Publications

Preprints

 

 

 

2024

Lutz, R.*, Grünschläger, F.*, Simon, M.*, Awwad, M.H.S., Bauer, M., Yousefian, S., Beumer, N., Jopp-Saile, L., Sedlmeier, A., Solé-Boldo, L., Avanesyan, B., Vonficht, D., Stelmach, P., Steinbuss, G., Boch, T., Steiger, S., Baertsch, M.-A., Prokoph, N., Rippe, K., Durie, B.G.M., Wickenhauser, C., Trumpp, A., Müller-Tidow, C., Hübschmann, D., Weinhold, N., Raab, M.-S., Brors, B.*, Goldschmidt, H.*, Imbusch, C.D.*, Hundemer, M.*, Haas, S.*, 2024. Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy. Nature Communications 15, 10396. https://doi.org/10.1038/s41467-024-54543-0

Hai, L., Friedel, D., Hinz, F., Hoffmann, D.C.F., Doubrovinskaia, S., Rohdjess, H., Weidenauer, K., Denisova, E., Scheffler, G.T., Kessler, T., Kourtesakis, A., Herold-Mende, C., Henegariu, O., Baehring, J.M., Dietrich, J., Brors, B., Wick, W., Sahm, F., Kaulen, L., 2024. Distinct epigenetic and transcriptional profiles of Epstein-Barr virus (EBV) positive and negative primary CNS lymphomas. Neuro-Oncology 2024, noae251. https://doi.org/10.1093/neuonc/noae251

Rafi, A.M., Nogina, D., Penzar, D., Lee, Dohoon, Lee, Danyeong, Kim, N., Kim, Sangyeup, Kim, D., Shin, Y., Kwak, I.-Y., Meshcheryakov, G., Lando, A., Zinkevich, A., Kim, B.-C., Lee, J., Kang, T., Vaishnav, E.D., Yadollahpour, P., Bornelöv, S., Svensson, F., Trapotsi, M.-A., Tran, D., Nguyen, T., Tu, X., Zhang, W., Qiu, W., Ghotra, R., Yu, Y., Labelson, E., Prakash, A., Narayanan, A., Koo, P., Chen, X., Jones, D.T., Tinti, M., Guan, Y., Ding, M., Chen, K., Yang, Y., Ding, K., Dixit, G., Wen, J., Zhou, Z., Dutta, P., Sathian, R., Surana, P., Ji, Y., Liu, H., Davuluri, R.V., Hiratsuka, Y., Takatsu, M., Chen, T.-M., Huang, C.-H., Wang, H.-K., Shih, E.S.C., Chen, S.-H., Wu, C.-H., Chen, J.-Y., Huang, K.-L., Alsaggaf, I., Greaves, P., Barton, C., Wan, C., Abad, N., Körner, C., Feuerbach, L., Brors, B., Li, Y., Röner, S., Dash, P.M., Schubach, M., Soylemez, O., Møller, A., Kavaliauskaite, G., Madsen, J., Lu, Z., Queen, O., Babjac, A., Emrich, S., Kardamiliotis, K., Kyriakidis, K., Malousi, A., Palaniappan, A., Gupta, K., Kumar S, P., Bradford, J., Perrin, D., Salomone, R., Schmitz, C., JiaXing, C., JingZhe, W., AiWei, Y., Kim, Sun, Albrecht, J., Regev, A., Gong, W., Kulakovskiy, I.V., Meyer, P., de Boer, C.G., 2024. A community effort to optimize sequence-based deep learning models of gene regulation. Nature Biotechnology epub ahead of print. https://doi.org/10.1038/s41587-024-02414-w

Oduselu, G.O., Elebiju, O.F., Ogunnupebi, T.A., Akash, S., Ajani, O.O., Adebiyi, E.F., 2024. Employing Hexahydroquinolines as PfCDPK4 Inhibitors to Combat Malaria Transmission: An Advanced Computational Approach. Advances and Applications in Bioinformatics and Chemistry 17, 83–105. https://doi.org/10.2147/AABC.S476404

Man, K.H., Wu, Y., Gao, Z., Spreng, A.-S., Keding, S.J.E., Mangei, J., Boskovic, P., Mallm, J.-P., Liu, H.-K., Imbusch, C.D., Lichter, P., Radlwimmer, B., 2024. SOX10 mediates glioblastoma cell-state plasticity. EMBO Reports 25, 5113–5140. https://doi.org/10.1038/s44319-024-00258-8

Manuilova, I., Bossenz, J., Weise, A.B., Boehm, D., Strantz, C., Unberath, P., Reimer, N., Metzger, P., Pauli, T., Werle, S.D., Schulze, S., Hiemer, S., Ustjanzew, A., Kestler, H.A., Busch, H., Brors, B., Christoph, J., 2024. Identifications of Similarity Metrics for Patients With Cancer: Protocol for a Scoping Review. JMIR Research Protocols 13, e58705. https://doi.org/10.2196/58705

An, J.*, Kurilov, R.*, Peccerella, T., Bergmann, F., Edderkaoui, M., Lim, A., Zhou, X., Pfütze, K., Schulz, A., Wolf, S., Hu, K., Springfeld, C., Mughal, S.S., Zezlina, L., Fortunato, F., Beyer, G., Mayerle, J., Roth, S., Hulkkonen, J., Merz, D., Ei, S., Mehrabi, A., Loos, M., Al-Saeedi, M., Michalski, C.W., Büchler, M.W., Hackert, T., Brors, B., Pandol, S.J., Bailey, P., Neoptolemos, J.P., 2024. Metavert synergises with standard cytotoxics in human PDAC organoids and is associated with transcriptomic signatures of therapeutic response. Translational Oncology 49, 102109. https://doi.org/10.1016/j.tranon.2024.102109

José Besso, M., Bitto, V., Koi, L., Wijaya Hadiwikarta, W., Conde-Lopez, C., Euler-Lange, R., Bonrouhi, M., Schneider, K., Linge, A., Krause, M., Baumann, M., Kurth, I., 2024. Transcriptomic and epigenetic landscape of nimorazole-enhanced radiochemotherapy in head and neck cancer. Radiotherapy and Oncology 199, 110348. https://doi.org/10.1016/j.radonc.2024.110348

Martín, R., Gaitán, N., Jarlier, F., Feuerbach, L., de Soyres, H., Arbonés, M., Gutman, T., Puiggròs, M., Ferriz, A., Gonzalez, A., Estelles, L., Gut, I., Capella-Gutierrez, S., Stein, L.D., Brors, B., Royo, R., Hupé, P., Torrents, D., 2024. ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. Cell Genomics 4, 100639. https://doi.org/10.1016/j.xgen.2024.100639

Ogunnupebi, T.A., Oduselu, G.O., Elebiju, O.F., Ajani, O.O., Adebiyi, E.F., 2024. In silico studies of benzothiazole derivatives as potential inhibitors of Anopheles funestus and Anopheles gambiae trehalase. Frontiers in Bioinformatics 4, 1428539. https://doi.org/10.3389/fbinf.2024.1428539

Simon, M., Stüve, P., Schmidleithner, L., Bittner, S., Beumer, N., Strieder, N., Schmidl, C., Pant, A., Gebhard, C., Eigenberger, A., Rehli, M., Prantl, L., Hehlgans, T., Brors, B., Imbusch, C.D., Delacher, M., Feuerer, M., 2024. Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells. Immunity 57, 1975-1993.e10. https://doi.org/10.1016/j.immuni.2024.06.015

Adebayo, G.P., Oduselu, G.O., Aderohunmu, D.V., Klika, K., Olasehinde, G.I., Ajani, O.O., Adebiyi, E.F., 2024. Structure-based design, and development of amidinyl, amidoximyl and hydroxamic acid based organic molecules as novel antimalarial drug candidates. Arabian Journal of Chemistry 17, 105573. https://doi.org/10.1016/j.arabjc.2023.105573

Adedeji, E.O., Beder, T., Damiani, C., Cappelli, A., Accoti, A., Tapanelli, S., Ogunlana, O.O., Fatumo, S., Favia, G., Koenig, R., Adebiyi, E.F., 2024. Combination of computational techniques and RNAi reveal targets in Anopheles gambiae for malaria vector control. PLoS ONE 19, e0305207-. https://doi.org/10.1371/journal.pone.0305207

Bitto, V., Hönscheid, P., Besso, M.J., Sperling, C., Kurth, I., Baumann, M., Brors, B., 2024. Enhancing mass spectrometry imaging accessibility using convolutional autoencoders for deriving hypoxia-associated peptides from tumors. npj Systems Biology and Applications 10, 57. https://doi.org/10.1038/s41540-024-00385-x

Elebiju, O.F., Oduselu, G.O., Ogunnupebi, T.A., Ajani, O.O., Adebiyi, E.F., 2024. In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance. Pharmaceuticals 17, 543. https://doi.org/10.3390/ph17050543

Rieckmann, L.-M., Spohn, M., Ruff, L., Agorku, D., Becker, L., Borchers, A., Krause, J., O’Reilly, R., Hille, J., Velthaus-Rusik, J.-L., Beumer, N., Günther, A., Willnow, L., Imbusch, C.D., Iglauer, P., Simon, R., Franzenburg, S., Winter, H., Thomas, M., Bokemeyer, C., Gagliani, N., Krebs, C.F., Sprick, M., Hardt, O., Riethdorf, S., Trumpp, A., Stoecklein, N.H., Peine, S., Rosenstiel, P., Pantel, K., Loges, S., Janning, M., 2024. Diagnostic leukapheresis reveals distinct phenotypes of NSCLC circulating tumor cells. Molecular Cancer 23, 93. https://doi.org/10.1186/s12943-024-01984-2

Kreis, J., Aybey, B., Geist, F., Brors, B., Staub, E., 2024. Stromal signals dominate gene expression signature scores that aim to describe cancer cell-intrinsic stemness or mesenchymality characteristics. Cancer Research Communications 4, 516–529. https://doi.org/10.1158/2767-9764.CRC-23-0383

Delacher, M., Schmidleithner, L., Simon, M., Stüve, P., Sanderink, L., Hotz-Wagenblatt, A., Wuttke, M., Schambeck, K., Ruhland, B., Hofmann, V., Bittner, S., Ritter, U., Pant, A., Helbich, S.S., Voss, M., Lemmermann, N.A., Bessiri-Schake, L., Bohn, T., Eigenberger, A., Menevse, A.N., Gebhard, C., Strieder, N., Abken, H., Rehli, M., Huehn, J., Beckhove, P., Hehlgans, T., Junger, H., Geissler, E.K., Prantl, L., Werner, J.M., Schmidl, C., Brors, B., Imbusch, C.D., Feuerer, M., 2024. The effector program of human CD8 T cells supports tissue remodeling. Journal of Experimental Medicine 221, e20230488. https://doi.org/10.1084/jem.20230488

Toussaint, P.A., Leiser, F., Thiebes, S., Schlesner, M., Brors, B., Sunyaev, A., 2024. Explainable artificial intelligence for omics data: a systematic mapping study. Briefings in Bioinformatics 25, 1–16. https://doi.org/10.1093/bib/bbad453

 

2023

Adegbite, G., Edeki, S., Isewon, I., Emmanuel, J., Dokunmu, T., Rotimi, S., Oyelade, J., Adebiyi, E.F., 2023. Mathematical modeling of malaria transmission dynamics in humans with mobility and control states. Infectious Disease Modelling 8, 1015–1031. https://doi.org/10.1016/j.idm.2023.08.005

Ademuwagun, I.A., Oduselu, G.O., Rotimi, S.O., Adebiyi, E.F., 2023. Pharmacophore-Aided Virtual Screening and Molecular Dynamics Simulation Identifies TrkB Agonists for Treatment of CDKL5-Deficiency Disorders. Bioinformatics and Biology Insights 17, 117793222311582-. https://doi.org/10.1177/11779322231158254

Alonso-Moreda, N., Berral-González, A., De La Rosa, E., González-Velasco, O., Sánchez-Santos, J.M., De Las Rivas, J., 2023. Comparative Analysis of Cell Mixtures Deconvolution and Gene Signatures Generated for Blood, Immune and Cancer Cells. International Journal of Molecular Sciences 24, 10765. https://doi.org/10.3390/ijms241310765

Aybey, B., Zhao, S., Brors, B., Staub, E., 2023. Immune cell type signature discovery and random forest classification for analysis of single cell gene expression datasets. Frontiers in Immunology 14, 1194745. https://doi.org/10.3389/fimmu.2023.1194745

Braband, K.L., Nedwed, A.S., Helbich, S.S., Simon, M., Beumer, N., Brors, B., Marini, F., Delacher, M., 2023. Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. Frontiers in Immunology 14, 1232511. https://doi.org/10.3389/fimmu.2023.1232511

Elebiju, O.F., Ajani, O.O., Oduselu, G.O., Ogunnupebi, T.A., Adebiyi, E.F., 2023. Recent advances in functionalized quinoline scaffolds and hybrids—Exceptional pharmacophore in therapeutic medicine. Frontiers in Chemistry 10, 1074331. https://doi.org/10.3389/fchem.2022.1074331

Falola, O., Adam, Y., Ajayi, O., Kumuthini, J., Adewale, S., Mosaku, A., Samtal, C., Adebayo, G., Emmanuel, J., Tchamga, M.S.S., Erondu, U., Nehemiah, A., Rasaq, S., Ajayi, M., Akanle, B., Oladipo, O., Isewon, I., Adebiyi, M., Oyelade, J., Adebiyi, E.F., 2023. SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets. Bioinformatics 39, btac791. https://doi.org/10.1093/bioinformatics/btac791

Kandala, S., Ramos, M., Voith von Voithenberg, L., Diaz-Jimenez, A., Chocarro, S., Keding, S.J.E., Brors, B., Imbusch, C.D., Sotillo, R., 2023. Chronic chromosome instability induced by Plk1 results in immune suppression in breast cancer. Cell Reports 42, 113266. https://doi.org/10.1016/j.celrep.2023.113266

Kaulen, L., Denisova, E., Hinz, F., Hai, L., Friedel, D., Henegariu, O., Hoffmann, D.C.F., Ito, J., Kourtesakis, A., Lehnert, P., Doubrovinskaia, S., Karschnia, P., von Baumgarten, L., Kessler, T., Baehring, J.M., Brors, B., Sahm, F., Wick, W., 2023. Integrated genetic analyses of immunodeficiency-associated Epstein-Barr virus- (EBV) positive primary CNS lymphomas. Acta Neuropathologica 146, 499–514. https://doi.org/10.1007/s00401-023-02613-w

