Innovation in cancer pharmacotherapy through integrative consideration of germline and tumor genomes

Authors: Tremmel, Roman ^{1, 2}, Hübschmann, Daniel ^{3, 4, 5, 6}, Schaeffeler, Elke ^{1, 2, 7}, Pirmann, Sebastian ³, Fröhling, Stefan ^{4, 8, 9, 10}, Schwab, Matthias ^{1, 2, 7, 11, 12, 13, ∗}

Source: In Pharmacological Reviews January 2025 77(1)

Precision oncology – Guideline of the Austrian, German and Swiss Societies for hematology and medical oncology

Authors: Rieke, Damian T. ^{a, ⁎}, Bitzer, Michael ^b, Bleckmann, Annalen ^c, Desuki, Alexander ^d, Ernst, Thomas ^e, Esposito, Irene ^f, Gerger, Armin ^g, Glimm, Hanno ^h, Horak, Peter ⁱ, Hübschmann, Daniel ^j, Illert, Anna Lena ^k, Kunzmann, Volker ^l, Loges, Sonja ^m, Pretzell, Ina ⁿ, Schmitz, Katja ^o, Seeber, Andreas ^p, Söhlke, Bärbel ^q, Wicki, Andreas ^r, Wolf, Jürgen ^s, Maschmeyer, Georg ^t

Source: In European Journal of Cancer 2 May 2025 220

Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 – 07/2023

Authors: Bundschuh, Christian, Weidner, Niklas, Klein, Julian, Rausch, Tobias, Azevedo, Nayara, Telzerow, Anja, Mallm, Jan-Philipp, Kim, Heeyoung, Steiger, Simon, Seufert, Isabelle, Börner, Kathleen, Bauer, Katharina, Hübschmann, Daniel, Jost, Katharina Laurence, Parthé, Sylvia, Schnitzler, Paul, Boutros, Michael, Rippe, Karsten, Müller, Barbara, Bartenschlager, Ralf, Kräusslich, Hans-Georg, Benes, Vladimir

Source: In Infection, Genetics and Evolution April 2024 119

SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results

Authors: Gu, Zuguang, Hübschmann, Daniel

Source: Genomics proteomics & bioinformatics. 21(1):190-202

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100194511922.0x000001&indx=1&recIds=ETOCvdc_100194511922.0x000001

Targeted therapy of advanced parathyroid carcinoma guided by genomic and transcriptomic profiling

Authors: Teleanu, Maria‐Veronica, Fuss, Carmina T., Paramasivam, Nagarajan, Pirmann, Sebastian, Mock, Andreas, Terkamp, Christoph, Kircher, Stefan, Landwehr, Laura‐Sophie, Lenschow, Christina, Schlegel, Nicolas, Stenzinger, Albrecht, Jahn, Arne, Fassnacht, Martin, Glimm, Hanno, Hübschmann, Daniel, Fröhling, Stefan, Kroiss, Matthias

Source: Molecular oncology. 17(7):1343-1355

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100186845409.0x000001&indx=1&recIds=ETOCvdc_100186845409.0x000001

Retained functional normal and preleukemic HSCs at diagnosis are associated with good prognosis in DNMT3AmutNPM1mut AMLs

Authors: Donato, Elisa ^∗, Correia, Nadia ^∗, Andresen, Carolin ^∗, Karpova, Darja, Würth, Roberto, Klein, Corinna, Sohn, Markus, Przybylla, Adriana, Zeisberger, Petra, Rothfelder, Kathrin, Salih, Helmut, Bonig, Halvard, Stasik, Sebastian, Röllig, Christoph, Dolnik, Anna, Bullinger, Lars, Buchholz, Frank, Thiede, Christian, Hübschmann, Daniel, Trumpp, Andreas

Source: In Blood Advances 28 March 2023 7(6):1011-1018

aRgus: Multilevel visualization of non-synonymous single nucleotide variants & advanced pathogenicity score modeling for genetic vulnerability assessment

