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Article

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.
Al-Diab, O., Sünkel, C., Blanc, E., Catar, R.A., Ashraf, M.I., Zhao, H., Wang, P., Rinschen, M.M., Fritsche-Guenther, R., Grahammer, F., Bachmann, S., Beule, D., Kirwan, J.A., Rajewsky, N., Huber, T.B., Gürgen, D. and Kusch, A.
Biology of Sex Differences 15 (1): 72. 15 September 2024

Microenvironmental acidification by pneumococcal sugar consumption fosters barrier disruption and immune suppression in the human alveolus.
Fatykhova, D., Fritsch, V.N., Siebert, K., Methling, K., Lalk, M., Busche, T., Kalinowski, J., Weiner, J., Beule, D., Bertrams, W., Kohler, T.P., Hammerschmidt, S., Löwa, A., Fischer, M., Mieth, M., Hellwig, K., Frey, D., Neudecker, J., Rueckert, J.C., Toennies, M., Bauer, T.T., Graff, M., Tran, H.L., Eggeling, S., Gruber, A.D., Antelmann, H., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal : 2301983. 4 September 2024 (In Press)

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Harnessing transcriptomic signals for amyotrophic lateral sclerosis to identify novel drugs and enhance risk prediction.
Pain, O., Jones, A., Al Khleifat, A., Agarwal, D., Hramyka, D., Karoui, H., Kubica, J., Llewellyn, D.J., Ranson, J.M., Yao, Z., Iacoangeli, A. and Al-Chalabi, A.
Heliyon 10 (15): e35342. 15 August 2024

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
Essex, M., Millet Pascual-Leone, B.L., Löber, U., Kuhring, M., Zhang, B., Brüning, U., Fritsche-Guenther, R., Krzanowski, M., Fiocca Vernengo, F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thibeault, C., Corman, V.M., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
NPJ Biofilms and Microbiomes 10 (1): 66. 1 August 2024

Intestinal retinol saturase is implicated in the development of obesity and epithelial homeostasis upon injury.
Kiefer, M.F., Meng, Y., Yang, N., Vahrenbrink, M., Wulff, S., Li, C., Wowro, S.J., Petricek, K.M., Sommerfeld, M., Flores, R.E., Obermayer, B., Piepelow, K., Klaus, S., Hartl, K., Guillot, A., Tacke, F., Sigal, M. and Schupp, M.
American Journal of Physiology Endocrinology and Metabolism 327 (2): E203-E216. August 2024

Microglia undergo molecular and functional adaptations to dark and light phases in male laboratory mice.
Mattei, D., Ivanov, A., Hammer, J., Ugursu, B., Schalbetter, S., Richetto, J., Weber-Stadlbauer, U., Mueller, F., Scarborough, J., Wolf, S.A., Kettenmann, H., Wollscheid, B., Beule, D. and Meyer, U.
Brain, Behavior and Immunity 210 : 571-583. August 2024

Robust detection of clinically relevant features in single-cell RNA profiles of patient-matched fresh and formalin-fixed paraffin-embedded (FFPE) lung cancer tissue.
Trinks, A., Milek, M., Beule, D., Kluge, J., Florian, S., Sers, C., Horst, D., Morkel, M. and Bischoff, P.
Cellular Oncology 47 (4): 1221-1231. August 2024

The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.
Ramberger, E., Sapozhnikova, V., Ng, Y.L.D., Dolnik, A., Ziehm, M., Popp, O., Sträng, E., Kull, M., Grünschläger, F., Krüger, J., Benary, M., Müller, S., Gao, X., Murgai, A., Haji, M., Schmidt, A., Lutz, R., Nogai, A., Braune, J., Laue, D., Langer, C., Khandanpour, C., Bassermann, F., Döhner, H., Engelhardt, M., Straka, C., Hundemer, M., Beule, D., Haas, S., Keller, U., Einsele, H., Bullinger, L., Knop, S., Mertins, P. and Krönke, J.
Nature Cancer 5 (8): 1267-1284. August 2024