Koi, L., Bitto, V., Weise, C., Möbius, L., Linge, A., Löck, S., Yaromina, A., Besso, M.J., Valentini, C., Pfeifer, M., Overgaard, J., Zips, D., Kurth, I., Krause, M., Baumann, M., 2023. Prognostic biomarkers for the response to the radiosensitizer nimorazole combined with RCTx: a pre-clinical trial in HNSCC xenografts. Journal of Translational Medicine 21, 576. https://doi.org/10.1186/s12967-023-04439-2

Körber, V., Stainczyk, S., Kurilov, R., Henrich, K.-O., Hero, B., Brors, B., Westermann, F., Höfer, T., 2023. Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome. Nature Genetics 55, 619–630. https://doi.org/10.1038/s41588-023-01332-y

Morfouace, M., Horak, P., Kreutzfeldt, S., Stevovic, A., de Rojas, T., Denisova, E., Hutter, B., Bautista, F., Oliveira, J., Defachelles, A.-S., White, J., Kasper, B., Preusser, M., Golfinopoulos, V., Pfister, S., Van der Graaf, W., Wardelmann, E., Shenjere, P., Fröhling, S., McCabe, M.G., 2023. Comprehensive molecular profiling of sarcomas in adolescent and young adult patients: Results of the EORTC SPECTA-AYA international proof-of-concept study. European Journal of Cancer 178, 216–226. https://doi.org/10.1016/j.ejca.2022.10.020

Münch, J., Sobol, M.S., Brors, B., Kaster, A.-K., 2023. Single-cell transcriptomics and data analyses for prokaryotes—Past, present and future concepts, in: Advances in Applied Microbiology. Elsevier, New York, NY [u.a.], pp. 1–39. https://doi.org/10.1016/bs.aambs.2023.04.002

Oduselu, G.O., Aderohunmu, D.V., Ajani, O.O., Elebiju, O.F., Ogunnupebi, T.A., Adebiyi, E.F., 2023a. Synthesis, in silico and in vitro antimicrobial efficacy of substituted arylidene-based quinazolin-4(3H)-one motifs. Frontiers in Chemistry 11, 1264824. https://doi.org/10.3389/fchem.2023.1264824

Oduselu, G.O., Afolabi, R., Ademuwagun, I., Vaughan, A., Adebiyi, E.F., 2023b. Structure-based pharmacophore modeling, virtual screening, and molecular dynamics simulation studies for identification of Plasmodium falciparum 5-aminolevulinate synthase inhibitors. Frontiers in Medicine 9, 1022429. https://doi.org/10.3389/fmed.2022.1022429

Ogunnupebi, T.A., Ajani, O.O., Oduselu, G.O., Elebiju, O.F., Adebiyi, E.F., 2023. Chemistry and pharmacological diversity of benzothiazepine—Excellent pathway to drug discovery. Journal of Molecular Structure 1280, 135071. https://doi.org/10.1016/j.molstruc.2023.135071

Owolabi, P., Adam, Y., Adebiyi, E.F., 2023. Personalizing medicine in Africa: current state, progress and challenges. Frontiers in Genetics 14, 1233338. https://doi.org/10.3389/fgene.2023.1233338

Riegel, D., Romero-Fernández, E., Simon, M., Adenugba, A.R., Singer, K., Mayr, R., Weber, F., Kleemann, M., Imbusch, C.D., Kreutz, M., Brors, B., Ugele, I., Werner, J.M., Siska, P.J., Schmidl, C., 2023. Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells. Molecular Cell 83, 622-636.e10. https://doi.org/10.1016/j.molcel.2022.12.029

Samarin, J., Fabrowski, P., Kurilov, R., Nuskova, H., Hummel-Eisenbeiss, J., Pink, H., Li, N., Weru, V., Alborzinia, H., Yildiz, U., Grob, L., Täubert, M.J., Czech, M., Morgen, M., Brandstädter, C., Becker, K., Mao, L., Jayavelu, A.K., Goncalves, A., Uhrig, U., Seiler, J.S., Lyu, Y., Diederichs, S., Klingmüller, U., Muckenthaler, M., Kopp-Schneider, A., Teleman, A., Miller, A., Gunkel, P.N., 2023. Low level of antioxidant capacity biomarkers but not target overexpression predicts vulnerability to ROS-inducing drugs. Redox Biology 62, 102639. https://doi.org/10.1016/j.redox.2023.102639

Schwartz, U., Llamazares Prada, M., Pohl, S.T., Richter, M., Tamas, R., Schuler, M., Keller, C., Mijosek, V., Muley, T., Schneider, M.A., Quast, K., Hey, J., Heußel, C.P., Warth, A., Winter, H., Serçin, Ö., Karmouty-Quintana, H., Jyothula, S.S., Patel, M.K., Herth, F., Koch, I., Petrosino, G., Titimeaua, A., Mardin, B.R., Weichenhan, D., Jurkowski, T.P., Imbusch, C.D., Brors, B., Benes, V., Jung, B., Wyatt, D., Stahl, H.F., Plass, C., Jurkowska, R.Z., 2023. High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD. The EMBO Journal 42, e111272. https://doi.org/10.15252/embj.2022111272

Wu, Y., Seufert, I., Al-Shaheri, F.N., Kurilov, R., Bauer, A.S., Manoochehri, M., Moskalev, E.A., Brors, B., Tjaden, C., Giese, N.A., Hackert, T., Büchler, M.W., Hoheisel, J., 2023. DNA-methylation signature accurately differentiates pancreatic cancer from chronic pancreatitis in tissue and plasma. Gut 72, 2344–2353. https://doi.org/10.1136/gutjnl-2023-330155

Yousuf, S., Qiu, M., Voith von Voithenberg, L., Hulkkonen, J., Macinkovic, I., Schulz, A.R., Hartmann, D., Mueller, F., Mijatovic, M., Ibberson, D., AlHalabi, K.T., Hetzer, J., Anders, S., Brüne, B., Mei, H.E., Imbusch, C.D., Brors, B., Heikenwälder, M., Gaida, M.M., Büchler, M.W., Weigert, A., Hackert, T., Roth, S., 2023. Spatially resolved multi-omics single-cell analyses inform mechanisms of immune-dysfunction in pancreatic cancer. Gastroenterology 165, 891-908.e14. https://doi.org/10.1053/j.gastro.2023.05.036

Zhou, X.*, An, J.*, Kurilov, R., Brors, B., Hu, K., Peccerella, T., Roessler, S., Pfütze, K., Schulz, A., Wolf, S., Hohmann, N., Theile, D., Sauter, M., Burhenne, J., Ei, S., Heger, U., Strobel, O., Barry, S.T., Springfeld, C., Tjaden, C., Bergmann, F., Büchler, M., Hackert, T., Fortunato, F., Neoptolemos, J.P., Bailey, P., 2023. Persister cell phenotypes contribute to poor patient outcomes after neoadjuvant chemotherapy in PDAC. Nature Cancer 4, 1362–1381. https://doi.org/10.1038/s43018-023-00628-6

Ziaei Jam, H., Li, Y., DeVito, R., Mousavi, N., Ma, N., Lujumba, I., Adam, Y., Maksimov, M., Huang, B., Dolzhenko, E., Qiu, Y., Kakembo, F.E., Joseph, H., Onyido, B., Adeyemi, J., Bakhtiari, M., Park, J., Javadzadeh, S., Jjingo, D., Adebiyi, E., Bafna, V., Gymrek, M., 2023. A deep population reference panel of tandem repeat variation. Nature Communications 14, 6711. https://doi.org/10.1038/s41467-023-42278-3

 

2022

Adam, Y., Sadeeq, S., Kumuthini, J., Ajayi, O., Wells, G., Solomon, R., Ogunlana, O., Adetiba, E., Iweala, E., Brors, B., Adebiyi, E.F., 2022. Polygenic Risk Score in African populations: progress and challenges. F1000Research 11, 175. https://doi.org/10.12688/f1000research.76218.2

Adedeji, E.O., Oduselu, G.O., Ogunlana, O.O., Fatumo, S., Koenig, R., Adebiyi, E.F., 2022. Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study. Insects 13, 1070. https://doi.org/10.3390/insects13111070

Beyene, M., Toussaint, P.A., Thiebes, S., Schlesner, M., Brors, B., Sunyaev, A., 2022. A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research. Journal of the American Medical Informatics Association 29, 1433–1444. https://doi.org/10.1093/jamia/ocac077

Boch, T., Frost, N., Sommer, L., Overbeck, T.R., Thomas Michaeli, C., Szuszies, C.J., Beumer, N., Imbusch, C.D., Winter, H., Thomas, M., Roeper, J., Janning, M., Griesinger, F., Wermke, M., Loges, S., 2022. Pathologic responses in oligometastatic NSCLC patients treated with neoadjuvant immune checkpoint blockade with and without chemotherapy followed by surgery. Lung Cancer 164, 46–51. https://doi.org/10.1016/j.lungcan.2021.11.009

Bogeska, R., Mikecin, A.-M., Kaschutnig, P.E., Fawaz, M., Büchler-Schäff, M., Le, D., Ganuza, M., Vollmer, A., Paffenholz, S., Asada, N., Rodriguez-Correa, E., Frauhammer, F., Büttner, F., Ball, M., Knoch, J., Stäble, S., Walter, D., Petri, A., Carreño-Gonzalez, M.J., Wagner, V., Brors, B., Haas, S., Lipka, D., Essers, M., Weru, V., Holland-Letz, T., Mallm, J.-P., Rippe, K., Krämer, S., Schlesner, M., McKinney Freeman, S., Florian, M.C., King, K.Y., Frenette, P.S., Rieger, M.A., Milsom, M., 2022. Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging. Cell Stem Cell 29, 1273-1284.e8. https://doi.org/10.1016/j.stem.2022.06.012

Burns, D., Anokian, E., Saunders, E.J., Bristow, R.G., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J., Weischenfeldt, J., Waszak, S.M., Corcoran, N.M., Jung, C.-H., Pope, B.J., Hovens, C.M., Cancel-Tassin, G., Cussenot, O., Loda, M., Sander, C., Hayes, V.M., Dalsgaard Sorensen, K., Lu, Y.-J., Hamdy, F.C., Foster, C.S., Gnanapragasam, V., Butler, A., Lynch, A.G., Massie, C.E., Woodcock, D.J., Cooper, C.S., Wedge, D.C., Brewer, D.S., Kote-Jarai, Z., Eeles, R.A., 2022. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. European Urology 82, 201–211. https://doi.org/10.1016/j.eururo.2022.05.007

Carter, J.A., Strömich, L., Peacey, M., Chapin, S.R., Velten, L., Steinmetz, L.M., Brors, B., Pinto, S., Meyer, H.V., 2022. Transcriptomic diversity in human medullary thymic epithelial cells. Nature Communications 13, 4296. https://doi.org/10.1038/s41467-022-31750-1

Denisova, E., Westphal, D., Surowy, H.M., Meier, F., Hutter, B., Reifenberger, J., Rütten, A., Schulz, A., Sergon, M., Ziemer, M., Brors, B., Betz, R.C., Redler, S., 2022. Whole-exome sequencing in eccrine porocarcinoma indicates promising therapeutic strategies. Cancer Gene Therapy 29, 697–708. https://doi.org/10.1038/s41417-021-00347-z

Giesen, N., Paramasivam, N., Toprak, U.H., Huebschmann, D., Xu, J., Uhrig, S., Samur, M., Bähr, S., Fröhlich, M., Mughal, S.S., Mai, E.K., Jauch, A., Müller-Tidow, C., Brors, B., Munshi, N., Goldschmidt, H., Weinhold, N., Schlesner, M., Raab, M.-S., 2022. Comprehensive genomic analysis of refractory multiple myeloma reveals a complex mutational landscape associated with drug resistance and novel therapeutic vulnerabilities. Haematologica 107, 1891–1901. https://doi.org/10.3324/haematol.2021.279360

Gladbach, Y., Sklarz, L.-M., Roolf, C., Beck, J., Schütz, E., Fuellen, G., Junghanss, C., Murua Escobar, H., Hamed, M., 2022. Molecular Characterization of the Response to Conventional Chemotherapeutics in Pro-B-ALL Cell Lines in Terms of Tumor Relapse. Genes 13, 1240. https://doi.org/10.3390/genes13071240

Heilig, C., Laßmann, A., Mughal, S.S., Mock, A., Pirmann, S., Teleanu, M.-V., Renner, M., Andresen, C., Köhler, B.C., Aybey, B., Bauer, S., Siveke, J., Hamacher, R., Folprecht, G., Richter, S., Schröck, E., Brandts, C.H., Ahrens, M., Hohenberger, P., Egerer, G., Kindler, T., Börries, M., Illert, A.L., von Bubnoff, N., Apostolidis, L., Jost, P.J., Westphalen, C.B., Weichert, W., Keilholz, U., Klauschen, F., Beck, K., Winter, U., Richter, D., Möhrmann, L., Bitzer, M., Schulze Osthoff, K., Brors, B., Mechtersheimer, G., Kreutzfeldt, S., Heining, C., Lipka, D., Stenzinger, A., Schlenk, R., Horak, P., Glimm, H., Hübschmann, D., Fröhling, S., 2022. Gene expression-based prediction of pazopanib efficacy in sarcoma. European Journal of Cancer 172, 107–118. https://doi.org/10.1016/j.ejca.2022.05.025

Hong, C., Thiele, R., Feuerbach, L., 2022. GenomeTornadoPlot: A novel R package for CNV visualization and focality analysis. Bioinformatics 38, 2036–2038. https://doi.org/10.1093/bioinformatics/btac037

Isewon, I., Soremekun, C., Adebiyi, M., Adetunji, C., Ogunleye, A.J., Bajeh, A.O., Asani, E.O., Gbadamosi, B., Soremekun, O., Udosen, B., Kintu, C., Ogundokun, R., Arowolo, M.O., Matiluko, O., Nashiru, O., Adebiyi, E., Ekenna, C., Fatumo, S., 2022. Strengthening Bioinformatics and Genomics Analysis Skills in Africa for Attainment of the Sustainable Development Goals: Report of the 2nd Conference of the Nigerian Bioinformatics and Genomics Network. The American Journal of Tropical Medicine and Hygiene 107, 21–23. https://doi.org/10.4269/ajtmh.21-1164