Authors: Schröter, Julian, Dattner, Tal, Hüllein, Jennifer, Jayme, Alejandra, Heuveline, Vincent, Hoffmann, Georg F., Kölker, Stefan, Lenz, Dominic, Opladen, Thomas, Popp, Bernt, Schaaf, Christian P., Staufner, Christian, Syrbe, Steffen, Uhrig, Sebastian, Hübschmann, Daniel, Brennenstuhl, Heiko

Source: In Computational and Structural Biotechnology Journal 2023 21:1077-1083

Gene expression-based prediction of pazopanib efficacy in sarcoma

Authors: Heilig, Christoph E., Laßmann, Andreas, Mughal, Sadaf S., Mock, Andreas, Pirmann, Sebastian, Teleanu, Veronica, Renner, Marcus, Andresen, Carolin, Köhler, Bruno C., Aybey, Bogac, Bauer, Sebastian, Siveke, Jens T., Hamacher, Rainer, Folprecht, Gunnar, Richter, Stephan, Schröck, Evelin, Brandts, Christian H., Ahrens, Marit, Hohenberger, Peter, Egerer, Gerlinde, Kindler, Thomas, Boerries, Melanie, Illert, Anna L., von Bubnoff, Nikolas, Apostolidis, Leonidas, Jost, Philipp J., Westphalen, C. Benedikt, Weichert, Wilko, Keilholz, Ulrich, Klauschen, Frederick, Beck, Katja, Winter, Ulrike, Richter, Daniela, Möhrmann, Lino, Bitzer, Michael, Schulze-Osthoff, Klaus, Brors, Benedikt, Mechtersheimer, Gunhild, Kreutzfeldt, Simon, Heining, Christoph, Lipka, Daniel B., Stenzinger, Albrecht, Schlenk, Richard F., Horak, Peter, Glimm, Hanno, Hübschmann, Daniel, Fröhling, Stefan

Source: European journal of cancer. 172:107-118

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100170792098.0x000001&indx=1&recIds=ETOCvdc_100170792098.0x000001

Bcl‐xL as prognostic marker and potential therapeutic target in cholangiocarcinoma

Authors: Hoffmeister‐Wittmann, Paula, Mock, Andreas, Nichetti, Federico, Korell, Felix, Heilig, Christoph E., Scherr, Anna‐Lena, Günther, Michael, Albrecht, Thomas, Kelmendi, Eblina, Xu, Kaiyu, Nader, Luisa, Kessler, Annika, Schmitt, Nathalie, Fritzsche, Sarah, Weiler, Sofia, Sobol, Benjamin, Stenzinger, Albrecht, Boeck, Stefan, Westphalen, Christoph B., Schulze‐Osthoff, Klaus, Trojan, Jörg, Kindler, Thomas, Weichert, Wilko, Spiekermann, Karsten, Bitzer, Michael, Folprecht, Gunnar, Illert, Anna L., Boerries, Melanie, Klauschen, Frederick, Ochsenreither, Sebastian, Siveke, Jens, Bauer, Sebastian, Glimm, Hanno, Brors, Benedikt, Hüllein, Jennifer, Hübschmann, Daniel, Uhrig, Sebastian, Horak, Peter, Kreutzfeldt, Simon, Banales, Jesus M., Springfeld, Christoph, Jäger, Dirk, Schirmacher, Peter, Roessler, Stephanie, Ormanns, Steffen, Goeppert, Benjamin, Fröhling, Stefan, Köhler, Bruno C.

