Publikationen

Preprints

González-Velasco Ó, Simon M, Yilmaz R, Parlato R, Weishaupt J, Imbusch CD, Brors B, 2024.Identifying similar populations across independent single cell studies without data integration. bioRxiv; 2024. DOI: 10.1101/2024.09.27.615367.

Abad NAB, Glas I, Hong C, Pageaud Y, Hutter B, Brors B, Körner C, Feuerbach L, 2024. Identifying, Prioritizing, and Visualizing Functional Promoter SNVs with the Recurrence-agnostic REMIND-Cancer Pipeline and pSNV Hunter. bioRxiv; 2024. doi: 10.1101/2024.09.10.612212.

Mughal SS, Reiss Y, Felsberg J, Meyer L, Macas J, Schlue S, Starzetz T, Köhrer K, Fehm T, Müller V, Lamszus K, Schadendorf D, Helfrich I, Wikman H, Berghoff A, Brors B, Plate KH, Reifenberger G, 2024. Identification and characterization of tertiary lymphoid structures in brain metastases. bioRxiv; 2024. doi: 10.1101/2024.09.30.614674.

Engel NL, Herzel L, Surmely J, Frieß H, Simon M, Brors B, Imbusch C, Feuerbach L. Quantifying immune cell telomere content at single-cell resolution in context of PD-1 checkpoint immunotherapy. bioRxiv; 2024. doi: 10.1101/2024.08.28.609339.

Abad NAB, Glas I, Hong C, Small A, Pageaud Y, Maia A, Weichenhan D, Plass C, Hutter B, Brors B, Körner C, Feuerbach L, 2024. The promoter mutation paucity as part of the dark matter of the cancer genome. bioRxiv; 2024. doi: 10.1101/2024.06.03.597231.

 