Jahn, A., Rump, A., Widmann, T., Heining, C., Horak, P., Hutter, B., Paramasivam, N., Uhrig, S., Gieldon, L., Drukewitz, S., Kübler, A., Bermudez, M., Hackmann, K., Porrmann, J., Wagner, J., Arlt, M., Franke, M., Fischer, J., Kowalzyk, Z., William, D., Weth, V., Oster, S., Fröhlich, M.A., Hüllein, J., Valle González, C., Kreutzfeldt, S., Mock, A., Heilig, C., Lipka, D., Möhrmann, L., Hanf, D., Teleanu, M.-V., Allgäuer, M., Ruhnke, L., Kutz, O., Knurr, A., Laßmann, A., Endris, V., Neumann, O., Penzel, R., Beck, K., Richter, D., Winter, U., Wolf, S., Pfütze, K., Geörg, C., Meissburger, B., Buchhalter, I., Augustin, M., Aulitzky, W.E., Hohenberger, P., Kroiss, M., Schirmacher, P., Schlenk, R., Keilholz, U., Klauschen, F., Folprecht, G., Bauer, S., Siveke, J., Brandts, C.H., Kindler, T., Börries, M., Illert, A.L., von Bubnoff, N., Jost, P.J., Metzeler, K.H., Bitzer, M., Schulze Osthoff, K., von Kalle, C., Brors, B., Stenzinger, A., Weichert, W., Hübschmann, D., Fröhling, S., Glimm, H., Schröck, E., Klink, B., 2022. Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers. Annals of Oncology 33, 1186–1199. https://doi.org/10.1016/j.annonc.2022.07.008

Li, X., Michels, B., Tosun, O.E., Jung, J., Kappes, J., Ibing, S., Nataraj, N.B., Sahay, S., Schneider, M., Wörner, A., Becki, C., Ishaque, N., Feuerbach, L., Heßling, B., Helm, D., Will, R., Yarden, Y., Müller-Decker, K., Wiemann, S., Körner, C., 2022. 5’isomiR-183-5p - +2 elicits tumor suppressor activity in a negative feedback loop with E2F1. Journal of Experimental & Clinical Cancer Research 41, 190. https://doi.org/10.1186/s13046-022-02380-8

Meier, R., Greve, G., Zimmer, D., Bresser, H., Berberich, B., Langova, R., Stomper, J., Rubarth, A., Feuerbach, L., Lipka, D., Hey, J., Grüning, B., Brors, B., Duyster, J., Plass, C., Becker, H., Lübbert, M., 2022. The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation. Blood Cancer Journal 12, 122. https://doi.org/10.1038/s41408-022-00715-4

Möhrmann, L., Werner, M., Oleś, M., Mock, A., Uhrig, S., Jahn, A., Kreutzfeldt, S., Fröhlich, M., Hutter, B., Paramasivam, N., Richter, D., Beck, K., Winter, U., Pfütze, K., Heilig, C., Teleanu, V., Lipka, D., Zapatka, M., Hanf, D., List, C., Allgäuer, M., Penzel, R., Rüter, G., Jelas, I., Hamacher, R., Falkenhorst, J., Wagner, S., Brandts, C.H., Börries, M., Illert, A.L., Metzeler, K.H., Westphalen, C.B., Desuki, A., Kindler, T., Folprecht, G., Weichert, W., Brors, B., Stenzinger, A., Schröck, E., Hübschmann, D., Horak, P., Heining, C., Fröhling, S., Glimm, H., 2022. Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity. Nature Communications 13, 4485. https://doi.org/10.1038/s41467-022-31866-4

Radke, J., Ishaque, N., Koll, R., Gu, Z., Schumann, E., Sieverling, L., Uhrig, S., Hübschmann, D., Toprak, U.H., López, 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., Jödicke, A., Trümper, L., Anagnostopoulos, I., Lenze, D., Küppers, R., Hummel, M., Schmitt, C.A., Wiestler, O., Wolf, S., Unterberg, A., Eils, R., Herold-Mende, C., Brors, B., Siebert, R., Wiemann, S., Heppner, F.L., Siebert, R., Wagner, S., Haake, A., Richter, J., Richter, G., Eils, R., Lawerenz, C., Eils, J., Kerssemakers, J., Jaeger-Schmidt, C., Scholz, I., Bergmann, A.K., Borst, C., Braulke, F., Burkhardt, B., Claviez, A., Dreyling, M., Eberth, S., Einsele, H., Frickhofen, N., Haas, S., Hansmann, M.-L., Karsch, D., Klepl, N., Kneba, M., Lisfeld, J., Mantovani-Löffler, L., Rohde, M., Ott, G., Stadler, C., Staib, P., Stilgenbauer, S., Zenz, T., Hansmann, M.-L., Kube, D., Haas, S., Klapper, W., Kostezka, U., Möller, P., Rosenwald, A., Ott, G., Szczepanowski, M., Ammerpohl, O., Aukema, S.M., Binder, V., Borkhardt, A., Haake, A., Hoell, J.I., Leich, E., Lichter, P., López, C., Nagel, I., Pischimariov, J., Radlwimmer, B., Richter, J., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schreiber, S., Vater, I., Wagener, R., Siebert, R., Bernhart, S.H., Binder, H., Doose, G., Eils, R., Hoffmann, S., Hopp, L., Kleinheinz, K., Kretzmer, H., Kreuz, M., Korbel, J., Langenberger, D., Loeffler, M., Rosolowski, M., Stadler, P.F., Sungalee, S., 2022. The genomic and transcriptional landscape of primary central nervous system lymphoma. Nature Communications 13, 2558. https://doi.org/10.1038/s41467-022-30050-y

 

2021

Adam, Y., Samtal, C., Brandenburg, J.-T., Falola, O., Adebiyi, E.F., 2021. Performing post-genome-wide association study analysis: overview, challenges and recommendations. F1000Research 10, 1002. https://doi.org/10.12688/f1000research.53962.1

Ademuwagun, I.A., Rotimi, S.O., Syrbe, S., Ajamma, Y.U., Adebiyi, E.F., 2021. Voltage Gated Sodium Channel Genes in Epilepsy: Mutations, Functional Studies, and Treatment Dimensions. Frontiers in Neurology 12, 600050. https://doi.org/10.3389/fneur.2021.600050

Afolabi, R., Chinedu, S., Ajamma, Y., Adam, Y., Koenig, R., Adebiyi, E.F., 2021. Computational identification of Plasmodium falciparum RNA pseudouridylate synthase as a viable drug target, its physicochemical properties, 3D structure prediction and prediction of potential inhibitors. Infection, Genetics and Evolution 97, 105194. https://doi.org/10.1016/j.meegid.2021.105194

Awwad, M.H.S., Mahmoud, A., Bruns, H., Echchannaoui, H., Kriegsmann, K., Lutz, R., Raab, M.-S., Bertsch, U., Munder, M., Jauch, A., Weisel, K., Maier, B., Weinhold, N., Salwender, H.J., Eckstein, V., Hänel, M., Fenk, R., Dürig, J., Brors, B., Benner, A., Müller-Tidow, C., Goldschmidt, H., Hundemer, M., 2021. Selective elimination of immunosuppressive T cells in patients with multiple myeloma. Leukemia 35, 2602–2615. https://doi.org/10.1038/s41375-021-01172-x

Beitzen-Heineke, A., Berenbrok, N., Waizenegger, J., Paesler, S., Gensch, V., Udonta, F., Vargas Delgado, M.E., Engelmann, J., Hoffmann, F., Schafhausen, P., von Amsberg, G., Riecken, K., Beumer, N., Imbusch, C.D., Lorens, J., Fischer, T., Pantel, K., Bokemeyer, C., Ben-Batalla, I., Loges, S., 2021. AXL Inhibition Represents a Novel Therapeutic Approach in BCR-ABL Negative Myeloproliferative Neoplasms. HemaSphere 5, e630. https://doi.org/10.1097/HS9.0000000000000630

Creason, A., Haan, D., Dang, K., Chiotti, K.E., Inkman, M., Lamb, A., Yu, T., Hu, Y., Norman, T.C., Buchanan, A., van Baren, J., Spangler, R., Rollins, M.R., Spellman, P.T., Rozanov, D., Zhang, J., Maher, C.A., Caloian, C., Watson, J.D., Uhrig, S., Haas, B.J., Jain, M., Akeson, M., Ahsen, M.E., Stolovitzky, G., Guinney, J., Boutros, P.C., Stuart, J.M., Ellrott, K., Zhang, H., Wang, Y., Guan, Y., Nguyen, C., Sugai, C., Jha, A., Li, J.W., Dobin, A., 2021. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Systems 12, 827-838.e5. https://doi.org/10.1016/j.cels.2021.05.021

Delacher, M.*, Simon, M.*, Sanderink, L.*, Hotz-Wagenblatt, A., Wuttke, M., Schambeck, K., Schmidleithner, L., Bittner, S., Pant, A., Ritter, U., Hehlgans, T., Riegel, D., Schneider, V., Groeber-Becker, F.K., Eigenberger, A., Gebhard, C., Strieder, N., Fischer, A., Rehli, M., Hoffmann, P., Edinger, M., Strowig, T., Huehn, J., Schmidl, C., Werner, J.M., Prantl, L., Brors, B., Imbusch, C.D., Feuerer, M., 2021. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. Immunity 54, 702-720.e17. https://doi.org/10.1016/j.immuni.2021.03.007

Espinet, E., Gu, Z., Imbusch, C.D., Giese, N.A., Büscher, 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., 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., 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, 638–659. https://doi.org/10.1158/2159-8290.CD-20-1202

Feuerbach, L., 2021. Formal reply to “Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX”. Nature Communications 12, 1551. https://doi.org/10.1038/s41467-021-21796-y

Ghazal, H., Adam, Y., Azami, A.I., Sehli, S., Nyarko, H.N., Chaouni, B., Olasehinde, G., Isewon, I., Adebiyi, M., Ajani, O., Matovu, E., Obembe, O., Ajamma, Y., Kuzamunu, G., Samson Pandam, S., Kayondo, J., Benkahla, A., Adebiyi, E.F., 2021. Plant Genomics in Africa: Present and prospects. The Plant Journal 107, 21–36. https://doi.org/10.1111/tpj.15272

Hartlieb, S., Sieverling, L., Nadler-Holly, M., Ziehm, M., Toprak, U.H., Herrmann, C., Ishaque, N., Okonechnikov, K., Gartlgruber, M., Park, Y.-G., Wecht, E.M., Savelyeva, L., Henrich, K.-O., Rosswog, C., Fischer, M., Hero, B., Jones, D.T.W., Pfaff, E., Witt, O., Pfister, S.M., Volckmann, R., Koster, J., Kiesel, K., Rippe, K., Taschner-Mandl, S., Ambros, P., Brors, B., Selbach, M., Feuerbach, L., Westermann, F., 2021. Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nature Communications 12, 1269. https://doi.org/10.1038/s41467-021-21247-8

Heilig, C., Horak, P., Kreutzfeldt, S., Teleanu, V., Mock, A., Renner, M., Bhatti, I.A., Hutter, B., Hüllein, J., Fröhlich, M., Uhrig, S., Süße, H., Heiligenthal, L., Ochsenreither, S., Illert, A.L., Vogel, A., Desuki, A., Heinemann, V., Heidegger, S., Bitzer, M., Scheytt, M., Brors, B., Hübschmann, D., Baretton, G., Stenzinger, A., Steindorf, K., Benner, A., Jäger, D., Heining, C., Glimm, H., Fröhling, S., Schlenk, R.F., 2021. Rationale and design of the CRAFT (Continuous ReAssessment with Flexible ExTension in Rare Malignancies) multicenter phase II trial. ESMO Open 6, 100310. https://doi.org/10.1016/j.esmoop.2021.100310

Hlevnjak, M., Schulze, M., Elgaafary, S., Fremd, C., Michel, L., Beck, K., Pfütze, K., Richter, D., Wolf, S., Horak, P., Kreutzfeldt, S., Pixberg, C., Hutter, B., Ishaque, N., Hirsch, S., Gieldon, L., Stenzinger, A., Springfeld, C., Smetanay, K., Seitz, J., Mavratzas, A., Brors, B., Kirsten, R., Schuetz, F., Fröhling, S., Sinn, H.-P., Jäger, D., Thewes, V., Zapatka, M., Lichter, P., Schneeweiss, A., 2021. CATCH: A Prospective Precision Oncology Trial in Metastatic Breast Cancer. JCO Precision Oncology 5, 676–686. https://doi.org/10.1200/PO.20.00248

Horak, P., Heining, C., Kreutzfeldt, S., Hutter, B., Mock, A., Hüllein, J., Fröhlich, M.A., Uhrig, S., Jahn, A., Rump, A., Gieldon, L., Möhrmann, L., Hanf, D., Teleanu, M.-V., Heilig, C., Lipka, D., Allgäuer, M., Ruhnke, L., Lassmann, A., Endris, V., Neumann, O., Penzel, R., Beck, K., Richter, D., Winter, U., Wolf, S., Pfütze, K., Geörg, C., Meissburger, B., Buchhalter, I., Augustin, M., Aulitzky, W.E., Hohenberger, P., Kroiss, M., Schirmacher, P., Schlenk, R., Keilholz, U., Klauschen, F., Folprecht, G., Bauer, S., Siveke, J., Brandts, C.H., Kindler, T., Börries, M., Illert, A.L., von Bubnoff, N., Jost, P.J., Spiekermann, K., Bitzer, M., Schulze Osthoff, K., von Kalle, C., Klink, B., Brors, B., Stenzinger, A., Schröck, E., Hübschmann, D., Weichert, W., Glimm, H., Fröhling, S., 2021. Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers. Cancer Discovery 11, 2780–2795. https://doi.org/10.1158/2159-8290.CD-21-0126

Hübschmann, D., Kleinheinz, K., Wagener, R., Bernhart, S.H., López, 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.E., Carrillo de Santa Pau, E., Claviez, A., Doose, G., Haake, A., Karsch, D., Haas, S., Hansmann, M.-L., Hoell, J.I., Hovestadt, V., Huang, B., Hummel, M., Jäger-Schmidt, C., Kerssemakers, J., 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., Martín-Subero, J.I., Szczepanowski, M., Warsow, G., Weniger, M.A., Zapatka, M., Valencia, A., Stunnenberg, H.G., Lichter, P., Möller, P., Loeffler, M., Eils, R., Klapper, W., Hoffmann, S., Trümper, L., Küppers, R., Schlesner, M., Siebert, R., 2021. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia 35, 2002–2016. https://doi.org/10.1038/s41375-021-01251-z