High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment.
Wei, T.T., Blanc, E., Peidli, S., Bischoff, P., Trinks, A., Horst, D., Sers, C., Blüthgen, N., Beule, D., Morkel, M. and Obermayer, B.
International Journal of Cancer 19 July 2024 (In Press)

Disrupting TSLP-TSLP receptor interactions via putative small molecule inhibitors yields a novel and efficient treatment option for atopic diseases.
Adhikary, P.P., Idowu, T., Tan, Z., Hoang, C., Shanta, S., Dumbani, M., Mappalakayil, L., Awasthi, B., Bermudez, M., Weiner, J., Beule, D., Wolber, G., Page, B.D. and Hedtrich, S.
EMBO Molecular Medicine 16 (7): 1630-1656. 15 July 2024

REEV: review, evaluate and explain variants.
Hramyka, D., Sczakiel, H.L., Zhao, M.X., Stolpe, O., Nieminen, M., Adam, R., Danyel, M., Einicke, L., Hägerling, R., Knaus, A., Mundlos, S., Schwartzmann, S., Seelow, D., Ehmke, N., Mensah, M.A., Boschann, F., Beule, D. and Holtgrewe, M.
Nucleic Acids Research 52 (W1): W148-W158. 5 July 2024

lncRNA CDKN2B-AS1 regulates collagen expression.
Shi, W., Song, J., Weiner, J.M., Chopra, A., Dommisch, H., Beule, D. and Schaefer, A.S.
Human Genetics 143 (7): 907-919. July 2024

IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota.
Röwekamp, I., Maschirow, L., Rabes, A., Fiocca Vernengo, F., Hamann, L., Heinz, G.A., Mashreghi, M.F., Caesar, S., Milek, M., Fagundes Fonseca, A.C., Wienhold, S.M., Nouailles, G., Yao, L., Mousavi, S., Bruder, D., Boehme, J.D., Puzianowska-Kuznicka, M., Beule, D., Witzenrath, M., Löhning, M., Klose, C.S.N., Heimesaat, M.M., Diefenbach, A. and Opitz, B.
Proceedings of the National Academy of Sciences of the United States of America 121 (22): e2310864121. 28 May 2024

Extracellular matrix remodeling in atopic dermatitis harnesses the onset of an asthmatic phenotype and is a potential contributor to the atopic march.
Graff, P., Woerz, D., Wilzopolski, J., Voss, A., Sarrazin, J., Blimkie, T.M., Weiner, J., Kershaw, O., Panwar, P., Hackett, T., Lau, S., Brömme, D., Beule, D., Lee, Y.A., Hancock, R.E.W., Gruber, A.D., Bäumer, W. and Hedtrich, S.
Journal of Investigative Dermatology 144 (5): 1010-1021. May 2024

Increased β(2)-adrenergic signaling promotes fracture healing through callus neovascularization in mice.
Jahn, D., Knapstein, P.R., Otto, E., Köhli, P., Sevecke, J., Graef, F., Graffmann, C., Fuchs, M., Jiang, S., Rickert, M., Erdmann, C., Appelt, J., Revend, L., Küttner, Q., Witte, J., Rahmani, A., Duda, G., Xie, W., Donat, A., Schinke, T., Ivanov, A., Tchouto, M.N., Beule, D., Frosch, K.H., Baranowsky, A., Tsitsilonis, S. and Keller, J.
Science Translational Medicine 16 (743): eadk9129. 17 April 2024

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.
Dörner, P.J., Anandakumar, H., Röwekamp, I., Fiocca Vernengo, F., Millet Pascual-Leone, B., Krzanowski, M., Sellmaier, J., Brüning, U., Fritsche-Guenther, R., Pfannkuch, L., Kurth, F., Milek, M., Igbokwe, V., Löber, U., Gutbier, B., Holstein, M., Heinz, G.A., Mashreghi, M.F., Schulte, L.N., Klatt, A.B., Caesar, S., Wienhold, S.M., Offermanns, S., Mack, M., Witzenrath, M., Jordan, S., Beule, D., Kirwan, J.A., Forslund, S.K., Wilck, N., Bartolomaeus, H., Heimesaat, M.M. and Opitz, B.
Nature Communications 15 (1): 2788. 30 March 2024

Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses.
Lebedin, M., Ratswohl, C., Garg, A., Schips, M., Vazquez Garcia, C., Spatt, L., Thibeault, C., Obermayer, B., Weiner, J., Moreno Velásquez, I., Gerhard, C., Stubbemann, P., Hanitsch, L.G., Pischon, T., Witzenrath, M., Sander, L.E., Kurth, F., Meyer-Hermann, M. and de la Rosa, K.
iScience 27 (3): 109330. 15 March 2024

Comparable CD8(+) T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals.
Tranter, Eva, Frentsch, Marco, Hütter-Krönke, Marie Luise, Vuong, Giang Lam, Busch, David, Loyal, Lucie, Henze, Larissa, Rosnev, Stanislav, Blau, Igor-Wolfgang, Thiel, Andreas, Beule, D., Bullinger, L., Obermayer, B. and Na, I.K.
Journal of Medical Virology 96 (3): e29539. March 2024

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J., Theisen, S., Dartsch, J., Fritsche-Guenther, R., Kirchner, M., Obermayer, B., Bauer, A., Kahlert, A.K., Rothe, M., Beule, D., Heuser, A., Mertins, P., Kirwan, J.A., Berndt, N., MacRae, C.A., Hubner, N. and Klaassen, S.
Cardiovascular Research 119 (18): 2902-2916. December 2023

miRNAs from inflamed gingiva link gene signaling to increased MET expression.
Zheng, L., Chopra, A., Weiner, J., Beule, D., Dommisch, H. and Schaefer, A.S.
Journal of Dental Research 102 (13): 1488-1497. December 2023

Generation of iPSC lines with SLC16A2:G401R or SLC16A2 knock out.
Ludwik, K.A., Opitz, R., Jyrch, S., Megges, M., Weiner, J., Beule, D., Kühnen, P. and Stachelscheid, H.
Stem Cell Research 73 : 103256. 21 November 2023

A colonic organoid model challenged with the large toxins of Clostridioides difficile TcdA and TcdB exhibit deregulated tight junction proteins.
Schneemann, M., Heils, L., Moos, V., Weiß, F., Krug, S.M., Weiner, J., Beule, D., Gerhard, R., Schulzke, J.D. and Bücker, R.
Toxins 15 (11): 643. 4 November 2023

Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.
Briest, F., Noerenberg, D., Hennch, C., Yoshida, K., Hablesreiter, R., Nimo, J., Sasca, D., Kirchner, M., Mansouri, L., Inoue, Y., Wiegand, L., Staiger, A.M., Casadei, B., Korkolopoulou, P., Weiner, J., Lopez-Guillermo, A., Warth, A., Schneider, T., Nagy, Á., Klapper, W., Hummel, M., Kanellis, G., Anagnostopoulos, I., Mertins, P., Bullinger, L., Rosenquist, R., Vassilakopoulos, T.P., Ott, G., Ogawa, S. and Damm, F.
Leukemia 37 (11): 2237-2249. November 2023

Leveraging large language models for decision support in personalized oncology.
Benary, M., Wang, X.D., Schmidt, M., Soll, D., Hilfenhaus, G., Nassir, M., Sigler, C., Knödler, M., Keller, U., Beule, D., Keilholz, U., Leser, U. and Rieke, D.T.
JAMA Network Open 6 (11): e2343689. November 2023

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E., Planas-Fèlix, M., Burkert, M., Puiggròs, M., Toedling, J., Thiessen, N., Blanc, E., Szymansky, A., Hertwig, F., Ishaque, N., Beule, D., Torrents, D., Eggert, A., Koche, R.P., Schwarz, R.F., Haase, K., Schulte, J.H. and Henssen, A.G.
Cell Genomics 3 (10): 100402. 11 October 2023

