, R. (2008). Systems biology and artificial life: Towards predictive modeling of biological systems. Artificial Life, 14(1), 1-2. doi: 10.1162/artl.2008.14.1.1

Oberthuer, A., Kaderali, L., Kahlert, Y., Hero, B., Westermann, F., Berthold, F., Brors, B., Eils, R., & Fischer, M. (2008). Subclassification and individual survival time prediction from gene expression data of neuroblastoma patients by using CASPAR. Clinical Cancer Research, 14(20), 6590-6601. doi: 10.1158/1078-0432.CCR-07-4377

Pinto, S., Dinkelacker, M., Derbinski, J., Rezavandy, E., Brors, B., Eils, R., & Kyewski, B. (2008). Phylogenetic conservation of promiscuous gene expression in thymic medullary epithelial cells. Wiener Klinische Wochenschrift, 120, 127-127.

Plaimas, K., Mallm, J.P., Oswald, M., Svara, F., Sourjik, V., Eils, R., & Konig, R. (2008). Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Systems Biology, 2, 67. doi: 10.1186/1752-0509-2-67

Schlaeger, C., Longerich, T., Schiller, C., Bewerunge, P., Mehrabi, A., Toedt, G., Kleeff, J., Ehemann, V., Eils, R., Lichter, P., Schirtnacher, P., & Radwimmer, B. (2008). Etiology-dependent molecular mechanisms in human hepatocarcinogenesis. Hepatology, 47(2), 511-520. doi: 10.1002/hep.22033

Schmidt-Glenewinkel, H., Vacheva, I., Hoeller, D., Dikic, I., & Eils, R. (2008). An ultrasensitive sorting mechanism for EGF receptor endocytosis. BMC Systems Biology, 2, 32. doi: 10.1186/1752-0509-2-32

Urlaub, D., Mesecke, S., Busch, H., Eils, R., & Watzl, C. (2008). Decision making in NK cells. Wiener Klinische Wochenschrift, 120, 23-23.

Yang, S., Illner, D., Teller, K., Solovei, I., van Driel, R., Joffe, B., Cremer, T., Eils, R., & Rohr, K. (2008). Structural analysis of interphase X-chromatin based on statistical shape theory. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1783(11), 2089-2099. doi: 10.1016/j.bbamcr.2008.08.007

Yang, S., Kohler, D., Teller, K., Cremer, T., Le Baccon, P., Heard, E., Eils, R., & Rohr, K. (2008). Nonrigid registration of 3-d multichannel microscopy images of cell nuclei. IEEE Trans Image Process, 17(4), 493-499. doi: 10.1109/TIP.2008.918017

Classen, S., Zander, T., Eggle, D., Chemnitz, J.M., Brors, B., Buchmann, I., Popov, A., Beyer, M., Eils, R., Debey, S., & Schultze, J.L. (2007). Human resting CD4(+) T cells are constitutively inhibited by TGF beta under steady-state conditions. Journal of Immunology, 178(11), 6931-6940.

Gladilin, E., Micoulet, A., Hosseini, B., Rohr, K., Spatz, J., & Eils, R. (2007). 3D finite element analysis of uniaxial cell stretching: from image to insight. Physical Biology, 4(2), 104-113. doi: Doi 10.1088/1478-3975/4/2/004

Kim, I.H., Nagel, J., Otten, S., Knerr, B., Eils, R., Rohr, K., & Dietzel, S. (2007). Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining. BMC Biotechnology, 7. doi: 10.1186/1472-6750-7-92

Lavrik, I.N., Golks, A., Riess, D., Bentele, M., Eils, R., & Krammer, P.H. (2007). Analysis of CD95 threshold signaling - Triggering of CD95 (FAS/APO-1) at low concentrations primarily results in survival signaling. Journal of Biological Chemistry, 282(18), 13664-13671. doi: 10.1074/jbc.M700434200

Oberthuer, A., Warnat, P., Kahlert, Y., Westermann, F., Spitz, R., Brors, B., Hero, B., Eils, R., Schwab, M., Berthold, F., & Fischer, M. (2007). Classification of neuroblastoma patients by published gene-expression markers reveals a low sensitivity for unfavorable courses of MYCN non-amplified disease. Cancer Letters, 250(2), 250-267. doi: 10.1016/j.canlet.2006.10.016

Schramm, G., Zapatka, M., Eils, R., & König, R. (2007). Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. BMC Bioinformatics, 8, 149.