Ibing, S., Michels, B.E., Mosdzien, M., Meyer, H.R., Feuerbach, L., Körner, C., 2021. On the impact of batch effect correction in TCGA isomiR expression data. NAR Cancer 3, zcab007. https://doi.org/10.1093/narcan/zcab007

Juul, R.I., Nielsen, M.M., Juul, M., Feuerbach, L., Pedersen, J.S., 2021. The landscape and driver potential of site-specific hotspots across cancer genomes. npj Genomic Medicine 6, 33. https://doi.org/10.1038/s41525-021-00197-6

Kayser, S., Hills, R.K., Langova, R., Kramer, M., Guijarro, F., Sustkova, Z., Estey, E.H., Shaw, C.M., Ráčil, Z., Mayer, J., Zak, P., Baer, M.R., Brunner, A.M., Szotkowski, T., Cetkovsky, P., Grimwade, D., Walter, R.B., Burnett, A.K., Ho, A.D., Ehninger, G., Müller-Tidow, C., Platzbecker, U., Thiede, C., Röllig, C., Schulz, A., Warsow, G., Brors, B., Esteve, J., Russell, N.H., Schlenk, R.F., Levis, M.J., 2021. Characteristics and outcome of patients with acute myeloid leukaemia and t(8;16)(p11;p13): results from an International Collaborative Study. British Journal of Haematology 192, 832–842. https://doi.org/10.1111/bjh.17336

Koelsche, C., Schrimpf, D., Stichel, D., Sill, M., Sahm, F., Reuss, D.E., Blattner, M., Worst, B., Heilig, C.E., Beck, K., Horak, P., Kreutzfeldt, S., Paff, E., Stark, S., Johann, P., Selt, F., Ecker, J., Sturm, D., Pajtler, K.W., Reinhardt, A., Wefers, A.K., Sievers, P., Ebrahimi, A., Suwala, A., Fernández-Klett, F., Casalini, B., Korshunov, A., Hovestadt, V., Kommoss, F.K.F., Kriegsmann, M., Schick, M., Bewerunge-Hudler, M., Milde, T., Witt, O., Kulozik, A.E., Kool, M., Romero-Pérez, L., Grünewald, T.G.P., Kirchner, T., Wick, W., Platten, M., Unterberg, A., Uhl, M., Abdollahi, A., Debus, J., Lehner, B., Thomas, C., Hasselblatt, M., Paulus, W., Hartmann, C., Staszewski, O., Prinz, M., Hench, J., Frank, S., Versleijen-Jonkers, Y.M.H., Weidema, M.E., Mentzel, T., Griewank, K., de Álava, E., Martín, J.D., Gastearena, M.A.I., Chang, K.T.-E., Low, S.Y.Y., Cuevas-Bourdier, A., Mittelbronn, M., Mynarek, M., Rutkowski, S., Schüller, U., Mautner, V.F., Schittenhelm, J., Serrano, J., Snuderl, M., Büttner, R., Klingebiel, T., Buslei, R., Gessler, M., Wesseling, P., Dinjens, W.N.M., Brandner, S., Jaunmuktane, Z., Lyskjær, I., Schirmacher, P., Stenzinger, A., Brors, B., Glimm, H., Heining, C., Tirado, O.M., Sáinz-Jaspeado, M., Mora, J., Alonso, J., Del Muro, X.G., Moran, S., Esteller, M., Benhamida, J.K., Ladanyi, M., Wardelmann, E., Antonescu, C., Flanagan, A., Dirksen, U., Hohenberger, P., Baumhoer, D., Hartmann, W., Vokuhl, C., Flucke, U., Petersen, I., Mechtersheimer, G., Capper, D., Jones, D.T.W., Fröhling, S., Pfister, S.M., von Deimling, A., 2021. Sarcoma classification by DNA methylation profiling. Nature Communications 12, 498. https://doi.org/10.1038/s41467-020-20603-4

Kreis, J., Nedić, B., Mazur, J., Urban, M., Schelhorn, S.-E., Grombacher, T., Geist, F., Brors, B., Zühlsdorf, M., Staub, E., 2021. RosettaSX: Reliable gene expression signature scoring of cancer models and patients. Neoplasia 23, 1069–1077. https://doi.org/10.1016/j.neo.2021.08.005

Maass, K., Schad, P., Finster, A., Puranachot, P., Rosing, F., Wedig, T., Schwarz, N., Stumpf, N., Pfister, S.M., Pajtler, K., 2021. From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube. Cancers 13, 3002. https://doi.org/10.3390/cancers13123002

Oduselu, G.O., Ajani, O.O., Ajamma, Y.U., Adebiyi, E.F., 2021. Structure-Based Drug Design in Discovering Target Specific Drugs against Plasmodium falciparum Adenylosuccinate LyaseOduselu. Tropical Journal of Natural Product Research 5, 739–743. https://doi.org/10.26538/tjnpr/v5i4.23

Simon, M., Mughal, S.S., Horak, P., Uhrig, S., Buchloh, J., Aybey, B., Stenzinger, A., Glimm, H., Fröhling, S., Brors, B., Imbusch, C.D., 2021. Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infiltrates with association to genomic aberrations. Journal of Translational Medicine 19, 204. https://doi.org/10.1186/s12967-021-02858-7

Uhrig, S., Ellermann, J., Walther, T., Burkhardt, P., Fröhlich, M., Hutter, B., Toprak, U.H., Neumann, O., Stenzinger, A., Scholl, C., Fröhling, S., Brors, B., 2021. Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research 31, 448–460. https://doi.org/10.1101/gr.257246.119

Velthaus, J.-L., Iglauer, P., Simon, R., Bokemeyer, C., Bannas, P., Beumer, N., Imbusch, C.D., Goekkurt, E., Loges, S., 2021. Lorlatinib Induces Durable Disease Stabilization in a Pancreatic Cancer Patient with a ROS1 p.L1950F Mutation: Case Report. Oncology Research and Treatment 44, 495–502. https://doi.org/10.1159/000517616

Wahjudi, L.W., Bernhardt, S., Abnaof, K.A., Horak, P., Kreutzfeldt, S., Heining, C., Borgoni, S., Becki, C., Berg, D., Richter, D., Hutter, B., Uhrig, S., Pfütze, K., Leichsenring, J., Glimm, H., Brors, B., von Kalle, C., Stenzinger, A., Korf, U., Fröhling, S., Wiemann, S., 2021. Integrating Proteomics into Precision Oncology. International Journal of Cancer 148, 1438–1451. https://doi.org/10.1002/ijc.33301

Xu, Z., Hu, K., Bailey, P., Springfeld, C., Roth, S., Kurilov, R., Brors, B., Gress, T., Buchholz, M., An, J., Wei, K., Peccerella, T., Büchler, M.W., Hackert, T., Neoptolemos, J.P., 2021. Clinical Impact of Molecular Subtyping of Pancreatic Cancer. Frontiers in Cell and Developmental Biology 9, 743908. https://doi.org/10.3389/fcell.2021.743908

 

2020

Delacher, M., Barra, M.M., Herzig, Y., Eichelbaum, K., Rafiee, M.-R., Richards, D.M., Träger, U., Hofer, A.-C., Kazakov, A., Braband, K., Gonzalez, M., Wöhrl, L., Schambeck, K., Imbusch, C.D., Abramson, J., Krijgsveld, J., Feuerer, M., 2020a. Quantitative Proteomics Identifies TCF1 as a Negative Regulator of Foxp3 Expression in Conventional T Cells. iScience 23, 101127. https://doi.org/10.1016/j.isci.2020.101127

Delacher, M., Imbusch, C.D., Hotz-Wagenblatt, A., Mallm, J.-P., Bauer, K., Simon, M., Riegel, D., Rendeiro, A.F., Bittner, S., Sanderink, L., Pant, A., Schmidleithner, L., Braband, K., Echtenachter, B., Fischer, A., Giunchiglia, V., Hoffmann, P., Edinger, M., Bock, C., Rehli, M., Brors, B., Schmidl, C., Feuerer, M., 2020b. Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF. Immunity 52, 295-312.e11. https://doi.org/10.1016/j.immuni.2019.12.002

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S., Gonzalez, S., Rosebrock, D., Mitchell, T.J., Rubanova, Y., Anur, P., Yu, K., Tarabichi, M., Deshwar, A., Wintersinger, J., Kleinheinz, K., Vázquez-García, 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., Lee, J., Schlesner, M., Boutros, P.C., Bowtell, D.D., Zhu, H., Getz, G., Imielinski, M., Beroukhim, R., Sahinalp, S.C., Ji, Y., Peifer, M., Markowetz, F., Mustonen, V., Yuan, K., Wang, W., Morris, Q.D., PCAWGEvolution&HeterogeneityWorkingGroup, Spellman, P.T., Wedge, D.C., Van Loo, P., PCAWGConsortium, 2020. The evolutionary history of 2,658 cancers. Nature 578, 122–128. https://doi.org/10.1038/s41586-019-1907-7

Heilig, C., Horak, P., Lipka, D.B., Mock, A., Uhrig, S., Kreutzfeldt, S., Richter, S., Gieldon, L., Fröhlich, M., Hutter, B., Hübschmann, D., Teleanu, V., Schmier, J.-W., Philipzen, J., Beuthien-Baumann, B., Schröck, E., Deimling, A., Bauer, S., Heining, C., Mechtersheimer, G., Stenzinger, A., Brors, B., Wardelmann, E., Glimm, H., Hartmann, W., Fröhling, S., 2020. Germline SDHB ‐inactivating mutation in gastric spindle cell sarcoma. Genes, Chromosomes & Cancer 59, 601–608. https://doi.org/10.1002/gcc.22876

Herrera-Rios, D., Mughal, S.S., Teuber-Hanselmann, S., Pierscianek, D., Sucker, A., Jansen, P., Schimming, T., Klode, J., Reifenberger, J., Felsberg, J., Keyvani, K., Brors, B., Sure, U., Reifenberger, G., Schadendorf, D., Helfrich, I., 2020. Macrophages/Microglia Represent the Major Source of Indolamine 2,3-Dioxygenase Expression in Melanoma Metastases of the Brain. Frontiers in Immunology 11, 120. https://doi.org/10.3389/fimmu.2020.00120

Horak, P., Uhrig, S., Witzel, M., Gil-Farina, I., Hutter, B., Rath, T., Gieldon, L., Balasubramanian, G.P., Pastor, X., Heilig, C.E., Richter, D., Schröck, E., Ball, C.R., Brors, B., Braun, C.J., Albert, M.H., Scholl, C., von Kalle, C., Schmidt, M., Fröhling, S., Klein, C., Glimm, H., 2020. Comprehensive genomic characterization of gene therapy-induced T-cell acute lymphoblastic leukemia. Leukemia 34, 2785–2789. https://doi.org/10.1038/s41375-020-0779-z

ICGC/TCGAPan-CancerAnalysisofWholeGenomesConsortium, 2020. Pan-cancer analysis of whole genomes. Nature 578, 82–93. https://doi.org/10.1038/s41586-020-1969-6

Jiao, W., Atwal, G., Polak, P., Karlic, R., Cuppen, E., PCAWGTumorSubtypesClinicalTranslationWorkingGroup, Danyi, A., de Ridder, J., van Herpen, C., Lolkema, M.P., Steeghs, N., Getz, G., Morris, Q., Stein, L.D., PCAWGConsortium, 2020. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications 11, 728. https://doi.org/10.1038/s41467-019-13825-8

Kim-Wanner, S.-Z., Assenov, Y., Nair, M.B., Weichenhan, D., Benner, A., Becker, N., Landwehr, K., Kuner, R., Sültmann, H., Esteller, M., Koch, I., Lindner, M., Meister, M., Thomas, M., Bieg, M., Klingmueller, U., Schlesner, M., Warth, A., Brors, B., Seifried, E., Bonig, H., Plass, C., Risch, A., Muley, T., 2020. Genome-wide DNA methylation profiling in early stage I lung adenocarcinoma reveals predictive aberrant methylation in the promoter region of the long non-coding RNA PLUT - an exploratory study. Journal of Thoracic Oncology 15, 1338–1350. https://doi.org/10.1016/j.jtho.2020.03.023

Kurilov, R., Haibe-Kains, B., Brors, B., 2020. Assessment of modelling strategies for drug response prediction in cell lines and xenografts. Scientific Reports 10, 2849. https://doi.org/10.1038/s41598-020-59656-2

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Bhandari, V., Li, C.H., Bristow, R.G., Boutros, P.C., PCAWGConsortium, 2020. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nature Communications 11, 737. https://doi.org/10.1038/s41467-019-14052-x

Busch, E., Kreutzfeldt, S., Agaimy, A., Mechtersheimer, G., Horak, P., Brors, B., Hutter, B., Fröhlich, M., Uhrig, S., Mayer, P., Schröck, E., Stenzinger, A., Glimm, H., Jäger, D., Springfeld, C., Fröhling, S., Zschäbitz, S., 2020. Successful BRAF/MEK inhibition in a patient with BRAFV600E-mutated extrapancreatic acinar cell carcinoma. Cold Spring Harbor Molecular Case Studies 6, a005553. https://doi.org/10.1101/mcs.a005553

