Research Group Pattern Recognition
and Digital Medicine

Daniel Hübschmann
Group Leader

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1. Articles

  • Groschel, S.*, Hübschmann, 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

  • Lopez, C.*, Kleinheinz, K.*, Aukema, S.M.*, Rohde, M.*, Bernhart, S.H.*, Hübschmann, D.*, Wagener, R., Toprak, U.H., Raimondi, F., Kreuz, M., Waszak, S.M., Huang, Z., 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.* (2019). Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun, 10(1), 1459. doi: 10.1038/s41467-019-08578-3

  • Hübschmann, D., & Schlesner, M. (2019). Evaluation of Whole Genome Sequencing Data. Methods Mol Biol, 1956, 321-336. doi: 10.1007/978-1-4939-9151-8_15
  • Horak, P., Weischenfeldt, J., von Amsberg, G., Beyer, B., Schutte, A., Uhrig, S., Gieldon, L., Klink, B., Feuerbach, L., Hübschmann, 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 Harb Mol Case Stud. doi: 10.1101/mcs.a003657

  • Wagener, R.*, Seufert, J.*, Raimondi, F., Bens, S., Kleinheinz, K., Nagel, I., Altmüller, J., Thiele, H., Hübschmann, D., & Kohler, C.W. (2019). The mutational landscape of Burkitt-like lymphoma with 11q aberration is distinct from that of Burkitt lymphoma. Blood, 133(9), 962-966. doi: 10.1182/blood-2018-07-864025

  • Korber, V., Yang, J., Barah, P., Wu, Y., Stichel, D., Gu, Z., Fletcher, M.N.C., Jones, D., Hentschel, B., Lamszus, K., Tonn, J.C., Schackert, G., Sabel, M., Felsberg, J., Zacher, A., Kaulich, K., Hübschmann, D., Herold-Mende, C., von Deimling, A., Weller, M., Radlwimmer, B., Schlesner, M., Reifenberger, G., Hofer, T., & Lichter, P. (2019). Evolutionary Trajectories of IDH(WT) Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis. Cancer Cell. doi: 10.1016/j.ccell.2019.02.007

  • Chudasama, P.*, Mughal, S.S.*, Sanders, M.A.*, Hübschmann, 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. Nat Commun, 9(1), 144. doi: 10.1038/s41467-017-02602-0

  • 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., Hübschmann, 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, 555(7696), 321-327. doi: 10.1038/nature25480

  • Wagener, R., Lopez, C., Kleinheinz, K., Bausinger, J., Aukema, S.M., Nagel, I., Toprak, U.H., Seufert, J., Altmuller, J., Thiele, H., Schneider, C., Kolarova, J., Park, J., Hübschmann, D., Murga Penas, E.M., Drexler, H.G., Attarbaschi, A., Hovland, R., Kjeldsen, E., Kneba, M., Kontny, U., de Leval, L., Nurnberg, P., Oschlies, I., Oscier, D., Schlegelberger, B., Stilgenbauer, S., Wossmann, W., Schlesner, M., Burkhardt, B., Klapper, W., Jaffe, E.S., Kuppers, R., & Siebert, R. (2018). IG-MYC (+) neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas. Blood, 132(21), 2280-2285. doi: 10.1182/blood-2018-03-842088

  • Warsow, G.*, Hübschmann, 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. Sci Rep, 8(1), 7477. doi: 10.1038/s41598-018-25544-z

  • Dieter, S.M., Heining, C., Agaimy, A., Hübschmann, 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. Ann Oncol, 28(1), 142-148. doi: 10.1093/annonc/mdw446

  • Giessler, K.M., Kleinheinz, K., Hübschmann, 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. J Exp Med, 214(7), 2073-2088. doi: 10.1084/jem.20162017

  • Horak, P., Klink, B., Heining, C., Groschel, S., Hutter, B., Frohlich, M., Uhrig, S., Hübschmann, 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. Int J Cancer, 141(5), 877-886. doi: 10.1002/ijc.30828

  • 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., Ishaque, N., Jager-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, 547(7663), 311-317. doi: 10.1038/nature22973

  • Sahm, F.*, Toprak, U.H.*, Hübschmann, 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., Harosh, C.B., 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 Neuropathol, 134(1), 155-158. doi: 10.1007/s00401-017-1715-9

  • Tagliaferri, L., Kunz, J.B., Happich, M., Esposito, S., Bruckner, T., Hübschmann, D., Okun, J.G., Hoffmann, G.F., Schulz, A., Kappe, J., Speckmann, C., Muckenthaler, M.U., & Kulozik, A.E. (2017). Newborn screening for severe combined immunodeficiency using a novel and simplified method to measure T-cell excision circles (TREC). Clin Immunol, 175, 51-55. doi: 10.1016/j.clim.2016.11.016

  • Groschel, S., Bommer, M., Hutter, B., Budczies, J., Bonekamp, D., Heining, C., Horak, P., Frohlich, M., Uhrig, S., Hübschmann, D., Georg, C., Richter, D., Pfarr, N., Pfutze, K., Wolf, S., Schirmacher, P., Jager, D., von Kalle, C., Brors, B., Glimm, H., Weichert, W., Stenzinger, A., & Frohling, S. (2016). Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with PDL1 amplification. Cold Spring Harb Mol Case Stud, 2(6), a001180. doi: 10.1101/mcs.a001180

  • Hoefflin, R., Lahrmann, B., Warsow, G., Hübschmann, D., Spath, C., Walter, B., Chen, X., Hofer, L., Macher-Goeppinger, S., & Tolstov, Y. (2016). Spatial niche formation but not malignant progression is a driving force for intratumoural heterogeneity. Nature communications, 7, ncomms11845.

     

2. Preprints

  • Hübschmann, D.*, Kurzawa, N.*, Steinhauser, S.*, Rentzsch, P.*, Kraemer, S., Andresen, C., Park, J., Eils, R., Schlesner, M., & Herrmann, C. (2017). Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers. BioRxiv, 199547. doi: 10.1101/199547

  • Kleinheinz, K., Bludau, I., Hübschmann, D., Heinold, M., Kensche, P., Gu, Z., Lopez, C., Hummel, M., Klapper, W., & Moeller, P. (2017). ACEseq-allele specific copy number estimation from whole genome sequencing. BioRxiv, 210807. doi: 10.1101/210807.

  • Whalley, J.P., Buchhalter, I., Rheinbay, E., Raine, K.M., Kleinheinz, K., Stobbe, M.D., Werner, J., Beltran, S., Gut, M., & Hübschmann, D. (2017). Framework for quality assessment of whole genome, cancer sequences. BioRxiv, 140921. doi: 10.1101/140921

     

3. Data sets

  • Hübschmann, D., Kurzawa, N., Steinhauser, S., Rentzsch, P., Krämer, S., Andresen, C., Park, J., Eils, R., Schlesner, M., and Herrmann, C. (2017). Bratwurst dataset. doi: 10.5281/zenodo.1003504

4. Book chapters

  • Hübschmann D, Kepper N, Cremer C, Kreth G:  Quantitative Approaches to Nuclear Architecture: Analysis and Modeling in Advances in Nuclear Architecture (Adams NM, Freemont PS (Eds.)), Springer (2010)

 

* indicates shared first or shared last authorship