Research Group Pattern Recognition
and Digital Medicine

Daniel Hübschmann
Group Leader

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1. Articles

  1. Sahm F*, Toprak U*, 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 CB, Eils R, Sturm D, Jones DTW, Pfister SM, Paulus W, Ram Z, Schlesner M, Grossman R, von Deimling A: Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature. Acta Neuropathol. 2017 May 4.
  2. 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., Schröck, E., Hoogenboezem, R. M., Kasper, B., Heilig, C. E., Egerer, G., Wolf, S., von Kalle, C., Eils, R., Stenzinger, A., Weichert, W., Glimm, H., Gröschel, 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., and Fröhling, S. (2018). Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nature Communications, 9(1):144.
  3. 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., Roth, W., Stenzinger, A., Perner, S., Hadaschik, B., Pahernik, S., Jäger, D., Grüllich, C., Duensing, A., Eils, R., Schlesner, M., Sültmann, H., Hohenfellner, M., and Duensing, S. (2018). Mutational heterogeneity and evidence for BRCAness in renal cell carcinoma with venous tumor thrombus. Scientific Reports, 8(1):7477.
  4. Cristina López*,Kortine Kleinheinz*, Sietse M. Aukema*, Marius Rohde*, Stephan H Bernhart*, Daniel Hübschmann*, Rabea Wagener*, Umut Toprak*, Francesco Raimondi, Markus Kreuz,Sebastian M. Waszak, Zhiqin Huang, Lina Sieverling, Nagarajan Paramasivam, Julian Seufert, Stephanie Sungalee, Robert B. Russell, Julia Bausinger, Helene Kretzmer, Ole Ammerpohl, Anke K. Bergmann, Hans Binder, Arndt Borkhardt, Benedikt Brors, Alexander Claviez, Gero Doose, Andrea Haake, Martin-Leo Hansmann, Jessica Hoell, Michael Hummel, Jan Korbel, Chris Lawerenz, Dido Lenze, Bernhard Radlwimmer, Julia Richter, Philip Rosenstiel, Andreas Rosenwald,Markus Schillhabel, Stephan Stilgenbauer, Peter F. Stadler, Monika Szczepanowski, Marc  A. Weniger, Marc Zapatka,Roland Eils, Peter Lichter, Markus Loeffler, Peter Möller, Lorenz Trümper, Wolfram Klapper, Steve Hoffmann, Ralf Küppers, Birgit Burhardt,Matthias Schlesner, Reiner Siebert (2018).Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma in children. Manuscript accepted at Nature Communications.
  5. Wagener R*, López C*, Kleinheinz K, Bausinger J, Aukema SM, Nagel I, Toprak UH, Seufert J, Altmüller J, Thiele H, Schneider C, Kolarova J, Park J, Hübschmann D, Murga Penas EM, Drexler HG, Attarbaschi A, Hovland R, Kjeldsen E, Kneba M, Kontny U, de Leval L, Nürnberg P, Oschlies I, Oscier D, Schlegelberger B, Stilgenbauer S, Wössmann W, Schlesner M, Burkhardt B, Klapper W, Jaffe ES, Küppers R, Siebert R:IG-MYC-positive neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas. Blood 2018 Oct 04. doi:
  6. Tagliaferri L, Kunz JB, Happich M, Esposito S, Bruckner T, Hübschmann D, Okun JG, Hoffmann GF, Schulz A, Kappe J, Speckmann C, Muckenthaler MU, Kulozik AE: Newborn screening for severe combined immunodeficiency using a novel and simplified method to measure T-cell excision circles (TREC). Clin. Immunol. 175, (2016)
  7. Dieter SM*, Heining C*, Agaimy A, Huebschmann D, Bonekamp D, Hutter B, Ehrenberg KR, Fröhlich M, Schlesner M, Scholl C, Schlemmer HP, Wolf S, Mavratzas A, Jung CS, Gröschel S, Kalle CV, Eils R, Brors B, Penzel R, Kriegsmann M, Reuss DE, Schirmacher P: Mutant KIT as Imatinib-Sensitive Target in Metastatic Sinonasal Carcinoma. Ann. Oncol. 10, (2016).
  8. Gröschel S, Bommer M, Hutter B, Budczies J, Bonekamp D, Heining C, Horak P, Fröhlich M, Uhrig S, Hübschmann D, Geörg C, Richter D, Pfarr N, Pfütze K, Wolf S, Schirmacher P, Jäger D, von Kalle C, Brors B, Glimm H, Weichert W, Stenzinger A, Fröhling S: Integration of genomics and histology revises diagnosis and enables effective therapy of refracory cancer of unknown primary with PDL1 amplification. Cold Spring Harb. Mol. Case Stud. 10, (2016).
  9. Hoefflin R, Lahrmann B, Warsow G, Hübschmann D, Spath C, Walter B, Chen X, Hofer L, Macher-Goeppinger S, Tolstov Y, Korzeniewski N, Duensing A, Grüllich C, Jäger D, Perner S, Schönberg G, Nyarangi-Dix J, Isaac S, Hatiboglu G, Teber D, Hadaschik B: Spatial niche formation but not malignant progression is a driving force for intratumoural heterogeneity. Nat. Commun. 7, (2016).
  10. Horak P, Klink B, Heining C, Gröschel S, Hutter B, Fröhlich M, Uhrig S, Hübschmann D, Schlesner M, Eils R, Richter D, Pfütze K, Geörg 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 RF, Schröck E, Brors B, von Kalle C, Glimm H, Fröhling S: Precision Oncology Based on Omics Data: The NCT Heidelberg Experience.  Int J Cancer. 2017 Jun 9
  11. Giessler KM, Kleinheinz K, Huebschmann D, Balasubramanian GP, Dubash TD, Dieter SM, Siegl C, Herbst F, Weber S, Hoffmann CM, Fronza R, Buchhalter I, Paramasivam N, Eils R, Schmidt M, von Kalle C, Schneider M, Ulrich A, Scholl C, Fröhling S, Weichert W, Brors B, Schlesner M, Ball CR, Glimm H: Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer. J Exp Med. 2017 Jun 1.
  12. Northcott PA*, Buchhalter I*, Morrissy AS*, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R*, Marra MA*, Pfister SM*, Taylor MD*, Lichter P*: The whole genome landscape of medulloblastoma subtypes. Nature 2017 Jul 19;547(7663):311-317. doi: 10.1038/nature22973.
  13. Groebner SN*, Worst BC*, Weischenfeldt J, Buchhalter I, Kleinheinz K, Johann PD, Balasubramanian P, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Oelmez S, Heinold M, Eils J, Lawerenz C, Blattmann C, Borkhardt A, Eggert A, Fulda S, Gessler M, Kappler R, Kirschner-Schwabe R, Kontny U, Kulozik A, Lohmann D, Nathrath M, Niemeyer C, Richter G, Siebert R, Westermann F, Witt H,  ICGC MMMLSeq Project, Burkhardt B, Kratz CP, Witt O, van Tilburg C, Jäger N, Kramm C, Fleischhack G, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Koster J, Resnick AC, Zwijnenburg DA, Raman P, Weber U, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L*, Zapatka M*, Pfister SM*: The landscape of genomic alterations and drug targets across childhood cancers. Nature 2018 Jul;559(7714):E10. doi: 10.1038/s41586-018-0167-2.

