Publications

Aschenbrenner, S.*, Kallenberger, S.*, 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), doi:10.1126/sciadv.aay0187 

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer Analysis of Whole Genomes, Nature, 578(7793), 82-93, doi: 10.1038/s41586-020-1969-6 

Yakneen, S.§, Waszak, S.M., PCAWG Technical Working Group, Gertz, M., Korbel, J. O.§, PCAWG Consortium (2020). Bulter enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, Epub ahead of print, doi: 10.1038/s41587-019-0360-3 

Zapatka, M.*, Borozan, I.*, Brewer, D.S.*, Iskar, M.*, Grundhoff, A., Alawi, M., Desai, N., Cooper, C.S., Eils, R., Ferretti, V. & Lichter, P.§ (2020). The landscape of viral association in human cancers. Nature Genetics, doi: 10.1101/465757 

Chan, C.W.Y., Gu, Z., Bieg, M., Eils, R. & Herrmann, C.§ (2019). Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC Medical Genomics, 12(1), 64. doi: 10.1186/s12920-019-0525-4 

Hoffmann, M. D., Aschenbrenner, S., Grosse, S., Rapti, K., Domenger, C., Mastel, M., 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 

Liu, L.*, Liu, C.*, Quintero, A.*, Wu, L*., Yuan, Y.*, Wang, M., Cheng, M., Leng, L., Xu, L., Dong, G., Li, R., Liu, Y., Wei, X., Xu, J., Chen, X., Lu, H., Chen, D., Wang, Q., Zhou, Q., Lin, X., Li, G., Liu, S., Wang, Q., Wang, H., Fink, J.L., Gao, Z., Liu, X., Hou, Y., Zhu, S., Yang, H., Ye, Y., Lin, G., Chen, F., Herrmann, C., Eils, R.§, Shang, Z.§ & Xu, X.§ (2019). Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nature Communications, 10(1), 470. doi: 10.1038/s41467-018-08205-7 

Mallm, J.-P.*, Iskar, M.*, Ishaque, N.*, Klett, L.C., Kugler, S.J., Muino, J.M., Teif, V.B., Poos, A.M., Großmann, S., Erdel, F., Tavernari, D., Koser, S.D., Schumacher, S., Brors, B., König, R., Remondini, D., Vingron, M., Stilgenbauer, S., Lichter, P., Zapatka, M., Mertens, D.§ & Rippe, K.§ (2019). Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology, 22;15(5):e8339. doi: 10.15252/msb.20188339 

Park, J.*, Choi, W.*, Tiesmeyer, S., Long, B., Borm, L.E., Garren, E., Nguyen, T.N., Codeluppi, S., Schlesner, M., Tasic, B., Eils, R.§ & Ishaque, N.§ (2019). Segmentation-free inference of cell types from in situ transcriptomics data. bioRxiv, doi: 10.1101/800748 

Smits, M., Zoldan, K., Ishaque, N., Gu, Z., 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.§ (2019). Follicular T helper cells shape the HCV-specific CD4 T cell repertoire after viral elimination. The Journal of Clinocal Investigation, 3;130(2):998-1009. doi: 10.1172/JCI129642 

Tirier, S. M., Park, J., Preusser, F., Amrhein, L., Gu, Z., Steiger, S., Mallm, J. P., Krieger, T., Waschow, M.,Chan, C.W.Y., Gu, Z., Bieg, M., Eils, R. & Herrmann, C.§ (2019). Impact of cancer mutational signatures on transcription factor motifs in the human genome. BMC Medical Genomics, 12(1), 64. doi: 10.1186/s12920-019-0525-4 

Hoffmann, M. D., Aschenbrenner, S., Grosse, S., Rapti, K., Domenger, C., Mastel, M., 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 

Liu, L.*, Liu, C.*, Quintero, A.*, Wu, L*., Yuan, Y.*, Wang, M., Cheng, M., Leng, L., Xu, L., Dong, G., Li, R., Liu, Y., Wei, X., Xu, J., Chen, X., Lu, H., Chen, D., Wang, Q., Zhou, Q., Lin, X., Li, G., Liu, S., Wang, Q., Wang, H., Fink, J.L., Gao, Z., Liu, X., Hou, Y., Zhu, S., Yang, H., Ye, Y., Lin, G., Chen, F., Herrmann, C., Eils, R.§, Shang, Z.§ & Xu, X.§ (2019). Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nature Communications, 10(1), 470. doi: 10.1038/s41467-018-08205-7 

Mallm, J.-P.*, Iskar, M.*, Ishaque, N.*, Klett, L.C., Kugler, S.J., Muino, J.M., Teif, V.B., Poos, A.M., Großmann, S., Erdel, F., Tavernari, D., Koser, S.D., Schumacher, S., Brors, B., König, R., Remondini, D., Vingron, M., Stilgenbauer, S., Lichter, P., Zapatka, M., Mertens, D.§ & Rippe, K.§ (2019). Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Molecular Systems Biology, 22;15(5):e8339. doi: 10.15252/msb.20188339 