Schramm, A., Vandesompele, J., Schulte, J.H., Dreesmann, S., Kaderali, L., Brors, B., Eils, R., Speleman, F., & Eggert, A. (2007). Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome. Clinical Cancer Research, 13(5), 1459-1465. doi: 10.1158/1078-0432.ccr-06-2032

Warnat, P., Oberthuer, A., Fischer, M., Westermann, F., Eils, R., & Brors, B. (2007). Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes. BMC Cancer, 7. doi: 10.1186/1471-2407-7-89

Astrahantseff, K., Melle, C., Bleul, A., Zapatka, M., Brors, B., Stuehler, K., Meyer, H.E., Eils, R., Schramm, A., von Eggeling, F., & Eggert, A. (2006). Serum profiling of neuroblastoma patients using SELDI-MS. Klinische Paediatrie, 218(3), 185-185.

Bacher, C.P., Guggiari, M., Brors, B., Augui, S., Clerc, P., Avner, P., Eils, R., & Heard, E. (2006). Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nature Cell Biology, 8(3), 293-299. doi: 10.1038/ncb1365

Bulashevska, A., & Eils, R. (2006). Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains. BMC Bioinformatics, 7, 13. doi: 10.1186/1471-2105-7-298

Debey, S., Zander, T., Brors, B., Popov, A., Eils, R., & Schultze, J.L. (2006). A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials. Genomics, 87(5), 653-664. doi: 10.1016/j.ygeno.2005.11.010

Jackson, D.B., Stein, M.A., Merino, A., & Eils, R. (2006). Microarrays meet the Voltaire challenge: Drug discovery on a chip? Drug Discov Today Technol, 3(2), 153-161. doi: 10.1016/j.ddtec.2006.06.014

Konig, R., Schramm, G., Oswald, M., Seitz, H., Sager, S., Zapatka, M., Reinelt, G., & Eils, R. (2006). Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. BMC Bioinformatics, 7. doi: 10.1186/1471-2105-7-119

Manoli, T., Gretz, N., Grone, H.-J., Kenzelmann, M., Eils, R., & Brors, B. (2006). Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics, 22(20), 2500-2506. doi: 10.1093/bioinformatics/btl424

Oberthuer, A., Berthold, F., Warnat, P., Hero, B., Kahlert, Y., Spitz, R., Ernestus, K., Konig, R., Haas, S., Eils, R., Schwab, M., Brors, B., Westermann, F., & Fischer, M. (2006). Customized oligonucleotide microarray gene expression based classification of neuroblastoma patients outperforms current clinical risk stratification. Journal of Clinical Oncology, 24, 5070-5078. doi: 10.1200/JCO.2006.06.1879

Oberthuer, A., Berthold, F., Warnat, P., Hero, B., Spitz, R., Ernestus, K., Konig, R., Eils, R., Schwab, M., Brors, B., Westermann, F., & Fischer, M. (2006). Gene-expression based classification of neuroblastoma patients using a customized oligonucleotide-microarray outperforms current clinical risk stratification. Klinische Paediatrie, 218, 192-192.

Schramm, A., Schulte, J.H., Apostolov, O., Sitek, B., Stuhler, K., Brors, B., Eils, J., Eils, R., Meyer, H.E., & Eggert, A. (2006). Combining transcriptome and proteome analysis for deciphering the effects of neurotrophin receptor expression and activation in neuroblastoma cells: A "Best of Both Worlds" approach. Klinische Paediatrie, 218(3), 194-194.