Calabrese, C., Davidson, N.R., Demircioğlu, D., Fonseca, N.A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C.M., Urban, L., Greger, L., Li, S., Liu, D., Perry, M.D., Xiang, Q., Zhang, F., Zhang, J., Bailey, P., Erkek, S., Hoadley, K.A., Hou, Y., Huska, M.R., Kilpinen, H., Korbel, J.O., Marin, M.G., Markowski, J., Nandi, T., Pan-Hammarström, Q., Pedamallu, C.S., Siebert, R., Stark, S.G., Su, H., Tan, P., Waszak, S.M., Yung, C., Zhu, S., Awadalla, P., Creighton, C.J., Meyerson, M., Ouellette, B.F.F., Wu, K., Yang, H., Brazma, A., Brooks, A.N., Göke, J., Rätsch, G., Schwarz, R.F., Stegle, O., Zhang, Z., Calabrese, C., Davidson, N.R., Demircioğlu, D., Fonseca, N.A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C.M., Urban, L., Fonseca, N.A., Kahles, A., Lehmann, K.-V., Urban, L., Soulette, C.M., Shiraishi, Y., Liu, F., He, Y., Demircioğlu, D., Davidson, N.R., Calabrese, C., Zhang, J., Perry, M.D., Xiang, Q., Greger, L., Li, S., Liu, D., Stark, S.G., Zhang, F., Amin, S.B., Bailey, P., Chateigner, A., Cortés-Ciriano, I., Craft, B., Erkek, S., Frenkel-Morgenstern, M., Goldman, M., Hoadley, K.A., Hou, Y., Huska, M.R., Khurana, E., Kilpinen, H., Korbel, J.O., Lamaze, F.C., Li, C., Li, Xiaobo, Li, Xinyue, Liu, X., Marin, M.G., Markowski, J., Nandi, T., Nielsen, M.M., Ojesina, A.I., Pan-Hammarström, Q., Park, P.J., Pedamallu, C.S., Pedersen, J.S., Siebert, R., Su, H., Tan, P., Teh, B.T., Wang, J., Waszak, S.M., Xiong, H., Yakneen, S., Ye, C., Yung, C., Zhang, X., Zheng, L., Zhu, J., Zhu, S., Awadalla, P., Creighton, C.J., Meyerson, M., Ouellette, B.F.F., Wu, K., Yang, H., Göke, J., Schwarz, R.F., Stegle, O., Zhang, Z., Brazma, A., Rätsch, G., Brooks, A.N., 2020. Genomic basis for RNA alterations in cancer. Nature 578, 129–136. https://doi.org/10.1038/s41586-020-1970-0

Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J.S., PCAWGConsortium, 2020. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology 3, 56. https://doi.org/10.1038/s42003-019-0741-7

Cmero, M., Yuan, K., Ong, C.S., Schröder, J., PCAWG, E., Heterogeneity Working, G., Corcoran, N.M., Papenfuss, T., Hovens, C.M., Markowetz, F., Macintyre, G., PCAWGConsortium, 2020. Inferring structural variant cancer cell fraction. Nature Communications 11, 730. https://doi.org/10.1038/s41467-020-14351-8

Cortés-Ciriano, I., Lee, J.J.-K., Xi, R., Jain, D., Jung, Y.L., Yang, L., Gordenin, D., Klimczak, L.J., Zhang, C.-Z., Pellman, D.S., Park, P.J., Akdemir, K.C., Alvarez, E.G., Baez-Ortega, A., Beroukhim, R., Boutros, P.C., Bowtell, D.D.L., Brors, B., Burns, K.H., Campbell, P.J., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A.J., Edwards, P.A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J.L., Frenkel-Morgenstern, M., Garsed, D.W., Gerstein, M., Gordenin, D.A., Haan, D., Haber, J.E., Hess, J.M., Hutter, B., Imielinski, M., Jones, D.T.W., Ju, Y.S., Kazanov, M.D., Klimczak, L.J., Koh, Y., Korbel, J.O., Kumar, K., Lee, E.A., Lee, J.J.-K., Li, Y., Lynch, A.G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F.C.P., Ossowski, S., Park, P.J., Pearson, J.V., Puiggròs, M., Rippe, K., Roberts, N.D., Roberts, S.A., Rodriguez-Martin, B., Schumacher, S.E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Sültmann, H., Torrents, D., Tubio, J.M.C., Villasante, I., Waddell, N., Wala, J.A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S.-S., Zamora, J., Zhang, C.-Z., 2020. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics 52, 331–341. https://doi.org/10.1038/s41588-019-0576-7

 

2019

Delacher, M., Schmidl, C., Herzig, Y., Breloer, M., Hartmann, W., Brunk, F., Kägebein, D., Träger, U., Hofer, A.-C., Bittner, S., Weichenhan, D., Imbusch, C.D., Hotz-Wagenblatt, A., Hielscher, T., Breiling, A., Federico, G., Gröne, H.-J., Schmid, R.M., Rehli, M., Abramson, J., Feuerer, M., 2019. Rbpj expression in regulatory T cells is critical for restraining TH2 responses. Nature Communications 10, 1621. https://doi.org/10.1038/s41467-019-09276-w

Feuerbach, L., Sieverling, L., Deeg, K.I., Ginsbach, P., Hutter, B., Buchhalter, I., Northcott, P.A., Mughal, S.S., Chudasama, P., Glimm, H., Scholl, C., Lichter, P., Fröhling, S., Pfister, S.M., Jones, D.T.W., Rippe, K., Brors, B., 2019. TelomereHunter - in silico estimation of telomere content and composition from cancer genomes. BMC Bioinformatics 20, 272. https://doi.org/10.1186/s12859-019-2851-0

Gröschel, S., Hübschmann, D., Raimondi, F., Horak, P., Warsow, G., Fröhlich, M., Klink, B., Gieldon, L., Hutter, B., Kleinheinz, K., Bonekamp, D., Marschal, O., Chudasama, P., Mika, J., Groth, M., Uhrig, S., Krämer, S., Heining, C., Heilig, C., Richter, D., Reisinger, E., Pfütze, K., Eils, R., Wolf, S., von Kalle, C., Brandts, C., Scholl, C., Weichert, W., Richter, S., Bauer, S., Penzel, R., Schröck, E., Stenzinger, A., Schlenk, R., Brors, B., Russell, R.B., Glimm, H., Schlesner, M., Fröhling, S., 2019. Defective homologous recombination DNA repair as therapeutic target in advanced chordoma. Nature Communications 10, 1635. https://doi.org/10.1038/s41467-019-09633-9

Horak, P., Weischenfeldt, J., von Amsberg, G., Beyer, B., Schütte, 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., Schröck, E., Glimm, H., Fröhling, 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, a003657. https://doi.org/10.1101/mcs.a003657

Hüllein, J., Słabicki, M., Rosolowski, M., Jethwa, A., Habringer, S., Tomska, K., Kurilov, R., Lu, J., Scheinost, S., Wagener, R., Huang, Z., Lukas, M., Yavorska, O., Helfrich, H., Scholtysik, R., Bonneau, K., Tedesco, D., Küppers, R., Klapper, W., Pott, C., Stilgenbauer, S., Burkhardt, B., Löffler, M., Trümper, L.H., Hummel, M., Brors, B., Zapatka, M., Siebert, R., Kreuz, M., Keller, U., Huber, W., Zenz, T., 2019. MDM4 is targeted by 1q gain and drives disease in Burkitt lymphoma. Cancer Research 79, 3125–3138. https://doi.org/10.1158/0008-5472.CAN-18-3438

Leichsenring, J., Horak, P., Kreutzfeldt, S., Heining, C., Christopoulos, P., Volckmar, A.-L., Neumann, O., Kirchner, M., Ploeger, C., Budczies, J., Heilig, C.E., Hutter, B., Fröhlich, M., Uhrig, S., Kazdal, D., Allgäuer, M., Harms, A., Rempel, E., Lehmann, U., Thomas, M., Pfarr, N., Azoitei, N., Bonzheim, I., Marienfeld, R., Möller, P., Werner, M., Fend, F., Boerries, M., von Bubnoff, N., Lassmann, S., Longerich, T., Bitzer, M., Seufferlein, T., Malek, N., Weichert, W., Schirmacher, P., Penzel, R., Endris, V., Brors, B., Klauschen, F., Glimm, H., Fröhling, S., Stenzinger, A., 2019. Variant classification in precision oncology. International Journal of Cancer 145, 2996–3010. https://doi.org/10.1002/ijc.32358

Longerich, T., Endris, V., Neumann, O., Rempel, E., Kirchner, M., Abadi, Z., Uhrig, S., Kriegsmann, M., Weiss, K.H., Breuhahn, K., Mehrabi, A., Weber, T.F., Wilkens, L., Straub, B.K., Rosenwald, A., Schulze, F., Brors, B., Froehling, S., Pellegrino, R., Budczies, J., Schirmacher, P., Stenzinger, A., 2019. RSPO2 gene rearrangement: a powerful driver of β-catenin activation in liver tumours. Gut 68, 1287–1296. https://doi.org/10.1136/gutjnl-2018-317632

López, C., Kleinheinz, K., Aukema, S.M., Rohde, M., Bernhart, S.H., Hübschmann, D., Wagener, R., Toprak, U., 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., Möller, P., Trümper, L., Klapper, W., Hoffmann, S., Küppers, 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-Löffler, 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., 2019. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nature Communications 10, 1459. https://doi.org/10.1038/s41467-019-08578-3

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 15, e8339-. https://doi.org/10.15252/msb.20188339

Mock, A., Heilig, C.E., Kreutzfeldt, S., Huebschmann, D., Heining, C., Schröck, E., Brors, B., Stenzinger, A., Jäger, D., Schlenk, R., Glimm, H., Fröhling, S., Horak, P., Apostolidis, L., Augustin, M., Aust, D., Bhatti, I.A., Bloehdorn, J., Brendel, C., Britschgi, C., Braess, J., Burdach, S., Busch, E., Casuscelli, J., Desuki, A., Deutsch, T., Dietrich, M., Ehmer, U., Ettrich, T.J., Falkenhorst, J., Fehm, T., Flörcken, A., Forschner, A., Fuxius, S., Gonzales-Carmona, M., Griesinger, F., Grill, S., Gröschel, S., Haag, G.M., Haag, U., Halama, N., Hebart, H., Heidger, N., Hermes, B., Hess, G., Hettmer, S., Hoechstetter, M., Hoffmann, M., Hüttner, F.J., Illert, A.L., Jenzer, M., Kasper, B., Kasper-Virchow, S., Kindler, T., Koscielniak, E., Krönke, J., Kühn, M., Kunzmann, V., Lang, A., Leichsenring, J., Livingstone, E., Liotta, L., Luley, K., Mack, E., Martens, U.M., Metzeler, K., Middeke, J.M., Möhrmann, L., Jayarama-Naidu, R., Pape, U.-F., Perkhofer, L., Pfeufer, A., Pixberg, C., Quante, M., Rendenbach, B., Rieke, D., Rothermundt, C., Sagerer, A.N., Salzmann, M., Saur, D., Schilling, B., Schleicher, J., Schlenska-Lange, A., Schmidt, T., Schmitz, S., Schölch, S., Shah, R., Shoumariyeh, K., Siebenhüner, A., Singh, M., Siveke, J., Springfeld, C., Starke, H., Strobel, S., Teleanu, V., Thon, N., Wagner, S., Walle, T., Westphalen, B., Whitlock, B., Winkler, E., Wirsik, N.M., Woydack, L., Bois, A.Z., Zschäbitz, S., 2019a. Community-driven development of a modified progression-free survival ratio for precision oncology. ESMO Open 4, e000583. https://doi.org/10.1136/esmoopen-2019-000583

Mock, A., Rapp, C., Warta, R., Abdollahi, A., Jäger, D., Sakowitz, O., Brors, B., von Deimling, A., Jungk, C., Unterberg, A., Herold-Mende, C., 2019b. Impact of post-surgical freezing delay on brain tumor metabolomics. Metabolomics 15, 78. https://doi.org/10.1007/s11306-019-1541-2

Mühlenberg, T., Ketzer, J., Heinrich, M.C., Grunewald, S., Mariño-Enríquez, A., Trautmann, M., Hartmann, W., Wardelmann, E., Treckmann, J., Worm, K., Bertram, S., Herold, T., Schildhaus, H.-U., Glimm, H., Stenzinger, A., Brors, B., Horak, P., Hohenberger, P., Fröhling, S., Fletcher, J.A., Bauer, S., 2019. KIT-dependent and -independent genomic heterogeneity of resistance in gastrointestinal stromal tumors - TORC1/2 inhibition as salvage strategy. Molecular Cancer Therapeutics 18, 1985–1996. https://doi.org/10.1158/1535-7163.MCT-18-1224

Oduselu, G.O., Ajani, O.O., Ajamma, Y.U., Brors, B., Adebiyi, E.F., 2019. Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor. Bioinformatics and Biology Insights 13, 117793221986553-. https://doi.org/10.1177/1177932219865533

Paramasivam, N., Hübschmann, 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., Werner, J., Uhrig, S., Wirsching, H.-G., Schick, M., Bewerunge-Hudler, M., Beck, K., Brehmer, S., Urbschat, S., Seiz-Rosenhagen, M., Hänggi, 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, 295–308. https://doi.org/10.1007/s00401-019-02008-w

Weichenhan, D., Imbusch, C.D., Wang, Q., Brors, B., Plass, C., 2019. Generation of Whole Genome Bisulfite Sequencing Libraries from Very Low DNA Input. Methods in Molecular Biology 1956, 229–248. https://doi.org/10.1007/978-1-4939-9151-8_10

Wick, W., Dettmer, S., Berberich, A., Kessler, T., Karapanagiotou-Schenkel, I., Wick, A., Winkler, F., Pfaff, E., Brors, B., Debus, J., Unterberg, A., Bendszus, M., Herold-Mende, C., Eisenmenger, A., von Deimling, A., Jones, D., Pfister, S., Sahm, F., Platten, M., 2019. N2M2 (NOA20) phase I/II trial of molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed non-MGMT hypermethylated glioblastoma. Neuro-Oncology 21, 95–105. https://doi.org/10.1093/neuonc/noy161

 

2018

Behjati Ardakani, F., Kattler, K., Nordström, K., Gasparoni, N., Gasparoni, G., Fuchs, S., Sinha, A., Barann, M., Ebert, P., Fischer, J., Hutter, B., Zipprich, G., Imbusch, C.D., Felder, B., Eils, J., Brors, B., Lengauer, T., Manke, T., Rosenstiel, P., Walter, J., Schulz, M.H., 2018. Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. Epigenetics & Chromatin 11, 66. https://doi.org/10.1186/s13072-018-0236-7

Chudasama, P., Mughal, S.S., Sanders, M.A., Hübschmann, D., Chung, I., Deeg, K., 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., Fröhling, S., 2018. Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nature Communications 9, 144. https://doi.org/10.1038/s41467-017-02602-0

Correia, M.P., Stojanovic, A., Bauer, K., Juraeva, D., Tykocinski, L.-O., Lorenz, H.-M., Brors, B., Cerwenka, A., 2018. Distinct human circulating NKp30+FcεRIγ+CD8+ T cell population exhibiting high natural killer-like antitumor potential. Proceedings of the National Academy of Sciences of the United States of America 115, E5980–E5989. https://doi.org/10.1073/pnas.1720564115