Park, J.*, Choi, W.*, Tiesmeyer, S., Long, B., Borm, L.E., Garren, E., Nguyen, T.N., Codeluppi, S., Schlesner, M., Tasic, B., Eils, R.§ & Ishaque, N.§ (2019). Segmentation-free inference of cell types from in situ transcriptomics data. bioRxiv, doi: 10.1101/800748 

Smits, M., Zoldan, K., Ishaque, N., Gu, Z., 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.§ (2019). Follicular T helper cells shape the HCV-specific CD4 T cell repertoire after viral elimination. The Journal of Clinocal Investigation, 3;130(2):998-1009. doi: 10.1172/JCI129642 

Tirier, S. M., Park, J., Preusser, F., Amrhein, L., Gu, Z., 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(1), 12367. doi: 10.1038/s41598-019-48771-4 

Upmeier zu Belzen, J., Bürgel, T., Holderbach, S., Bubeck, F., Adam, L., Gandor, C., Klein, M., Mathony, J., Pfuderer, P. L., Platz, L., Przybilla, M., Schwendemann, M., Heid, D., Hoffmann, M. D., Jendrusch, M., Schmelas, C., Waldhauer, M., Lehmann, I., Niopek, D.§ & Eils, R.§ (2019). Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. Nature Machine Intelligence 1, 225-235. doi: 10.1038/s42256-019-0049-9 

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(1), 12367. doi: 10.1038/s41598-019-48771-4 

Upmeier zu Belzen, J., Bürgel, T., Holderbach, S., Bubeck, F., Adam, L., Gandor, C., Klein, M., Mathony, J., Pfuderer, P. L., Platz, L., Przybilla, M., Schwendemann, M., Heid, D., Hoffmann, M. D., Jendrusch, M., Schmelas, C., Waldhauer, M., Lehmann, I., Niopek, D.§ & Eils, R.§ (2019). Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. Nature Machine Intelligence 1, 225-235. doi: 10.1038/s42256-019-0049-9 

Bubeck, F., Hoffmann, M. D., Harteveld, Z., Aschenbrenner, S., Bietz, A., Waldhauer, M. C., Börner, 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), 924-927, doi:10.1038/s41592-018-0178-9 

Gröbner, S.N.*, Worst, B.C.*, Weischenfeldt, J., Buchhalter, I., Kleinheinz, K., Rudneva, V.A., Johann, P.D., Balasubramanian, G.P., Segura-Wang, M., Brabetz, S., Bender, S., Hutter, B., Sturm, D., Pfaff, E., Hubschmann, D., Zipprich, G., Heinold, M., Eils, J., Lawerenz, C., Erkek, S., Lambo, S., Waszak, S., Blattmann, C., Borkhardt, A., Kuhlen, M., Eggert, A., Fulda, S., Gessler, M., Wegert, J., Kappler, R., Baumhoer, D., Burdach, S., Kirschner-Schwabe, R., Kontny, U., Kulozik, A.E., Lohmann, D., Hettmer, S., Eckert, C., Bielack, S., Nathrath, M., Niemeyer, C., Richter, G.H., Schulte, J., Siebert, R., Westermann, F., Molenaar, J.J., Vassal, G., Witt, H., Burkhardt, B., Kratz, C.P., Witt, O., van Tilburg, C.M., Kramm, C.M., Fleischhack, G., Dirksen, U., Rutkowski, S., Fruhwald, M., von Hoff, K., Wolf, S., Klingebiel, T., Koscielniak, E., Landgraf, P., Koster, J., Resnick, A.C., Zhang, J., Liu, Y., Zhou, X., Waanders, A.J., Zwijnenburg, D.A., Raman, P., Brors, B., Weber, U.D., Northcott, P.A., Pajtler, K.W., Kool, M., Piro, R.M., Korbel, J.O., Schlesner, M., Eils, R., Jones, D.T.W., Lichter, P., Chavez, L.§, Zapatka, M.§, Pfister, S.M.§ (2018). The landscape of genomic alterations across childhood cancers. Nature, 559(7714), 321-327, doi: 10.1038/s41586-018-0167-2 

Ishaque, N.*, Abba, M.L.*, Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Kleinheinz, K., Toprak, U.H., Hutter, B., Benner, A., Shavinskaya, A., Zhou, C., Gu, Z., Kerssemakers, J., Marx, A., Moniuszko, M., Kozlowski, M., Reszec, J., Niklinski, J., Eils, J., Schlesner, M., Eils, R., Brors, B. & Allgayer, H.§ (2018). Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nature Communications, 9(1), 4782. doi: 10.1038/s41467-018-07041-z 

Kumar S.*, Warrel J.*, Shantao L., McGillivray P., Meyerson W., Salichos L., Harmanci, A., Martinez-FGundichely, A., Chan, C. W. Y., Nielsen, M. M., Locjovsky, L., Zhang, Y., Li, X., Pedersen, J. S., Herrmann C., Getz G., Khurana E. & Gerstein M. B.§ (2018). Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences, Cell, in Press, bioRxiv, doi: 10.1101/280446 