Schuster, S., Eils, R., & Prank, K. (2006). 5th International Conference on Systems Biology (ICSB 2004), Heidelberg, October 9-13, 2004. BioSystems, 83(2-3), 71-74. doi: 10.1016/j.biosystems.2005.08.003

Shahi, P., Loukianiouk, S., Bohne-Lang, A., Kenzelmann, M., Kueffer, S., Maertens, S., Eils, R., Groene, H.-J., Gretz, N., & Brors, B. (2006). Argonaute - a database for gene regulation by mammalian microRNAs. Nucleic Acids Research, 34, D115-D118. doi: 10.1093/nar/gkj093

Stange, D.E., Radlwimmer, B., Schubert, F., Traub, F., Pich, A., Toedt, G., Mendrzyk, F., Lehmann, U., Eils, R., Kreipe, H., & Lichter, P. (2006). High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer. Clinical Cancer Research, 12(2), 345-352. doi: 10.1158/1078-0432.ccr-05-1633

Thuerigen, O., Schneeweiss, A., Toedt, G., Warnat, P., Hahn, M., Kramer, H., Brors, B., Rudlowski, C., Benner, A., Schuetz, F., Tews, B., Eils, R., Sinn, H.P., Sohn, C., & Lichter, P. (2006). Gene expression signature predicting pathologic complete response with gemcitabine, epirubicin, and docetaxel in primary breast cancer. Journal of Clinical Oncology, 24(12), 1839-1845. doi: 10.1200/jco.2005.04.7019

Ulrich, M., Kappel, C., Beaudouin, J., Hezel, S., Ulrich, J., & Eils, R. (2006). Tropical-parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images. Bioinformatics, 22(21), 2709-2710. doi: 10.1093/bioinformatics/btl456

Vinayagam, A., del Val, C., Schubert, F., Eils, R., Glatting, K.H., Suhai, S., & Konig, R. (2006). GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics, 7, 161. doi: 10.1186/1471-2105-7-161

Baldessari, D., Shin, Y., Krebs, O., Konig, R., Koide, T., Vinayagam, A., Fenger, U., Mochii, M., Terasaka, C., Kitayama, A., Peiffer, D., Ueno, N., Eils, R., Cho, K.W., & Niehrs, C. (2005). Global gene expression profiling and cluster analysis in Xenopus laevis. Mechanisms of Development, 122(3), 441-475. doi: 10.1016/j.mod.2004.11.007

Bentele, M., & Eils, R. (2005). Systems biology of apoptosis. Systems Biology: Definitions and Perspectives, 13, 349-372.

Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Muller, S., Eils, R., Cremer, C., Speicher, M.R., & Cremer, T. (2005). Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biology, 3(5), 826-842. doi: 10.1371/journal.pbio.0030157

Bulashevska, S., & Eils, R. (2005). Inferring genetic regulatory logic from expression data. Bioinformatics, 21(11), 2706-2713. doi: 10.1093/bioinformatics/bti388

Kronenwett, R., Butterweck, U., Steidl, U., Kliszewski, S., Neumann, F., Bork, S., Blanco, E.D., Roes, N., Graf, T., Brors, B., Eils, R., Maercker, C., Kobbe, G., Gattermann, N., & Haas, R. (2005). Distinct molecular phenotype of malignant CD34+hematopoietic stem and progenitor cells in chronic myelogenous leukemia. Oncogene, 24(34), 5313-5324. doi: 10.1038/sj.onc.1208596

Lenart, P., Bacher, C.P., Daigle, N., Hand, A.R., Eils, R., Terasaki, M., & Ellenberg, J. (2005). A contractile nuclear actin network drives chromosome congression in oocytes. Nature, 436(7052), 812-818. doi: 10.1038/nature03810

Murmann, A.E., Gao, J.T., Encinosa, M., Gautier, M., Peter, M.E., Eils, R., Lichter, P., & Rowley, J.D. (2005). Local gene density predicts the spatial position of genetic loci in the interphase nucleus. Experimental Cell Research, 311(1), 14-26. doi: 10.1016/j.yexcr.2005.07.020