Fuchs, K., Cardona Gloria, Y., Wolz, O.-O., Herster, F., Sharma, L., Dillen, C.A., Täumer, C., Dickhöfer, S., Bittner, Z., Dang, T.-M., Singh, A., Haischer, D., Schlöffel, M.A., Koymans, K.J., Sanmuganantham, T., Krach, M., Roger, T., Le Roy, D., Schilling, N.A., Frauhammer, F., Miller, L.S., Nürnberger, T., LeibundGut-Landmann, S., Gust, A.A., Macek, B., Frank, M., Gouttefangeas, C., Dela Cruz, C.S., Hartl, D., Weber, A.N., 2018. The fungal ligand chitin directly binds TLR2 and triggers inflammation dependent on oligomer size. EMBO Reports 19, e201846065-. https://doi.org/10.15252/embr.201846065

Gerhäuser, C., Favero, F., Risch, T., Simon, R., Feuerbach, L., Assenov, Y., Heckmann, D., Sidiropoulos, N., Waszak, S.M., Hübschmann, D., Urbanucci, A., Girma, E.G., Kuryshev, V., Klimczak, L.J., Saini, N., Stütz, A.M., Weichenhan, D., Böttcher, L.-M., Toth, R., Hendriksen, J.D., Koop, C., Lutsik, P., Matzk, S., Warnatz, H.-J., Amstislavskiy, 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.-M., Eils, R., Schlesner, M., Strand, D.W., Bristow, R.G., Boutros, P.C., von Kalle, C., Gordenin, D., Sültmann, 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, 996-1011.e8. https://doi.org/10.1016/j.ccell.2018.10.016

Gröbner, S., Worst, B., Weischenfeldt, J., Buchhalter, I., Kleinheinz, K., Rudneva, V.A., Johann, P., 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., Frühwald, 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., Northcott, P.A., Pajtler, K., Kool, M., Piro, R.M., Korbel, J.O., Schlesner, M., Eils, R., Jones, D., Lichter, P., Chavez, L., Zapatka, M., Pfister, S., 2018. The landscape of genomic alterations across childhood cancers. Nature 555, 321–327. https://doi.org/10.1038/nature25480

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., Jäger, D., Ellenrieder, V., Bergh, B., Yahyapour, R., Eils, R., Consortium, H., Marschollek, M., 2018. HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries. Methods of Information in Medicine 57, e66–e81. https://doi.org/10.3414/ME18-02-0002

Heining, C., Horak, P., Uhrig, S., Codo, P.L., Klink, B., Hutter, B., Fröhlich, M.A., Bonekamp, D., Richter, D., Steiger, K., Penzel, R., Endris, V., Ehrenberg, K.R., Frank, S., Kleinheinz, K., Toprak, U., Schlesner, M., Mandal, R., Schulz, L., Lambertz, H., Fetscher, S., Bitzer, M., Malek, N.P., Horger, M., Giese, N.A., Strobel, O., Hackert, T., Springfeld, C., Feuerbach, L., Bergmann, F., Schröck, E., von Kalle, C., Weichert, W., Scholl, C., Ball, C., Stenzinger, A., Brors, B., Fröhling, S., Glimm, H., 2018. NRG1 Fusions in KRAS Wild-Type Pancreatic Cancer. Cancer Discovery 8, 1087–1095. https://doi.org/10.1158/2159-8290.CD-18-0036

Iorgulescu, J.B., Van Ziffle, J., Stevers, M., Grenert, J.P., Bastian, B.C., Chavez, L., Stichel, D., Buchhalter, I., Samuel, D., Nicolaides, T., Banerjee, A., Mueller, S., Gupta, N., Tihan, T., Bollen, A.W., Northcott, P.A., Kool, M., Pfister, S., Korshunov, A., Perry, A., Solomon, D.A., 2018. Deep sequencing of WNT-activated medulloblastomas reveals secondary SHH pathway activation. Acta Neuropathologica 135, 635–638. https://doi.org/10.1007/s00401-018-1819-x

Ishaque, N., Abba, M.L., Hauser, C., Patil, N., Paramasivam, N., Huebschmann, D., Leupold, J.H., Balasubramanian, G.P., Kleinheinz, K., Toprak, U., 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, 4782. https://doi.org/10.1038/s41467-018-07041-z

Jian, Z., Cheng, T., Zhang, Z., Raulefs, S., Shi, K., Steiger, K., Maeritz, N., Kleigrewe, K., Hofmann, T., Benitz, S., Bruns, P.E., Lamp, D., Jastroch, M., Akkan, J., Jäger, C., Huang, P., Nie, S., Shen, S., Zou, X., Ceyhan, G.O., Michalski, C.W., Friess, H., Kleeff, J., Kong, B., 2018. Glycemic Variability Promotes Both Local Invasion and Metastatic Colonization by Pancreatic Ductal Adenocarcinoma. Cellular and Molecular Gastroenterology and Hepatology 6, 429–449. https://doi.org/10.1016/j.jcmgh.2018.07.003

Lier, A., Penzel, R., Heining, C., Horak, P., Fröhlich, M., Uhrig, S., Budczies, J., Kirchner, M., Volckmar, A.-L., Hutter, B., Kreutzfeldt, S., Endris, V., Richter, D., Wolf, S., Pfütze, K., Neumann, O., Buchhalter, I., Morais de Oliveira, C.M., Singer, S., Leichsenring, J., Herpel, E., Klauschen, F., Jost, P.J., Metzeler, K.H., Schulze-Osthoff, K., Kopp, H.-G., Kindler, T., Rieke, D.T., Lamping, M., Brandts, C., Falkenhorst, J., Bauer, S., Schröck, E., Folprecht, G., Boerries, M., von Bubnoff, N., Weichert, W., Brors, B., Lichter, P., von Kalle, C., Schirmacher, P., Glimm, H., Fröhling, S., Stenzinger, A., 2018. Validating Comprehensive Next-Generation Sequencing Results for Precision Oncology: The NCT/DKTK Molecularly Aided Stratification for Tumor Eradication Research Experience. JCO Precision Oncology 2, 1–13. https://doi.org/10.1200/PO.18.00171

Mock, A., Warta, R., Dettling, S., Brors, B., Jäger, D., Herold-Mende, C., 2018. MetaboDiff: an R package for differential metabolomic analysis. Bioinformatics 34, 3417–3418. https://doi.org/10.1093/bioinformatics/bty344

Perera-Bel, J., Hutter, B., Heining, C., Bleckmann, A., Fröhlich, M.A., Fröhling, S., Glimm, H., Brors, B., Beißbarth, T., 2018. From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Medicine 10, 18. https://doi.org/10.1186/s13073-018-0529-2

Pfaff, E., Kessler, T., Balasubramanian, G.P., Berberich, A., Schrimpf, D., Wick, A., Debus, J., Unterberg, A., Bendszus, M., Herold-Mende, C., Capper, D., Schenkel, I., Eisenmenger, A., Dettmer, S., Brors, B., Platten, M., Pfister, S., von Deimling, A., Jones, D., Wick, W., Sahm, F., 2018. Feasibility of real-time molecular profiling for patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation-the NCT Neuro Master Match (N2M2) pilot study. Neuro-Oncology 20, 826–837. https://doi.org/10.1093/neuonc/nox216

Robinson, G.W., Rudneva, V.A., Buchhalter, I., Billups, C.A., Waszak, S.M., Smith, K.S., Bowers, D.C., Bendel, A., Fisher, P.G., Partap, S., Crawford, J.R., Hassall, T., Indelicato, D.J., Boop, F., Klimo, P., Sabin, N.D., Patay, Z., Merchant, T.E., Stewart, C.F., Orr, B.A., Korbel, J.O., Jones, D., Sharma, T., Lichter, P., Kool, M., Korshunov, A., Pfister, S., Gilbertson, R.J., Sanders, R.P., Onar-Thomas, A., Ellison, D.W., Gajjar, A., Northcott, P.A., 2018. Risk-adapted therapy for young children with medulloblastoma (SJYC07): therapeutic and molecular outcomes from a multicentre, phase 2 trial. The Lancet Oncology 19, 768–784. https://doi.org/10.1016/S1470-2045(18)30204-3

Rodríguez-Paredes, M., Bormann, F., Raddatz, G., Gutekunst, J., Lucena-Porcel, C., Köhler, F., Wurzer, E., Schmidt, K., Gallinat, S., Wenck, H., Röwert-Huber, J., Denisova, E., Feuerbach, L., Park, J., Brors, B., Herpel, E., Nindl, I., Hofmann, T., Winnefeld, M., Lyko, F., 2018. Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin. Nature Communications 9, 577. https://doi.org/10.1038/s41467-018-03025-1

Terziev, D., Hutter, B., Klink, B., Stenzinger, A., Stögbauer, F., Glimm, H., Fröhling, S., Wickenhauser, C., Jordan, K., Hurtz, H.-J., Müller, L.P., Rüssel, J., Weber, T., 2018. Nivolumab maintenance after salvage autologous stem cell transplantation results in long-term remission in multiple relapsed primary CNS lymphoma. European Journal of Haematology 101, 115–118. https://doi.org/10.1111/ejh.13072

Tomska, K., Kurilov, R., Lee, K.S., Hüllein, J., Lukas, M., Sellner, L., Walther, T., Wagner, L., Oleś, M., Brors, B., Huber, W., Zenz, T., 2018. Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma. Scientific Reports 8, 12046. https://doi.org/10.1038/s41598-018-30509-3

Waszak, S.M., Northcott, P.A., Buchhalter, I., Robinson, G.W., Sutter, C., Groebner, S., Grund, K.B., Brugières, L., Jones, D., Pajtler, K., 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., Hernáiz Driever, P., 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., Schüz, J., Johansen, C., Andersen, T.V., Röösli, 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., 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., 2018. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. The Lancet Oncology 19, 785–798. https://doi.org/10.1016/S1470-2045(18)30242-0

Zorea, J., Prasad, M., Cohen, L., Li, N., Schefzik, R., Ghosh, S., Rotblat, B., Brors, B., Elkabets, M., 2018. IGF1R upregulation confers resistance to isoform-specific inhibitors of PI3K in PIK3CA-driven ovarian cancer. Cell Death & Disease 9, 944. https://doi.org/10.1038/s41419-018-1025-8

 

2017

Ball, C., Oppel, F., Ehrenberg, K.R., Dubash, T.D., Dieter, S., Hoffmann, C.M., Abel, U., Herbst, F., Koch, M., Werner, J., Bergmann, F., Ishaque, N., Schmidt, M., von Kalle, C., Scholl, C., Fröhling, S., Brors, B., Weichert, W., Weitz, J., Glimm, H., 2017. Succession of transiently active tumor-initiating cell clones in human pancreatic cancer xenografts. EMBO Molecular Medicine 9, 918–932. https://doi.org/10.15252/emmm.201607354

Brocks, D., Schmidt, C.R., Daskalakis, M., Jang, H.S., Shah, N.M., Li, D., Li, J., Zhang, B., Hou, Y., Laudato, S., Lipka, D., Schott, J., Bierhoff, H., Assenov, Y., Helf, M., Ressnerova, A., Islam, M.S., Lindroth, A.M., Haas, S., Essers, M., Imbusch, C.D., Brors, B., Oehme, I., Witt, O., Lübbert, M., Mallm, J.-P., Rippe, K., Will, R., Weichenhan, D., Stoecklin, G., Gerhäuser, C., Oakes, C.C., Wang, T., Plass, C., 2017. DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nature Genetics 49, 1052–1060. https://doi.org/10.1038/ng.3889

Budczies, J., Mechtersheimer, G., Denkert, C., Klauschen, F., Mughal, S.S., Chudasama, P., Bockmayr, M., Jöhrens, K., Endris, V., Lier, A., Lasitschka, F., Penzel, R., Dietel, M., Brors, B., Gröschel, S., Glimm, H., Schirmacher, P., Renner, M., Fröhling, S., Stenzinger, A., 2017. PD-L1 (CD274) copy number gain, expression, and immune cell infiltration as candidate predictors for response to immune checkpoint inhibitors in soft-tissue sarcoma. OncoImmunology 6, e1279777-. https://doi.org/10.1080/2162402X.2017.1279777

Chudasama, P., Renner, M., Straub, M., Mughal, S.S., Hutter, B., Kosaloglu-Yalcin, Z., Schweßinger, R., Scheffler, M., Alldinger, I., Schimmack, S., Persigehl, T., Kobe, C., Jäger, D., von Kalle, C., Schirmacher, P., Beckhaus, M.-K., Wolf, S., Heining, C., Gröschel, S., Wolf, J., Brors, B., Weichert, W., Glimm, H., Scholl, C., Mechtersheimer, G., Specht, K., Fröhling, S., 2017. Targeting Fibroblast Growth Factor Receptor 1 for Treatment of Soft-Tissue Sarcoma. Clinical Cancer Research 23, 962–973. https://doi.org/10.1158/1078-0432.CCR-16-0860

Czink, E., Kloor, M., Goeppert, B., Fröhling, S., Uhrig, S., Weber, T.F., Meinel, J., Sutter, C., Weiss, K.H., Schirmacher, P., von Knebel Doeberitz, M., Jäger, D., Springfeld, C., 2017. Successful immune checkpoint blockade in a patient with advanced stage microsatellite-unstable biliary tract cancer. Cold Spring Harbor Molecular Case Studies 3, a001974-. https://doi.org/10.1101/mcs.a001974

Delacher, M., Imbusch, C.D., Weichenhan, D., Breiling, A., Hotz-Wagenblatt, A., Träger, U., Hofer, A.-C., Kägebein, D., Wang, Q., Frauhammer, F., Mallm, J.-P., Bauer, K., Herrmann, C., Lang, P.A., Brors, B., Plass, C., Feuerer, M., 2017. Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. Nature Immunology 18, 1160–1172. https://doi.org/10.1038/ni.3799

Dieter, S., Giessler, K., Kriegsmann, M., Dubash, T.D., Möhrmann, L., Schulz, E., Siegl, C., Weber, S., Strakerjahn, H., Oberlack, A., Heger, U., Gao, J., Hartinger, E.-M., Oppel, F., Hoffmann, C.M., Ha, N., Brors, B., Lasitschka, F., Ulrich, A., Strobel, O., Schmidt, M., von Kalle, C., Schneider, M., Weichert, W., Ehrenberg, K.R., Glimm, H., Ball, C., 2017a. Patient-derived xenografts of gastrointestinal cancers are susceptible to rapid and delayed B-lymphoproliferation. International Journal of Cancer 140, 1356–1363. https://doi.org/10.1002/ijc.30561