2. Preprints

  1. Daniel Hübschmann*, Nils Kurzawa*, Sebastian Steinhauser*, Philipp Rentzsch*, Stephen Krämer, Carolin Andresen, Jeongbin Park, Roland Eils, Matthias Schlesner*, Carl Herrmann*: Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers. bioRxiv, doi: https://doi.org/10.1101/199547
  2. Justin P. Whalley, Ivo Buchhalter, Esther Rheinbay, Keiran M. Raine, Kortine Kleinheinz, Miranda D. Stobbe, Johannes Werner, Sergi Beltran, Marta Gut, Daniel Huebschmann, Barbara Hutter, Dimitri Livitz, Marc Perry, Mara Rosenberg, Gordon Saksena, Jean-Rémi Trotta, Roland Eils, Jan Korbel, Daniela S. Gerhard, Peter Campbell, Gad Getz, Matthias Schlesner, Ivo G. Gut: Framework For Quality Assessment Of Whole Genome Cancer Sequences. bioRxiv, doi: https://doi.org/10.1101/140921
  3. Kleinheinz, K., Bludau, I., Hübschmann, D., Heinold, M., Kensche, P., Gu, Z., Lopez, C., Hummel, M., Klapper, W., Moeller, P., Vater, I., Wagener, R., Brors, B., Siebert, R., Eils, R., and Schlesner, M. (2017). ACEseq - allele specific copy number estimation from whole genome sequencing. bioRxiv, https://doi.org/10.1101/210807.

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. https://doi.org/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)