Neben, K., Schnittger, S., Brors, B., Tews, B., Kokocinski, F., Haferlach, T., Muller, J., Hahn, M., Hiddemann, W., Eils, R., Lichter, P., & Schoch, C. (2005). Distinct gene expression patterns associated with FLT3- and NRAS-activating mutations in acute myeloid leukemia with normal karyotype. Oncogene, 24(9), 1580-1588. doi: 10.1038/sj.onc.1208344

Neumann, F., Teutsch, N., Kliszewski, S., Bork, S., Brors, B., Schimkus, N., Roes, N., Germing, U., Hildebrandt, B., Royer-Pokora, B., Eils, R., Gattermann, N., Haas, R., & Kronenwett, R. (2005). Gene expression profiling of Philadelphia chromosome (Ph)-negative CD34+ hematopoietic stem and progenitor cells of patients with Ph-positive CML in major molecular remission during therapy with imatinib. Leukemia, 19(3), 458-460. doi: 10.1038/sj.leu.2403615

Schardt, J.A., Meyer, M., Hartmann, C.H., Schubert, F., Schmidt-Kittler, O., Fuhrmann, C., Polzer, B., Petronio, M., Eils, R., & Klein, C.A. (2005). Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer. Cancer Cell, 8(3), 227-239. doi: 10.1016/j.ccr.2005.08.003

Schramm, A., Schulte, J.H., Klein-Hitpass, L., Havers, W., Sieverts, H., Berwanger, B., Christiansen, H., Warnat, P., Brors, B., Eils, J., Eils, R., & Eggert, A. (2005). Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Oncogene, 24(53), 7902-7912. doi: 10.1038/sj.onc.1208936

Schubert, F., Tausch, B., Joos, S., & Eils, R. (2005). CGH-profiler: Data mining based on genomic aberration profiles. BMC Bioinformatics, 6. doi: 10.1186/1471-2105-6-188

Schulte, J.H., Schramm, A., Klein-Hitpass, L., Klenk, M., Wessels, H., Hauffa, B.P., Eils, J.R., Eils, R., Brodeur, G.M., Schweigerer, L., Havers, W., & Eggert, A. (2005). Microarray analysis reveals differential gene expression patterns and regulation of single target genes contributing to the opposing phenotype of TrkA- and TrkB-expressing neuroblastomas. Oncogene, 24(1), 165-177. doi: 10.1038/sj.onc.1208000

Warnat, P., Eils, R., & Brors, B. (2005). Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics, 6. doi: 10.1186/1471-2105-6-265

Athale, C.A., Christensen, M.O., Eils, R., Boege, F., & Mielke, C. (2004). Inferring a system model of subcellular Topoisomerase II beta localization dynamics. Omics-a Journal of Integrative Biology, 8(2), 167-175. doi: 10.1089/1536231041388339

Bacher, C.P., Reichenzeller, M., Athale, C., Herrmann, H., & Eils, R. (2004). 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin-poor tracks. BMC Cell Biology, 5, 14. doi: 10.1186/1471-2121-5-45

Bentele, M., Lavrik, I., Ulrich, M., Stosser, S., Heermann, D.W., Kalthoff, H., Krammer, P.H., & Eils, R. (2004). Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. Journal of Cell Biology, 166(6), 839-851. doi: 10.1083/jcb.200404158

Bulashevska, S., Szakacs, O., Brors, B., Eils, R., & Kovacs, G. (2004). Pathways of urothelial cancer progression suggested by Bayesian network analysis of allelotyping data. International Journal of Cancer, 110(6), 850-856. doi: 10.1002/ijc.20180

Conrad, C., Erfle, H., Warnat, P., Daigle, N., Lorch, T., Ellenberg, J., Pepperkok, R., & Eils, R. (2004). Automatic identification of subcellular phenotypes on human cell arrays. Genome Research, 14(6), 1130-1136. doi: 10.1101/gr.2383804