Source: Liver international. 42(12):2855-2870

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100168408872.0x000001&indx=1&recIds=ETOCvdc_100168408872.0x000001

MGMT inactivation as a new biomarker in patients with advanced biliary tract cancers

Authors: Niger, Monica, Nichetti, Federico, Casadei‐Gardini, Andrea, Morano, Federica, Pircher, Chiara, Tamborini, Elena, Perrone, Federica, Canale, Matteo, Lipka, Daniel B., Vingiani, Andrea, Agnelli, Luca, Dobberkau, Anna, Hüllein, Jennifer, Korell, Felix, Heilig, Christoph E., Pusceddu, Sara, Corti, Francesca, Droz, Michele, Ulivi, Paola, Prisciandaro, Michele, Antista, Maria, Bini, Marta, Cattaneo, Laura, Milione, Massimo, Glimm, Hanno, Köhler, Bruno C., Pruneri, Giancarlo, Hübschmann, Daniel, Fröhling, Stefan, Mazzaferro, Vincenzo, Pietrantonio, Filippo, Di Bartolomeo, Maria, Braud, Filippo

Source: Molecular oncology. 16(14):2733-2746

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100167236486.0x000001&indx=1&recIds=ETOCvdc_100167236486.0x000001

Pkgndep: a tool for analyzing dependency heaviness of R packages

Authors: Gu, Zuguang, Hübschmann, Daniel

Source: Bioinformatics. 38(17):4248-4251

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100159689958.0x000001&indx=1&recIds=ETOCvdc_100159689958.0x000001

Antigen presentation safeguards the integrity of the hematopoietic stem cell pool

Authors: Hernández-Malmierca, Pablo, Vonficht, Dominik, Schnell, Alexandra, Uckelmann, Hannah J., Bollhagen, Alina, Mahmoud, Mohamed A.A., Landua, Sophie-Luise, van der Salm, Elise, Trautmann, Christine L., Raffel, Simon, Grünschläger, Florian, Lutz, Raphael, Ghosh, Michael, Renders, Simon, Correia, Nádia, Donato, Elisa, Dixon, Karin O., Hirche, Christoph, Andresen, Carolin, Robens, Claudia, Werner, Paula S., Boch, Tobias, Eisel, David, Osen, Wolfram, Pilz, Franziska, Przybylla, Adriana, Klein, Corinna, Buchholz, Frank, Milsom, Michael D., Essers, Marieke A.G., Eichmüller, Stefan B., Hofmann, Wolf-Karsten, Nowak, Daniel, Hübschmann, Daniel, Hundemer, Michael, Thiede, Christian, Bullinger, Lars, Müller-Tidow, Carsten, Armstrong, Scott A., Trumpp, Andreas, Kuchroo, Vijay K., Haas, Simon

Source: In Cell Stem Cell 5 May 2022 29(5):760-775

The proteogenomic subtypes of acute myeloid leukemia

Authors: Jayavelu, Ashok Kumar, Wolf, Sebastian, Buettner, Florian, Alexe, Gabriela, Häupl, Björn, Comoglio, Federico, Schneider, Constanze, Doebele, Carmen, Fuhrmann, Dominik C., Wagner, Sebastian, Donato, Elisa, Andresen, Carolin, Wilke, Anne C., Zindel, Alena, Jahn, Dominique, Splettstoesser, Bianca, Plessmann, Uwe, Münch, Silvia, Abou-El-Ardat, Khali, Makowka, Philipp, Acker, Fabian, Enssle, Julius C., Cremer, Anjali, Schnütgen, Frank, Kurrle, Nina, Chapuy, Björn, Löber, Jens, Hartmann, Sylvia, Wild, Peter J., Wittig, Ilka, Hübschmann, Daniel, Kaderali, Lars, Cox, Jürgen, Brüne, Bernhard, Röllig, Christoph, Thiede, Christian, Steffen, Björn, Bornhäuser, Martin, Trumpp, Andreas, Urlaub, Henning, Stegmaier, Kimberly, Serve, Hubert, Mann, Matthias, Oellerich, Thomas