Jabs, J., Zickgraf, F. M., Park, J., Wagner, S., Jiang, X., Jechow, K., Kleinheinz, K., Toprak, U. H., Schneider, M. A., Meister, M., Spaich, S., Sütterlin, 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):955. doi: 10.15252/msb.20177697 

Northcott, P. A.*, Buchhalter, I.*, Morrissy, A. S.*, Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., Warnatz, H. J., Sidiropoulos, N., Phillips, A. H., Schumacher, S., Kleinheinz, K., Waszak, S. M., Erkek, S., Jones, D. T. W., Worst, B. C., Kool, M., Zapatka, M., Jäger, N., Chavez, L., Hutter, B., Bieg, M., Paramasivam, N., Heinold, M., Gu, Z., Ishaque, N., Jäger-Schmidt, C., Imbusch, C. D., Jugold, A., Hübschmann, D., Risch, T., Amstislavskiy, V., Gonzalez, F. G. R., Weber, U. D., Wolf, S., Robinson, G. W., Zhou, X., Wu, G., Finkelstein, D., Liu, Y., Cavalli, F. M. G., Luu, B., Ramaswamy, V., Wu, X., Koster, J., Ryzhova, M., Cho, Y. J., Pomeroy, S. L., Herold-Mende, C., Schuhmann, M., Ebinger, M.,  Liau, L. M., Mora, J., McLendon, R. E., Jabado, N., Kumabe, T., Chuah, E., Ma, Y., Moore, R. A., Mungall, A. J., Mungall, K. L., Thiessen, N., Tse, K., Wong, T., Jones, S. J. M., Witt, O., Milde, T., Von Deimling, A., Capper, D., Korshunov, A., Yaspo, M. L., Kriwacki, R., Gajjar, A., Zhang, J., Beroukhim, R., Fraenkel, E., Korbel, J. O., Brors, B., Schlesner, M., Eils, R.§, Marra, M. A.§, Pfister, S. M.§, Taylor, M. D.§ & Lichter, P.§ (2017). The whole-genome landscape of medulloblastoma subtypes. Nature. 2017 Jul 19;547(7663):311-317. doi: 10.1038/nature22973 

Reisinger, E.§, Genthner, L., Kerssemakers, J., Kensche, P., Borufka, S., Jugold, A., Kling, A., Prinz, M., Scholz, I., Zipprich, G., Eils, R., Lawerenz, C., Eils, J. (2017). OTP: An automatized system for managing and processing NGS data. Journal of Biotechnology, 10(261), 53-62, doi: 10.1016/j.jbiotec.2017.08.006 

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 

Niopek, D., Wehler, P., Roensch, J., Eils, R.§ & Di Ventura, B.§ (2016). Optogenetic Control of Nuclear Protein Export. Nature Communication. 7. doi: 10.1038/ncomms10624 

Peifer, M.*§, Hertwig, F.*, Roels, F.*, Dreidax, D.*, Gartlgruber, M.*, Menon, R., Krämer, A., Roncaioli, J.L., Sand, F., Heukmann J. M., Ikram, F., Ackermann, S., Engesser, A., Kahlert, Y., Altmüller, J., Nürnberg, P., Thierry-Mieg, J., Thierry-Mieg, D., Mariappan, A., Heynck, S., Mariotti, E., Henrich, K.-O., Gloeckner, C., Bosco, G., Leuscher, I., Schweiger, M. R., Savelyeya, L., Watkins, S. C., Shao, C., Bell, E., Höfer, T., Achter, V., Lang, U., Theissen, J., Volland, R., Saadati, M., Eggert, A., de Wilde, B., Peng, Z., Zhao, C., Shi, L., Ortmann, M., Büttner, R., Perner, S., Hero, B., Schramm, A., Schulte, J. H., Herrmann C., O’Sullivan R., Westermann F.§, Thomas R. K.§ & Fischer M.§ (2015). Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature, 526(7575), 700–704. doi: 10.1038/nature14980 

Wachsmuth, M., Conrad, C., Bulkescher, J., Koch, B., Mahen, R., Isokane R., Pepperkok, R.§ & Ellenberg, J.§ (2015). High-throughput fluorescence correlation spectroscopy enables analysis of proteome dynamics in living cells. Nature Biotechnology, 33(4), 384-389, doi: 10.1038/nbt.3146 

Wegert, J.*, Ishaque, N.*, Vardapour, R., Geörg, C., Gu, Z., 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, 9;27(2):298-311. doi: 10.1016/j.ccell.2015.01.002  

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 

Conrad, C., Wünsche, A., Tan, T. H., Bulkescher, J., Sieckmann, F., Verissimo, F., Edelstein, A., Walter, T., Liebel, U., Pepperkok, R.§ & Ellenberg, J.§ (2011) Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nature Methods, 8(3), 246–249, doi: 10.1038/nmeth.1558 

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