Konig, R., Baldessari, D., Pollet, N., Niehrs, C., & Eils, R. (2004). Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Research, 32(3), 21. doi: 10.1093/nar/gnh027

Konig, R., & Eils, R. (2004). Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics, 20(10), 1500-1505. doi: 10.1093/bioinformatics/bth109

Martin-Sanchez, F., Iakovidis, I., Noraer, S., Maojo, V., de Groen, P., Van der Lei, J., Jones, T., Abraham-Fuchs, K., Apweiler, R., Babic, A., Baud, R., Breton, V., Cinquin, P., Doupi, P., Dugas, M., Eils, R., Engelbrecht, R., Ghazal, P., Jehenson, P., Kulikowski, C., Lampe, K., De Moor, G., Orphanoudakis, S., Rossing, N., Sarachan, B., Sousa, A., Spekowius, G., Thireos, G., Zahlmann, G., Zvarova, J., Hermosilla, I., & Vicente, F.J. (2004). Synergy between medical informatics and facilitating genomic medicine for future bioinformatics: health care. Journal of Biomedical Informatics, 37(1), 30-42. doi: 10.1016/j.jbi.2003.09.003

Scheuermann, M.O., Tajbakhsh, H., Kurz, A., Saracoglu, K., Eils, R., & Lichter, P. (2004). Topology of genes and nontranscribed sequences in human interphase nuclei. Experimental Cell Research, 301(2), 266-279. doi: 10.1016/j.yexcr.2004.08.031

Vinayagam, A., Konig, R., Moormann, J., Schubert, F., Eils, R., Glatting, K.H., & Suhai, S. (2004). Applying support vector machines for gene ontology based gene function prediction. BMC Bioinformatics, 5, 14. doi: 10.1186/1471-2105-5-116

Barz, T., Ackermann, K., Dubois, G., Eils, R., & Pyerin, W. (2003). Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling. Journal of Cell Science, 116(8), 1563-1577. doi: 10.1242/jcs.00352

Eils, R., & Athale, C. (2003). Computational imaging in cell biology. Journal of Cell Biology, 161(3), 477-481. doi: 10.1083/jcb.200302097

Gerlich, D., Mattes, J., & Eils, R. (2003). Quantitative motion analysis and visualization of cellular structures. Methods, 29(1), 3-13. doi: 10.1016/S1046-2023(20)00287-6

Gerlich, D., Beaudouin, J., Kalbfuss, B., Daigle, N., Eils, R., & Ellenberg, J. (2003). Global chromosome positions are transmitted through mitosis in mammalian cells. Cell, 112(6), 751-764. doi: 10.1016/s0092-8674(03)00189-2

Molenaar, C., Wiesmeijer, K., Verwoerd, N.P., Khazen, S., Eils, R., Tanke, H.J., & Dirks, R.W. (2003). Visualizing telomere dynamics in living mammalian cells using PNA probes. EMBO Journal, 22(24), 6631-6641. doi: 10.1093/emboj/cdg633

Schmidt-Kittler, O., Ragg, T., Daskalakis, A., Granzow, M., Ahr, A., Blankenstein, T.J.F., Kaufmann, M., Diebold, J., Arnholdt, H., Muller, P., Bischoff, J., Harich, D., Schlimok, G., Riethmuller, G., Eils, R., & Klein, C.A. (2003). From latent disseminated cells to overt metastasis: Genetic analysis of systemic breast cancer progression. Proceedings of the National Academy of Sciences of the United States of America, 100(13), 7737-7742. doi: 10.1073/pnas.1331931100

Wiemer, J., Schubert, F., Granzow, M., Ragg, T., Fieres, J., Mattes, J., & Eils, R. (2003). Informatics united - Exemplary studies combining medical informatics, neuroinformatics, and bioinformatics. Methods of Information in Medicine, 42(2), 126-133.