Source: In Cancer Cell 14 March 2022 40(3):301-317

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Authors: Altmüller, Janine, Angelov, Angel, Aschenbrenner, Anna C., Bals, Robert, Bartholomäus, Alexander, Becker, Anke, Becker, Matthias, Bezdan, Daniela, Bitzer, Michael, Blumert, Conny, Bonifacio, Ezio, Bork, Peer, Boyke, Bunk, Blum, Helmut, Casadei, Nicolas, Clavel, Thomas, Colome-Tatche, Maria, Cornberg, Markus, De La Rosa Velázquez, Inti Alberto, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Förstner, Konrad, Franzenburg, Sören, Frick, Julia-Stefanie, Gabernet, Gisela, Gagneur, Julien, Ganzenmueller, Tina, Gauder, Marie, Geißert, Janina, Goesmann, Alexander, Göpel, Siri, Grundhoff, Adam, Grundmann, Hajo, Hain, Torsten, Hanses, Frank, Hehr, Ute, Heimbach, André, Hoeper, Marius, Horn, Friedemann, Hübschmann, Daniel, Hummel, Michael, Iftner, Thomas, Iftner, Angelika, Illig, Thomas, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keller, Andreas, Keppler, Oliver T., Kim-Hellmuth, Sarah, Klein, Christoph, Knop, Michael, Kohlbacher, Oliver, Köhrer, Karl, Korbel, Jan, Kremsner, Peter G., Kühnert, Denise, Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin U., Makarewicz, Oliwia, Marini, Federico, Marz, Manja, McHardy, Alice C., Mertes, Christian, Münchhoff, Maximilian, Nahnsen, Sven, Nöthen, Markus, Ntoumi, Francine, Nürnberg, Peter, Ossowski, Stephan, Overmann, Jörg, Peter, Silke, Pfeffer, Klaus, Pink, Isabell, Poetsch, Anna R., Protzer, Ulrike, Pühler, Alfred, Rajewsky, Nikolaus, Ralser, Markus, Reiche, Kristin, Rieß, Olaf, Ripke, Stephan, Nunes da Rocha, Ulisses, Rosenstiel, Philip, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Scheithauer, Simone, Schiffer, Philipp, Schmid-Burgk, Jonathan, Schneider, Wulf, Schulte, Eva-Christina, Schultze, Joachim L., Sczyrba, Alexander, Sharaf, Mariam L., Singh, Yogesh, Sonnabend, Michael, Stegle, Oliver, Stoye, Jens, Theis, Fabian, Ulas, Thomas, Vehreschild, Janne, Velavan, Thirumalaisamy P., Vogel, Jörg, Volland, Sonja, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, Winkler, Sylke, Ziebuhr, John, Krämer, Benjamin, Knoll, Rainer, Bonaguro, Lorenzo, ToVinh, Michael, Raabe, Jan, Astaburuaga-García, Rosario, Schulte-Schrepping, Jonas, Kaiser, Kim Melanie, Rieke, Gereon J., Bischoff, Jenny, Monin, Malte B., Hoffmeister, Christoph, Schlabe, Stefan, De Domenico, Elena, Reusch, Nico, Händler, Kristian, Reynolds, Gary, Blüthgen, Nils, Hack, Gudrun, Finnemann, Claudia, Nischalke, Hans D., Strassburg, Christian P., Stephenson, Emily, Su, Yapeng, Gardner, Louis, Yuan, Dan, Chen, Daniel, Goldman, Jason, Rosenstiel, Philipp, Schmidt, Susanne V., Latz, Eicke, Hrusovsky, Kevin, Ball, Andrew J., Johnson, Joe M., Koenig, Paul-Albert, Schmidt, Florian I., Haniffa, Muzlifah, Heath, James R., Kümmerer, Beate M., Keitel, Verena, Jensen, Björn, Stubbemann, Paula, Kurth, Florian, Sander, Leif E., Nattermann, Jacob

Source: In Immunity 9 November 2021 54(11):2650-2669

RSPO2 inhibits BMP signaling to promote self-renewal in acute myeloid leukemia

Authors: Sun, Rui, He, Lixiazi, Lee, Hyeyoon, Glinka, Andrey, Andresen, Carolin, Hübschmann, Daniel, Jeremias, Irmela, Müller-Decker, Karin, Pabst, Caroline, Niehrs, Christof

Source: In Cell Reports 17 August 2021 36(7)

Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model

Authors: Simovic, Milena, Bolkestein, Michiel, Moustafa, Mahmoud, Wong, John K L, Körber, Verena, Benedetto, Sarah, Khalid, Umar, Schreiber, Hannah Sophia, Jugold, Manfred, Korshunov, Andrey, Hübschmann, Daniel, Mack, Norman, Brons, Stephan, Wei, Pei-Chi, Breckwoldt, Michael O, Heiland, Sabine, Bendszus, Martin, Debus, Jürgen, Höfer, Thomas, Zapatka, Marc, Kool, Marcel, Pfister, Stefan M, Abdollahi, Amir, Ernst, Aurélie

Source: Neuro-oncology. 23(12):2028-2041

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100136087823.0x000001&indx=1&recIds=ETOCvdc_100136087823.0x000001

Analysis of mutational signatures with yet another package for signature analysis

Authors: Hübschmann, Daniel, Jopp‐Saile, Lea, Andresen, Carolin, Krämer, Stephen, Gu, Zuguang, Heilig, Christoph E., Kreutzfeldt, Simon, Teleanu, Veronica, Fröhling, Stefan, Eils, Roland, Schlesner, Matthias

Source: Genes, chromosomes & cancer. 60(5):314-331

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100116943214.0x000001&indx=1&recIds=ETOCvdc_100116943214.0x000001

Poly(ADP‐ribose) polymerase inhibition in pancreatic cancer

Authors: Singh, Hans Martin, Bailey, Peter, Hübschmann, Daniel, Berger, Anne Katrin, Neoptolemos, John P., Jäger, Dirk, Siveke, Jens, Springfeld, Christoph

Source: Genes, chromosomes & cancer. 60(5):373-384

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100116943234.0x000001&indx=1&recIds=ETOCvdc_100116943234.0x000001

Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas

Authors: Hübschmann, Daniel, Kleinheinz, Kortine, Wagener, Rabea, Bernhart, Stephan H., López, Cristina, Toprak, Umut H., Sungalee, Stephanie, Ishaque, Naveed, Kretzmer, Helene, Kreuz, Markus, Waszak, Sebastian M., Paramasivam, Nagarajan, Ammerpohl, Ole, Aukema, Sietse M., Beekman, Renée, Bergmann, Anke K., Bieg, Matthias, Binder, Hans, Borkhardt, Arndt, Borst, Christoph, Brors, Benedikt, Bruns, Philipp, Carrillo de Santa Pau, Enrique, Claviez, Alexander, Doose, Gero, Haake, Andrea, Karsch, Dennis, Haas, Siegfried, Hansmann, Martin-Leo, Hoell, Jessica I., Hovestadt, Volker, Huang, Bingding, Hummel, Michael, Jäger-Schmidt, Christina, Kerssemakers, Jules N. A., Korbel, Jan O., Kube, Dieter, Lawerenz, Chris, Lenze, Dido, Martens, Joost H. A., Ott, German, Radlwimmer, Bernhard, Reisinger, Eva, Richter, Julia, Rico, Daniel, Rosenstiel, Philip, Rosenwald, Andreas, Schillhabel, Markus, Stilgenbauer, Stephan, Stadler, Peter F., Martín-Subero, José I., Szczepanowski, Monika, Warsow, Gregor, Weniger, Marc A., Zapatka, Marc, Valencia, Alfonso, Stunnenberg, Hendrik G., Lichter, Peter, Möller, Peter, Loeffler, Markus, Eils, Roland, Klapper, Wolfram, Hoffmann, Steve, Trümper, Lorenz, Küppers, Ralf, Schlesner, Matthias, Siebert, Reiner

Source: Leukemia. 35(7):2002-2016

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100193007000.0x000001&indx=1&recIds=ETOCvdc_100193007000.0x000001

Make Interactive Complex Heatmaps in R

Authors: Gu, Zuguang, Hübschmann, Daniel

Source: Bioinformatics. 38(5):1460-1462

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100141304708.0x000001&indx=1&recIds=ETOCvdc_100141304708.0x000001