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

Li, C.H., Prokopec, S.D., Sun, R.X., Yousif, F., Schmitz, N., Al-Shahrour, F., Atwal, G., Bailey, P.J., Biankin, A.V., Boutros, P.C., Campbell, P.J., Chang, D.K., Cooke, S.L., Deshpande, V., Faltas, B.M., Faquin, W.C., Garraway, L., Getz, G., Grimmond, S.M., Haider, S., Hoadley, K.A., Jiao, W., Kaiser, V.B., Karlić, R., Kato, M., Kübler, K., Lazar, A.J., Li, C.H., Louis, D.N., Margolin, A., Martin, S., Nahal-Bose, H.K., Nielsen, G.P., Nik-Zainal, S., Omberg, L., P’ng, C., Perry, M.D., Polak, P., Rheinbay, E., Rubin, M.A., Semple, C.A., Sgroi, D.C., Shibata, T., Siebert, R., Smith, J., Stein, L.D., Stobbe, M.D., Sun, R.X., Thai, K., Wright, D.W., Wu, C.-L., Yuan, K., Zhang, Junjun, Boutros, P.C., Aaltonen, L.A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D.J., Agrawal, N., Ahn, K.S., Ahn, S.-M., Aikata, H., Akbani, R., Akdemir, K.C., Al-Ahmadie, H., Al-Sedairy, S.T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L.B., Ally, A., Alsop, K., Alvarez, E.G., Amary, 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T., Boice, L., Bonizzato, G., De Bono, J.S., Boot, A., Bootwalla, M.S., Borg, A., Borkhardt, A., Boroevich, K.A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P.C., Bova, G.S., Bowen, D.T., Bowlby, R., Bowtell, D.D.L., Boyault, S., Boyce, R., Boyd, J., Brazma, A., Brennan, P., Brewer, D.S., Brinkman, A.B., Bristow, R.G., Broaddus, R.R., Brock, J.E., Brock, M., Broeks, A., Brooks, A.N., Brooks, D., Brors, B., Brunak, S., Bruxner, T.J.C., Bruzos, A.L., Buchanan, A., Buchhalter, I., Buchholz, C., Bullman, S., Burke, H., Burkhardt, B., Burns, K.H., Busanovich, J., Bustamante, C.D., Butler, A.P., Butte, A.J., Byrne, N.J., Børresen-Dale, A.-L., Caesar-Johnson, S.J., Cafferkey, A., Cahill, D., Calabrese, C., Caldas, C., Calvo, F., Camacho, N., Campbell, P.J., Campo, E., Cantù, C., Cao, S., Carey, T.E., Carlevaro-Fita, J., Carlsen, R., Cataldo, I., Cazzola, M., Cebon, J., Cerfolio, R., Chadwick, D.E., Chakravarty, D., Chalmers, D., Chan, C., Chan, K., Chan-Seng-Yue, M., Chandan, V.S., Chang, D.K., Chanock, S.J., Chantrill, L.A., Chateigner, A., Chatterjee, N., Chayama, K., Chen, H.-W., Chen, J., Chen, K., Chen, Y., Chen, Z., Cherniack, A.D., Chien, J., Chiew, Y.-E., Chin, S.-F., Cho, J., Cho, S., Choi, J.K., Choi, W., Chomienne, C., Chong, Z., Choo, S.P., Chou, A., Christ, A.N., Christie, E.L., Chuah, E., Cibulskis, C., Cibulskis, K., Cingarlini, S., Clapham, P., Claviez, A., Cleary, S., Cloonan, N., Cmero, M., Collins, C.C., Connor, A.A., Cooke, S.L., Cooper, C.S., Cope, L., Corbo, V., Cordes, M.G., Cordner, S.M., Cortés-Ciriano, I., Covington, K., Cowin, P.A., Craft, B., Craft, D., Creighton, C.J., Cun, Y., Curley, E., Cutcutache, I., Czajka, K., Czerniak, B., Dagg, R.A., Danilova, L., Davi, M.V., Davidson, N.R., Davies, H., Davis, I.J., Davis-Dusenbery, B.N., Dawson, K.J., De La Vega, F.M., De Paoli-Iseppi, R., Defreitas, T., Dei Tos, A.P., Delaneau, O., Demchok, J.A., Demeulemeester, J., Demidov, G.M., Demircioğlu, D., Dennis, N.M., Denroche, R.E., Dentro, S., Desai, N., Deshpande, V., Deshwar, A.G., Desmedt, C., Deu-Pons, J., Dhalla, N., Dhani, N.C., Dhingra, P., Dhir, R., DiBiase, A., Diamanti, K., Ding, L., Ding, S., Dinh, H.Q., Dirix, L., Doddapaneni, H., Donmez, N., Dow, M.T., Drapkin, R., Drechsel, O., Drews, R.M., Serge, S., Dudderidge, T., Dueso-Barroso, A., Dunford, A.J., Dunn, M., Dursi, L.J., Duthie, F.R., Dutton-Regester, K., Eagles, J., Easton, D.F., Edmonds, S., Edwards, P.A., Edwards, S.E., Eeles, R.A., Ehinger, A., Eils, J., Eils, R., El-Naggar, A., Eldridge, M., Ellrott, K., Erkek, S., Escaramis, G., Espiritu, S.M.G., Estivill, X., Etemadmoghadam, D., Eyfjord, J.E., Faltas, B.M., Fan, D., Fan, Y., Faquin, W.C., Farcas, C., Fassan, M., Fatima, A., Favero, F., Fayzullaev, N., Felau, I., Fereday, S., Ferguson, M.L., Ferretti, V., Feuerbach, L., Field, M.A., Fink, J.L., Finocchiaro, G., Fisher, C., Fittall, M.W., Fitzgerald, A., Fitzgerald, R.C., Flanagan, A.M., Fleshner, N.E., Flicek, P., Foekens, J.A., Fong, K.M., Fonseca, N.A., Foster, C.S., Fox, N.S., Fraser, M., Frazer, S., Frenkel-Morgenstern, M., Friedman, W., Frigola, J., Fronick, C.C., Fujimoto, A., Fujita, M., Fukayama, M., Fulton, L.A., Fulton, R.S., Furuta, M., Futreal, P.A., Füllgrabe, A., Gabriel, S.B., Gallinger, S., Gambacorti-Passerini, C., Gao, J., Gao, S., Garraway, L., Garred, Ø., Garrison, E., Garsed, D.W., Gehlenborg, N., Gelpi, J.L.L., George, J., Gerhard, D.S., Gerhäuser, C., Gershenwald, J.E., Gerstein, M., Gerstung, M., Getz, G., Ghori, M., Ghossein, R., Giama, N.H., Gibbs, R.A., Gill, A.J., Gill, P., Giri, D.D., Glodzik, D., Gnanapragasam, V.J., Goebler, M.E., Goldman, M.J., Gomez, C., Gonzalez, S., Gonzalez-Perez, A., Gordenin, D.A., Gossage, J., Gotoh, K., Govindan, R., Grabau, D., Graham, J.S., Grant, R.C., Green, A.R., Green, E., Greger, L., Grehan, N., Grimaldi, S., Grimmond, S.M., Grossman, R.L., Grundhoff, A., Gundem, G., Guo, Q., Gupta, M., Gupta, S., Gut, I.G., Gut, M., Göke, J., Ha, G., Haake, A., Haan, D., Haas, S., Haase, K., Haber, J.E., Habermann, N., Hach, F., Haider, S., Hama, N., Hamdy, F.C., Hamilton, A., Hamilton, M.P.,