Beaudouin, J., Gerlich, D., Daigle, N., Eils, R., & Ellenberg, J. (2002). Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina. Cell, 108(1), 83-96. doi: 10.1016/s0092-8674(01)00627-4

Brown, J., Jawad, M., Twigg, S.R.F., Saracoglu, K., Sauerbrey, A., Thomas, A.E., Eils, R., Harbott, J., & Kearney, L. (2002). A cryptic t(5;11)(q35;p15.5) in 2 children with acute myeloid leukemia with apparently normal karyotypes, identified by a multiplex fluorescence in situ hybridization telomere assay. Blood, 99(7), 2526-2531. doi: 10.1182/blood.V99.7.2526

Fritz, B., Schubert, F., Wrobel, G., Schwaenen, C., Wessendorf, S., Nessling, M., Korz, C., Rieker, R.J., Montgomery, K., Kucherlapati, R., Mechtersheimer, G., Eils, R., Joos, S., & Lichter, P. (2002). Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma. Cancer Research, 62(11), 2993-2998.

Muratani, M., Gerlich, D., Janicki, S.M., Gebhard, M., Eils, R., & Spector, D.L. (2002). Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4(2), 106-110. doi: 10.1038/ncb740

Schoch, C., Kohlmann, A., Schnittger, S., Brors, B., Dugas, M., Mergenthaler, S., Kern, W., Hiddemann, W., Eils, R., & Haferlach, T. (2002). Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 99(15), 10008-10013. doi: 10.1073/pnas.142103599

Berrar, D., Dubitzky, W., Solinas-Toldo, S., Bulashevska, S., Granzow, M., Conrad, C., Kalla, J., Lichter, P., & Eils, R. (2001). A database system for comparative genomic hybridization analysis. IEEE Engineering in Medicine and Biology Magazine, 20(4), 75-83. doi: 10.1109/51.940052

Brown, J., Saracoglu, K., Uhrig, S., Speicher, M.R., Eils, R., & Kearney, L. (2001). Subtelomeric chromosome rearrangements are detected using an innovative 12-color FISH assay (M-TEL). Nature Medicine, 7(4), 497-501. doi: 10.1038/86581

Fauth, C., Zhang, H.G., Harabacz, S., Brown, J., Saracoglu, K., Lederer, G., Rittinger, O., Rost, I., Eils, R., Kearney, L., & Speicher, M.R. (2001). A new strategy for the detection of subtelomeric rearrangements. Human Genetics, 109(6), 576-583. doi: 10.1007/s00439-001-0629-7

Gerlich, D., Beaudouin, J., Gebhard, M., Ellenberg, J., & Eils, R. (2001). Four-dimensional imaging and quantitative reconstruction to analyse complex spatiotemporal processes in live cells. Nature Cell Biology, 3(9), 852-855. doi: 10.1038/ncb0901-852

Saracoglu, K., Brown, J., Kearney, L., Uhrig, S., Azofeifa, J., Fauth, C., Speicher, M.R., & Eils, R. (2001). New concepts to improve resolution and sensitivity of molecular cytogenetic diagnostics by multicolor fluorescence in situ hybridization. Cytometry, 44(1), 7-15. doi: 10.1002/1097-0320(20010501)44:1<7::aid-cyto1076>3.0.co;2-g

Brown, J., Horsley, S.W., Jung, C., Saracoglu, K., Janssen, B., Brough, M., Daschner, M., Beedgen, B., Kerkhoffs, G., Eils, R., Harris, P.C., Jauch, A., & Kearney, L. (2000). Identification of a subtle t(16;19)(p13.3;p13.3) in an infant with multiple congenital abnormalities using a 12-colour multiplex FISH telomere assay, M-TEL. European Journal of Human Genetics, 8(12), 903-910. doi: 10.1038/sj.ejhg.5200545

Castleman, K.R., Eils, R., Morrison, L., Piper, J., Saracoglu, K., Schulze, M.A., & Speicher, M.R. (2000). Classification accuracy in multiple color fluorescence imaging microscopy. Cytometry, 41(2), 139-147.