Dieter, S., Heining, C., Agaimy, A., Huebschmann, D., Bonekamp, D., Hutter, B., Ehrenberg, K.R., Fröhlich, M., Schlesner, M., Scholl, C., Schlemmer, H.-P., Wolf, S., Mavratzas, A., Jung, C.S., Gröschel, 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., Fröhling, S., 2017b. Mutant KIT as imatinib-sensitive target in metastatic sinonasal carcinoma. Annals of Oncology 28, 142–148. https://doi.org/10.1093/annonc/mdw446

Forschner, A., Niessner, H., Möller, Y., Horak, P., Fröhlich, M.A., Warsow, G., Stenzinger, A., Fröhling, S., Glimm, H., Klumpp, B., Garbe, C., Sinnberg, T., 2017. Genomics of Immunotherapy-Associated Hyperprogressors-Letter. Clinical Cancer Research 23, 6374–6375. https://doi.org/10.1158/1078-0432.CCR-17-1480

Giessler, K., 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., Fröhling, 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, 2073–2088. https://doi.org/10.1084/jem.20162017

Horak, P., Klink, B., Heining, C., Gröschel, S., Hutter, B., Fröhlich, M.A., 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, R., Schröck, E., Brors, B., von Kalle, C., Glimm, H., Fröhling, S., 2017. Precision oncology based on omics data: The NCT Heidelberg experience. International Journal of Cancer 141, 877–886. https://doi.org/10.1002/ijc.30828

Hoßfeld, U., Jacobsen, H.-J., Plass, C., Brors, B., Wackernagel, W., 2017. 150 years of Johann Gregor Mendel’s “Versuche über Pflanzen-Hybriden”. Molecular Genetics and Genomics 292, 1–3. https://doi.org/10.1007/s00438-016-1254-4

Linhart, H., Bormann, F., Hutter, B., Brors, B., Lyko, F., 2017. Genetic and epigenetic profiling of a solitary Peutz-Jeghers colon polyp. Cold Spring Harbor Molecular Case Studies 3, a001610. https://doi.org/10.1101/mcs.a001610

Michel, C., Miller, C.N., Küchler, R., Brors, B., Anderson, M.S., Kyewski, B., Pinto, S., 2017. Revisiting the Road Map of Medullary Thymic Epithelial Cell Differentiation. The Journal of Immunology 199, 3488–3503. https://doi.org/10.4049/jimmunol.1700203

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., Worst, B., 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., 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., Taylor, M.D., Lichter, P., 2017. The whole-genome landscape of medulloblastoma subtypes. Nature 547, 311–317. https://doi.org/10.1038/nature22973

Schmidt, F., Gasparoni, N., Gasparoni, G., Gianmoena, K., Cadenas, C., Polansky, J.K., Ebert, P., Nordström, K., Barann, M., Sinha, A., Fröhler, S., Xiong, J., Dehghani Amirabad, A., Behjati Ardakani, F., Hutter, B., Zipprich, G., Felder, B., Eils, J., Brors, B., Chen, W., Hengstler, J.G., Hamann, A., Lengauer, T., Rosenstiel, P., Walter, J., Schulz, M.H., 2017. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. Nucleic Acids Research 45, 54–66. https://doi.org/10.1093/nar/gkw1061

Treutlein, J., Frank, J., Streit, F., Reinbold, C.S., Juraeva, D., Degenhardt, F., Rietschel, L., Witt, S.H., Forstner, A.J., Ridinger, M., Strohmaier, J., Wodarz, N., Dukal, H., Foo, J.C., Hoffmann, P., Herms, S., Heilmann-Heimbach, S., Soyka, M., Maier, W., Gaebel, W., Dahmen, N., Scherbaum, N., Müller-Myhsok, B., Lucae, S., Ising, M., Stickel, F., Berg, T., Roggenbuck, U., Jöckel, K.-H., Scholz, H., Zimmermann, U.S., Buch, S., Sommer, W.H., Spanagel, R., Brors, B., Cichon, S., Mann, K., Kiefer, F., Hampe, J., Rosendahl, J., Nöthen, M.M., Rietschel, M., 2017. Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis. Genes 8, 183. https://doi.org/10.3390/genes8070183

 

2016

Bender, S., Gronych, J., Warnatz, H.-J., Hutter, B., Gröbner, S., Ryzhova, M., Pfaff, E., Hovestadt, V., Weinberg, F., Halbach, S., Kool, M., Northcott, P.A., Sturm, D., Bjerke, L., Zichner, T., Stütz, 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., Brahim, D.H.-B., Trabelsi, S., Ng, H.-K., Zagzag, D., Allen, J.C., Karajannis, M.A., Gottardo, N.G., Jones, C., Korbel, J.O., 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., Lichter, P., Jones, D., 2016. Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nature Medicine 22, 1314–1320. https://doi.org/10.1038/nm.4204

Czink, E., Heining, C., Weber, T.F., Lasitschka, F., Schemmer, P., Schirmacher, P., Weiss, K.H., Glimm, H., Brors, B., Weichert, W., Jäger, D., Fröhling, S., Springfeld, C., 2016. [Durable remission under dual HER2 blockade with Trastuzumab and Pertuzumab in a patient with metastatic gallbladder cancer]. Zeitschrift für Gastroenterologie 54, 426–430. https://doi.org/10.1055/s-0042-103498

Durek, P., Nordström, K., Gasparoni, G., Salhab, A., Kressler, C., de Almeida, M., Bassler, K., Ulas, T., Schmidt, F., Xiong, J., Glažar, P., Klironomos, F., Sinha, A., Kinkley, S., Yang, X., Arrigoni, L., Amirabad, A.D., Ardakani, F.B., Feuerbach, L., Gorka, O., Ebert, P., Müller, F., Li, N., Frischbutter, S., Schlickeiser, S., Cendon, C., Fröhler, S., Felder, B., Gasparoni, N., Imbusch, C.D., Hutter, B., Zipprich, G., Tauchmann, Y., Reinke, S., Wassilew, G., Hoffmann, U., Richter, A.S., Sieverling, L., Chang, H.-D., Syrbe, U., Kalus, U., Eils, J., Brors, B., Manke, T., Ruland, J., Lengauer, T., Rajewsky, N., Chen, W., Dong, J., Sawitzki, B., Chung, H.-R., Rosenstiel, P., Schulz, M.H., Schultze, J.L., Radbruch, A., Walter, J., Hamann, A., Polansky, J.K., 2016. Epigenomic Profiling of Human CD4(+) T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity 45, 1148–1161. https://doi.org/10.1016/j.immuni.2016.10.022

Hezaveh, K., Kloetgen, A., Bernhart, S.H., Mahapatra, K.D., 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., Küppers, R., Lawerenz, C., Leich, E., Loeffler, M., Mantovani-Loeffler, L., López, C., McHardy, A.C., Möller, P., Rohde, M., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schlesner, M., Scholz, I., Stadler, P.F., Stilgenbauer, S., Sungalee, S., Szczepanowski, M., Trümper, L., Weniger, M.A., Siebert, R., Borkhardt, A., Hummel, M., Hoell, J.I., 2016. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica 101, 1380–1389. https://doi.org/10.3324/haematol.2016.143891

Kordes, M., Röring, M., Heining, C., Braun, S., Hutter, B., Richter, D., Geörg, C., Scholl, C., Gröschel, S., Roth, W., Rosenwald, A., Geissinger, E., von Kalle, C., Jäger, D., Brors, B., Weichert, W., Grüllich, C., Glimm, H., Brummer, T., Fröhling, S., 2016. Cooperation of BRAF(F595L) and mutant HRAS in histiocytic sarcoma provides new insights into oncogenic BRAF signaling. Leukemia 30, 937–946. https://doi.org/10.1038/leu.2015.319

Lang, M., Leménager, T., Streit, F., Fauth-Bühler, M., Frank, J., Juraeva, D., Witt, S.H., Degenhardt, F., Hofmann, A., Heilmann-Heimbach, S., Kiefer, F., Brors, B., Grabe, H.-J., John, U., Bischof, A., Bischof, G., Völker, U., Homuth, G., Beutel, M., Lind, P.A., Medland, S.E., Slutske, W.S., Martin, N.G., Völzke, H., Nöthen, M.M., Meyer, C., Rumpf, H.-J., Wurst, F.M., Rietschel, M., Mann, K.F., 2016. Genome-wide association study of pathological gambling. European Psychiatry 36, 38–46. https://doi.org/10.1016/j.eurpsy.2016.04.001

Oakes, C.C., Seifert, M., Assenov, Y., Gu, L., Przekopowitz, M., Ruppert, A.S., Wang, Q., Imbusch, C.D., Serva, A., Koser, S., Brocks, D., Lipka, D., Bogatyrova, O., Weichenhan, D., Brors, B., Rassenti, L., Kipps, T.J., Mertens, D., Zapatka, M., Lichter, P., Döhner, H., Küppers, R., Zenz, T., Stilgenbauer, S., Byrd, J.C., Plass, C., 2016. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nature Genetics 48, 253–264. https://doi.org/10.1038/ng.3488

Rattay, K., Meyer, H.V., Herrmann, C., Brors, B., Kyewski, B., 2016. Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells. Journal of Autoimmunity 67, 65–75. https://doi.org/10.1016/j.jaut.2015.10.001

Sahm, F., Schrimpf, D., Jones, D., Meyer, J., Kratz, A., Reuss, D., Capper, D., Koelsche, C., Korshunov, A., Wiestler, B.P.O., Buchhalter, I., Milde, T., Selt, F., Sturm, D., Kool, M., Hummel, M., Bewerunge-Hudler, M., Mawrin, C., Schüller, U., Jungk, C., Wick, A., Witt, O., Platten, M., Herold-Mende, C., Unterberg, A., Pfister, S., Wick, W., von Deimling, A., 2016. Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets. Acta Neuropathologica 131, 903–910. https://doi.org/10.1007/s00401-015-1519-8

Stunnenberg, H.G., Hirst, M., Abrignani, S., Adams, D., de Almeida, M., Altucci, L., Amin, V., Amit, I., Antonarakis, S.E., Aparicio, S., Arima, T., Arrigoni, L., Arts, R., Asnafi, V., Esteller, M., Bae, J.-B., Bassler, K., Beck, S., Berkman, B., Bernstein, B.E., Bilenky, M., Bird, A., Bock, C., Boehm, B., Bourque, G., Breeze, C.E., Brors, B., Bujold, D., Burren, O., Bussemakers, M.J., Butterworth, A., Campo, E., Carrillo-de-Santa-Pau, E., Chadwick, L., Chan, K.M., Chen, W., Cheung, T.H., Chiapperino, L., Choi, N.H., Chung, H.-R., Clarke, L., Connors, J.M., Cronet, P., Danesh, J., Dermitzakis, M., Drewes, G., Durek, P., Dyke, S., Dylag, T., Eaves, C.J., Ebert, P., Eils, R., Eils, J., Ennis, C.A., Enver, T., Feingold, E.A., Felder, B., Ferguson-Smith, A., Fitzgibbon, J., Flicek, P., Foo, R.S.-Y., Fraser, P., Frontini, M., Furlong, E., Gakkhar, S., Gasparoni, N., Gasparoni, G., Geschwind, D.H., Glažar, P., Graf, T., Grosveld, F., Guan, X.-Y., Guigo, R., Gut, I.G., Hamann, A., Han, B.-G., Harris, R.A., Heath, S., Helin, K., Hengstler, J.G., Heravi-Moussavi, A., Herrup, K., Hill, S., Hilton, J.A., Hitz, B.C., Horsthemke, B., Hu, M., Hwang, J.-Y., Ip, N.Y., Ito, T., Javierre, B.-M., Jenko, S., Jenuwein, T., Joly, Y., Jones, S.J.M., Kanai, Y., Kang, H.G., Karsan, A., Kiemer, A.K., Kim, S.C., Kim, B.-J., Kim, H.-H., Kimura, H., Kinkley, S., Klironomos, F., Koh, I.-U., Kostadima, M., Kressler, C., Kreuzhuber, R., Kundaje, A., Küppers, R., Larabell, C., Lasko, P., Lathrop, M., Lee, D.H.S., Lee, S., Lehrach, H., Leitão, E., Lengauer, T., Lernmark, Å., Leslie, R.D., Leung, G.K.K., Leung, D., Loeffler, M., Ma, Y., Mai, A., Manke, T., Marcotte, E.R., Marra, M.A., Martens, J.H.A., Martin-Subero, J.I., Maschke, K., Merten, C., Milosavljevic, A., Minucci, S., Mitsuyama, T., Moore, R.A., Müller, F., Mungall, A.J., Netea, M.G., Nordström, K., Norstedt, I., Okae, H., Onuchic, V., Ouellette, F., Ouwehand, W., Pagani, M., Pancaldi, V., Pap, T., Pastinen, T., Patel, R., Paul, D.S., Pazin, M.J., Pelicci, P.G., Phillips, A.G., Polansky, J., Porse, B., Pospisilik, J.A., Prabhakar, S., Procaccini, D.C., Radbruch, A., Rajewsky, N., Rakyan, V., Reik, W., Ren, B., Richardson, D., Richter, A., Rico, D., Roberts, D.J., Rosenstiel, P., Rothstein, M., Salhab, A., Sasaki, H., Satterlee, J.S., Sauer, S., Schacht, C., Schmidt, F., Schmitz, G., Schreiber, S., Schröder, C., Schübeler, D., Schultze, J.L., Schulyer, R.P., Schulz, M., Seifert, M., Shirahige, K., Siebert, R., Sierocinski, T., Siminoff, L., Sinha, A., Soranzo, N., Spicuglia, S., Spivakov, M., Steidl, C., Strattan, J.S., Stratton, M., Südbeck, P., Sun, H., Suzuki, N., Suzuki, Y., Tanay, A., Torrents, D., Tyson, F.L., Ulas, T., Ullrich, S., Ushijima, T., Valencia, A., Vellenga, E., Vingron, M., Wallace, C., Wallner, S., Walter, J., Wang, H., Weber, S., Weiler, N., Weller, A., Weng, A., Wilder, S., Wiseman, S.M., Wu, A.R., Wu, Z., Xiong, J., Yamashita, Y., Yang, X., Yap, D.Y., Yip, K.Y., Yip, S., Yoo, J.-I., Zerbino, D., Zipprich, G., 2016. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell 167, 1145–1149. https://doi.org/10.1016/j.cell.2016.11.007