Eils, R., Gerlich, D., Tvarusko, W., Spector, D.L., & Misteli, T. (2000). Quantitative imaging of pre-mRNA splicing factors in living cells. Molecular Biology of the Cell, 11(2), 413-418.

Rustom, A., Gerlich, D., Rudolf, R., Heinemann, C., Eils, R., & Gerdes, H.H. (2000). Analysis of fast dynamic processes in living cells: High-resolution and high-speed dual-color imaging combined with automated image analysis. BioTechniques, 28(4), 722-+.

Solovei, I., Kienle, D., Little, G., Eils, R., Savelyeva, L., Schwab, M., Jager, W., Cremer, C., & Cremer, T. (2000). Topology of double minutes (dmins) and homogeneously staining regions (HSRs) in nuclei of human neuroblastoma cell lines. Genes Chromosomes & Cancer, 29(4), 297-308. doi: 10.1002/1098-2264(2000)9999:9999<::aid-gcc1046>3.0.co;2-h

Speicher, M.R., Petersen, S., Uhrig, S., Jentsch, I., Fauth, C., Eils, R., & Petersen, I. (2000). Analysis of chromosomal alterations in non-small cell lung cancer by multiplex-FISH, comparative genomic hybridization, and multicolor bar coding. Laboratory Investigation, 80(7), 1031-1041. doi: 10.1038/labinvest.3780108

Dietzel, S., Schiebel, K., Little, G., Edelmann, P., Rappold, G.A., Eils, R., Cremer, C., & Cremer, T. (1999). The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity. Experimental Cell Research, 252(2), 363-375. doi: 10.1006/excr.1999.4635

Munkel, C., Eils, R., Dietzel, S., Zink, D., Mehring, C., Wedemann, G., Cremer, T., & Langowski, J. (1999). Compartmentalization of interphase chromosomes observed in simulation and experiment. Journal of Molecular Biology, 285(3), 1053-1065. doi: 10.1006/jmbi.1998.2361

Tvarusko, W., Bentele, M., Misteli, T., Rudolf, R., Kaether, C., Spector, D.L., Gerdes, H.H., & Eils, R. (1999). Time-resolved analysis and visualization of dynamic processes in living cells. Proceedings of the National Academy of Sciences of the United States of America, 96(14), 7950-7955. doi: 10.1073/pnas.96.14.7950

Bornfleth, H., Satzler, K., Eils, R., & Cremer, C. (1998). High-precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy. Journal of Microscopy, 189, 118-136. doi: 10.1046/j.1365-2818.1998.00276.x

Dietzel, S., Jauch, A., Kienle, D., Qu, G.Q., Holtgreve-Grez, H., Eils, R., Munkel, C., Bittner, M., Meltzer, P.S., Trent, J.M., & Cremer, T. (1998). Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei. Chromosome Research, 6(1), 25-33. doi: 10.1023/a:1009262223693

Dietzel, S., Eils, R., Sätzler, K., Bornfleth, H., Jauch, A., Cremer, C., & Cremer, T. (1998). Evidence against a looped structure of the inactive human X-chromosome territory. Experimental Cell Research, 240(2), 187-196. doi: 10.1006/excr.1998.3934

Eils, R., Uhrig, S., Saracoglu, K., Satzler, K., Bolzer, A., Petersen, I., Chassery, J.M., Ganser, M., & Speicher, M.R. (1998). An optimized, fully automated system for fast and accurate identification of chromosomal rearrangements by multiplex-FISH (M-FISH). Cytogenetics and Cell Genetics, 82(3-4), 160-171. doi: 10.1159/000015092

Scherthan, H., Eils, R., Trelles-Sticken, E., Dietzel, S., Cremer, T., Walt, H., & Jauch, A. (1998). Aspects of three-dimensional chromosome reorganization during the onset of human male meiotic prophase. Journal of Cell Science, 111, 2337-2351.

Visser, A.E., Eils, R., Jauch, A., Little, G., Bakker, P.J.M., Cremer, T., & Aten, J.A. (1998). Spatial distributions of early and late replicating chromatin in interphase chromosome territories. Experimental Cell Research, 243(2), 398-407. doi: 10.1006/excr.1998.4144

Sätzler, K., & Eils, R. (1997). Resolution improvement by 3-D reconstructions from tilted views in axial tomography and confocal theta microscopy. Bioimaging, 5(4), 171-182. doi: 10.1002/1361-6374(199712)5:4<171::AID-BIO1>3.0.CO;2-K

Cremer, C., Munkel, C., Granzow, M., Jauch, A., Dietzel, S., Eils, R., Guan, X.Y., Meltzer, P.S., Trent, J.M., Langowski, J., & Cremer, T. (1996). Nuclear architecture and the induction of chromosomal aberrations. Mutation Research-Reviews in Genetic Toxicology, 366(2), 97-116. doi: 10.1016/s0165-1110(96)90031-7

Eils, R., Dietzel, S., Bertin, E., Schrock, E., Speicher, M.R., Ried, T., Robert-Nicoud, M., Cremer, C., & Cremer, T. (1996). Three-dimensional reconstruction of painted human interphase chromosomes: Active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. Journal of Cell Biology, 135(6), 1427-1440. doi: 10.1083/jcb.135.6.1427

Visser, A.E., Eils, R., Bornfleth, H., Jauch, A., Bakker, P.J.M., Cremer, T., & Aten, J.A. (1996). Double labelling of replication DNA combined with FISH to investigate the organisation of the interphase cell nucleus. Molecular Biology of the Cell, 7, 594-594.

Wijmenga, C., Gregory, P.E., Hajra, A., Schrock, E., Ried, T., Eils, R., Liu, P.P., & Collins, F.S. (1996). Core binding factor beta-smooth muscle myosin heavy chain chimeric protein involved in acute myeloid leukemia forms unusual nuclear rod-like structures in transformed NIH 3T3 cells. Proceedings of the National Academy of Sciences of the United States of America, 93(4), 1630-1635. doi: 10.1073/pnas.93.4.1630

Dietzel, S., Weilandt, E., Eils, R., Münkel, C., Cremer, C., & Cremer, T. (1995). Three-dimensional distribution of centromeric or paracentromeric heterochromatin of chromosomes 1, 7, 15 and 17 in human lymphocyte nuclei studied with light microscopic axial tomography. Bioimaging, 3(3), 121-133. doi: 10.1002/1361-6374(199509)3:3<121::AID-BIO3>3.0.CO;2-E

Eils, R., Saracoglu, K., Munkel, C., Imhoff, J., Satzler, K., Bertin, E., Dietzel, S., Schrock, E., Ried, T., Cremer, T., & Cremer, C. (1995). 3-Dimensional Imaging Approaches and Monte-Carlo Simulations - Development Of Tools To Study The Morphology and Distribution of Chromosome Territories and Subchromosomal Targets in Human Cell-Nuclei. Zoological Studies, 34, 7-10.

Eils, R., Bertin, E., Saracoglu, K., Rinke, B., Schrock, E., Parazza, F., Usson, Y., Robertnicoud, M., Stelzer, E.H.K., Chassery, J.M., Cremer, T., & Cremer, C. (1995). Application of confocal laser microscopy and three-dimensional Voronoi diagrams for volume and surface estimates of interphase chromosomes. Journal of Microscopy, 177, 150-161. doi: 10.1111/j.1365-2818.1995.tb03545.x

Munkel, C., Eils, R., Imhoff, J., Dietzel, S., Cremer, C., & Cremer, T. (1995). Simulation of the distribution of chromosome targets. Bioimaging, 3(3), 108-120. doi: 10.1002/1361-6374(199509)3:3<108::AID-BIO2>3.0.CO;2-Z

Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9. Molecular Therapy, 27(4), 297-297.  Nur in diesem Format gefunden, siehe Link. Ich vermute Corresponding Author

*these authors contributed equally