Suryawanshi, V., Talke, I.N., Weber, M., Eils, R., Brors, B., Clemens, S., Krämer, U., 2016. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genomics 17, 1034. https://doi.org/10.1186/s12864-016-3319-5

Wallner, S., Schröder, C., Leitão, E., Berulava, T., Haak, C., Beißer, D., Rahmann, S., Richter, A.S., Manke, T., Bönisch, U., Arrigoni, L., Fröhler, S., Klironomos, F., Chen, W., Rajewsky, N., Müller, F., Ebert, P., Lengauer, T., Barann, M., Rosenstiel, P., Gasparoni, G., Nordström, K., Walter, J., Brors, B., Zipprich, G., Felder, B., Klein-Hitpass, L., Attenberger, C., Schmitz, G., Horsthemke, B., 2016. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics & Chromatin 9, 33. https://doi.org/10.1186/s13072-016-0079-z

Wang, Q., Satomi, K., Oh, J.E., Hutter, B., Brors, B., Diessl, N., Liu, H.-K., Wolf, S., Wiestler, O., Kleihues, P., Koelsch, B., Kindler-Röhrborn, A., Ohgaki, H., 2016. Braf Mutations Initiate the Development of Rat Gliomas Induced by Postnatal Exposure to N-Ethyl-N-Nitrosourea. The American Journal of Pathology 186, 2569–2576. https://doi.org/10.1016/j.ajpath.2016.05.024

 

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., Jäger, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C., Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Gröbner, 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, V., Valdés-Mas, R., Nakken, S., Vodák, D., Bower, L., Lynch, A.G., Anderson, C.L., Waddell, N., Pearson, J.V., Grimmond, S.M., Peto, M., Spellman, P., He, M., Kandoth, C., Lee, S., Zhang, J., Létourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D.A., López-Otín, C., Campo, E., Campbell, P.J., Boutros, P.C., Puente, X.S., Gerhard, D.S., Pfister, S., McPherson, J.D., Hudson, T.J., Schlesner, M., Lichter, P., Eils, R., Jones, D., Gut, I.G., 2015. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications 6, 10001. https://doi.org/10.1038/ncomms10001

Dietrich, S., Hüllein, J., Lee, S.C.-W., Hutter, B., Gonzalez, D., Jayne, S., Dyer, M.J.S., Oleś, M., Else, M., Liu, X., Słabicki, M., Wu, B., Troussard, X., Dürig, J., Andrulis, M., Dearden, C., von Kalle, C., Granzow, M., Jauch, A., Fröhling, S., Huber, W., Meggendorfer, M., Haferlach, T., Ho, A.D., Richter, D., Brors, B., Glimm, H., Matutes, E., Abdel Wahab, O., Zenz, T., 2015. Recurrent CDKN1B (p27) mutations in hairy cell leukemia. Blood 126, 1005–1008. https://doi.org/10.1182/blood-2015-04-643361

Fontebasso, A.M., Shirinian, M., Khuong-Quang, D.-A., Bechet, D., Gayden, T., Kool, M., De Jay, N., Jacob, K., Gerges, N., Hutter, B., Şeker-Cin, H., Witt, H., Montpetit, A., Brunet, S., Lepage, P., Bourret, G., Klekner, A., Bognár, L., Hauser, P., Garami, M., Farmer, J.-P., Montes, J.-L., Atkinson, J., Lambert, S., Kwan, T., Korshunov, A., Tabori, U., Collins, V.P., Albrecht, S., Faury, D., Pfister, S., Paulus, W., Hasselblatt, M., Jones, D., Jabado, N., 2015. Non-random aneuploidy specifies subgroups of pilocytic astrocytoma and correlates with older age. OncoTarget 6, 31844–31856. https://doi.org/10.18632/oncotarget.5571

Geisenberger, C., Mock, A., Warta, R., Rapp, C., Schwager, C., Korshunov, A., Nied, A.-K., Capper, D., Brors, B., Jungk, C., Jones, D., Collins, V.P., Ichimura, K., Bäcklund, L.M., Schnabel, E., Mittelbron, M., Lahrmann, B., Zheng, S., Verhaak, R.G.W., Grabe, N., Pfister, S., Hartmann, C., von Deimling, A., Debus, J., Unterberg, A., Abdollahi, A., Herold-Mende, C., 2015. Molecular profiling of long-term survivors identifies a subgroup of glioblastoma characterized by chromosome 19/20 co-gain. Acta Neuropathologica 130, 419–434. https://doi.org/10.1007/s00401-015-1427-y

Gu, L., Frommel, S.C., Oakes, C.C., Simon, R., Grupp, K., Gerig, C.Y., Bär, D., Robinson, M.D., Baer, C., Weiss, M., Gu, Z., Schapira, M., Kuner, R., Sültmann, H., Provenzano, M., Yaspo, M.-L., Brors, B., Korbel, J., Schlomm, T., Sauter, G., Eils, R., Plass, C., Santoro, R., 2015. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature Genetics 47, 22–30. https://doi.org/10.1038/ng.3165

Haller, F., Bieg, M., Moskalev, E.A., Barthelmeß, S., Geddert, H., Boltze, C., Diessl, N., Braumandl, K., Brors, B., Iro, H., Hartmann, A., Wiemann, S., Agaimy, A., 2015. Recurrent mutations within the amino-terminal region of β-catenin are probable key molecular driver events in sinonasal hemangiopericytoma. The American Journal of Pathology 185, 563–571. https://doi.org/10.1016/j.ajpath.2014.10.019

Isewon, I., Oyelade, J., Brors, B., Adebiyi, E., 2015. In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum. Evolutionary Bioinformatics 11, 231–238. https://doi.org/10.4137/EBO.S25585

Juraeva, D., Treutlein, J., Scholz, H., Frank, J., Degenhardt, F., Cichon, S., Ridinger, M., Mattheisen, M., Witt, S.H., Lang, M., Sommer, W.H., Hoffmann, P., Herms, S., Wodarz, N., Soyka, M., Zill, P., Maier, W., Jünger, E., Gaebel, W., Dahmen, N., Scherbaum, N., Schmäl, C., Steffens, M., Lucae, S., Ising, M., Smolka, M.N., Zimmermann, U.S., Müller-Myhsok, B., Nöthen, M.M., Mann, K., Kiefer, F., Spanagel, R., Brors, B., Rietschel, M., 2015. XRCC5 as a risk gene for alcohol dependence: evidence from a genome-wide gene-set-based analysis and follow-up studies in Drosophila and humans. Neuropsychopharmacology 40, 361–371. https://doi.org/10.1038/npp.2014.178

Künstlinger, H., Fassunke, J., Schildhaus, H.-U., Brors, B., Heydt, C., Ihle, M.A., Mechtersheimer, G., Wardelmann, E., Büttner, R., Merkelbach-Bruse, S., 2015. FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro. OncoTarget 6, 20215–20230. https://doi.org/10.18632/oncotarget.4046

Lau, D.T., Flemming, C.L., Gherardi, S., Perini, G., Oberthuer, A., Fischer, M., Juraeva, D., Brors, B., Xue, C., Norris, M.D., Marshall, G.M., Haber, M., Fletcher, J.I., Ashton, L.J., 2015. MYCN amplification confers enhanced folate dependence and methotrexate sensitivity in neuroblastoma. OncoTarget 6, 15510–15523. https://doi.org/10.18632/oncotarget.3732

Mudduluru, G., Abba, M.L., Batliner, J., Patil, N.S., Scharp, M., Lunavat, T.R., Leupold, J.H., Oleksiuk, O., Juraeva, D., Thiele, W., Rothley, M., Benner, A., Ben-Neriah, Y., Sleeman, J., Allgayer, H., 2015. A Systematic Approach to Defining the microRNA Landscape in Metastasis. Cancer Research 75, 3010–3019. https://doi.org/10.1158/0008-5472.CAN-15-0997

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., Bénard, J., Valent, A., Avigad, S., Yaniv, I., Grundy, R.G., Ortmann, M., Shao, C., 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, 1904–1915. https://doi.org/10.1158/1078-0432.CCR-14-0817

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., Jücker, M., Eils, R., Fehm, T., Trumpp, A., Johnsen, S.A., Klefström, J., Wilmanns, M., Müller, V., Pantel, K., Wikman, H., 2015a. Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic Acid-induced 2. Cancer Discovery 5, 506–519. https://doi.org/10.1158/2159-8290.CD-14-1042

Werner, S., Stamm, H., Pandjaitan, M., Kemming, D., Brors, B., Pantel, K., Wikman, H., 2015b. Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells. BMC Cancer 15, 896. https://doi.org/10.1186/s12885-015-1907-4

Yamano, T., Nedjic, J., Hinterberger, M., Steinert, M., Koser, S., Pinto, S., Gerdes, N., Lutgens, E., Ishimaru, N., Busslinger, M., Brors, B., Kyewski, B., Klein, L., 2015. Thymic B Cells Are Licensed to Present Self Antigens for Central T Cell Tolerance Induction. Immunity 42, 1048–1061. https://doi.org/10.1016/j.immuni.2015.05.013

Zhang, Wenqian, Yu, Y., Hertwig, F., Thierry-Mieg, J., Zhang, Wenwei, Thierry-Mieg, D., Wang, Jian, Furlanello, C., Devanarayan, V., Cheng, J., Deng, Y., Hero, B., Hong, H., Jia, M., Li, L., Lin, S.M., Nikolsky, Y., Oberthuer, A., Qing, T., Su, Z., Volland, R., Wang, C., Wang, M.D., Ai, J., Albanese, D., Asgharzadeh, S., Avigad, S., Bao, W., Bessarabova, M., Brilliant, M.H., Brors, B., Chierici, M., Chu, T.-M., Zhang, J., Grundy, R.G., He, M.M., Hebbring, S., Kaufman, H.L., Lababidi, S., Lancashire, L.J., Li, Y., Lu, X.X., Luo, H., Ma, X., Ning, B., Noguera, R., Peifer, M., Phan, J.H., Roels, F., Rosswog, C., Shao, S., Shen, J., Theissen, J., Tonini, G.P., Vandesompele, J., Wu, P.-Y., Xiao, W., Xu, J., Xu, W., Xuan, J., Yang, Y., Ye, Z., Dong, Z., Zhang, K.K., Yin, Y., Zhao, C., Zheng, Y., Wolfinger, R.D., Shi, T., Malkas, L.H., Berthold, F., Wang, Jun, Tong, W., Shi, L., Peng, Z., Fischer, M., 2015. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biology 16, 133. https://doi.org/10.1186/s13059-015-0694-1

 

2014

Brocks, D., Assenov, Y., Minner, S., Bogatyrova, O., Simon, R., Koop, C., Oakes, C., Zucknick, M., Lipka, D., Weischenfeldt, J., Feuerbach, L., Cowper-Sal Lari, R., Lupien, M., Brors, B., Korbel, J., Schlomm, T., Tanay, A., Sauter, G., Gerhäuser, C., Plass, C., Project, I.E.O.P.C., 2014. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer.080. Cell Reports 8, 798–806. https://doi.org/10.1016/j.celrep.2014.06.053

Cabezas-Wallscheid, N., Klimmeck, D., Hansson, J., Lipka, D., Reyes, A., Wang, Q., Weichenhan, D., Lier, A., von Paleske, L., Renders, S., Wünsche, P., Zeisberger, P., Brocks, D., Gu, L., Herrmann, C., Haas, S., Essers, M., Brors, B., Eils, R., Huber, W., Milsom, M., 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, 507–522. https://doi.org/10.1016/j.stem.2014.07.005

Gerola, S., Nittka, S., Kähler, 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, 769–778. https://doi.org/10.1002/gcc.22185

Gu, Z., Gu, L., Eils, R., Schlesner, M., Brors, B., 2014. circlize Implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812. https://doi.org/10.1093/bioinformatics/btu393

Haller, F., Moskalev, E.A., Faucz, F.R., Barthelmeß, S., Wiemann, S., Bieg, M., Assie, G., Bertherat, J., Schaefer, I.-M., Otto, C., Rattenberry, E., Maher, E.R., Ströbel, P., Werner, M., Carney, J.A., Hartmann, A., Stratakis, C.A., Agaimy, A., 2014. Aberrant DNA hypermethylation of SDHC: a novel mechanism of tumor development in Carney triad. Endocrine Related Cancer 21, 567–577. https://doi.org/10.1530/ERC-14-0254

Hovestadt, V., Jones, D., Picelli, S., Wang, W., Kool, M., Northcott, P.A., Sultan, M., Stachurski, K., Ryzhova, M., Warnatz, H.-J., Ralser, M., Brun, S., Bunt, J., Jäger, N., Kleinheinz, K., Erkek, S., Weber, U., 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., Lichter, P., 2014. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 510, 537–541. https://doi.org/10.1038/nature13268

Juraeva, D., Haenisch, B., Zapatka, M., Frank, J., Witt, S.H., Mühleisen, T.W., Treutlein, J., Strohmaier, J., Meier, S., Degenhardt, F., Giegling, I., Ripke, S., Leber, M., Lange, C., Schulze, T.G., Mössner, R., Nenadic, I., Sauer, H., Rujescu, D., Maier, W., Børglum, A., Ophoff, R., Cichon, S., Nöthen, M.M., Rietschel, M., Mattheisen, M., Brors, B., 2014. Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia. PLoS Genetics 10, e1004345-. https://doi.org/10.1371/journal.pgen.1004345

Lipka, D., Wang, Q., Cabezas-Wallscheid, N., Klimmeck, D., Weichenhan, D., Herrmann, C., Lier, A., Brocks, D., von Paleske, L., Renders, S., Wünsche, P., Zeisberger, P., Gu, L., Haas, S., Essers, M., Brors, B., Eils, R., Trumpp, A., Milsom, M., 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, 3476–3487. https://doi.org/10.4161/15384101.2014.973334

Martins, V.C., Busch, K., Juraeva, D., Blum, C., Ludwig, C., Rasche, V., Lasitschka, F., Mastitsky, S.E., Brors, B., Hielscher, T., Fehling, H.J., Rodewald, H.-R., 2014. Cell competition is a tumour suppressor mechanism in the thymus. Nature 509, 465–470. https://doi.org/10.1038/nature13317

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