Pharmacological inhibition of bromodomain and extra-terminal proteins induces an NRF-2-mediated antiviral state that is subverted by SARS-CoV-2 infection.
Mhlekude, B., Postmus, D., Stenzel, S., Weiner, J., Jansen, J., Zapatero-Belinchón, F.J., Olmer, R., Richter, A., Heinze, J., Heinemann, N., Mühlemann, B., Schroeder, S., Jones, T.C., Müller, M.A., Drosten, C., Pich, A., Thiel, V., Martin, U., Niemeyer, D., Gerold, G., Beule, D. and Goffinet, C.
PLoS Pathogens 19 (9): e1011657. 25 September 2023

Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice.
Monsorno, K., Ginggen, K., Ivanov, A., Buckinx, A., Lalive, A.L., Tchenio, A., Benson, S., Vendrell, M., D'Alessandro, A., Beule, D., Pellerin, L., Mameli, M. and Paolicelli, R.C.
Nature Communications 14 (1): 5749. 16 September 2023

Tumour mutational burden and survival with molecularly matched therapy.
de Bortoli, T., Benary, M., Horak, P., Lamping, M., Stintzing, S., Tinhofer, I., Leyvraz, S., Schäfer, R., Klauschen, F., Keller, U., Stenzinger, A., Fröhling, S., Kurzrock, R., Keilholz, U., Rieke, D.T. and Jelas, I.
European Journal of Cancer 190 : 112925. September 2023

SODAR: managing multiomics study data and metadata.
Nieminen, M., Stolpe, O., Kuhring, M., Weiner, J., Pett, P., Beule, D. and Holtgrewe, M.
GigaScience 12 : giad052. 27 July 2023

A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease.
Boeddrich, A., Haenig, C., Neuendorf, N., Blanc, E., Ivanov, A., Kirchner, M., Schleumann, P., Bayraktaroğlu, I., Richter, M., Molenda, C.M., Sporbert, A., Zenkner, M., Schnoegl, S., Suenkel, C., Schneider, L.S., Rybak-Wolf, A., Kochnowsky, B., Byrne, L.M., Wild, E.J., Nielsen, J.E., Dittmar, G., Peters, O., Beule, D. and Wanker, E.E.
Genome Medicine 15 (1): 50. 20 July 2023

Thrifty energy phenotype predicts weight regain in postmenopausal women with overweight or obesity and is related to FGFR1 signaling.
Spranger, L., Weiner, J., Bredow, J., Zeitz, U., Grittner, U., Boschmann, M., Dickmann, S., Stobäus, N., Schwartzenberg, R.J., Brachs, M., Spranger, J. and Mai, K.
Clinical Nutrition 42 (4): 559-567. April 2023

Mouse models of human multiple myeloma subgroups.
Winkler, W., Farré Díaz, C., Blanc, E., Napieczynska, H., Langner, P., Werner, M., Walter, B., Wollert-Wulf, B., Yasuda, T., Heuser, A., Beule, D., Mathas, S., Anagnostopoulos, I., Rosenwald, A., Rajewsky, K. and Janz, M.
Proceedings of the National Academy of Sciences of the United States of America 120 (10): e2219439120. 7 March 2023

TREX1 p.A129fs and p.Y305C variants in a large multi-ethnic cohort of CADASIL-like unrelated patients.
Foddis, M., Blumenau, S., Holtgrewe, M., Paquette, K., Westra, K., Alonso, I., Macario, M.d.C., Morgadinho, A.S., Velon, A.G., Santo, G., Santana, I., Mönkäre, S., Kuuluvainen, L., Schleutker, J., Pöyhönen, M., Myllykangas, L., Pavlovic, A., Kostic, V., Dobricic, V., Lohmann, E., Hanagasi, H., Santos, M., Guven, G., Bilgic, B., Bras, J., Beule, D., Dirnagl, U., Guerreiro, R. and Sassi, C.
Neurobiology of Aging 123 : 208-215. March 2023

Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19.
Mothes, R., Pascual-Reguant, A., Koehler, R., Liebeskind, J., Liebheit, A., Bauherr, S., Philipsen, L., Dittmayer, C., Laue, M., von Manitius, R., Elezkurtaj, S., Durek, P., Heinrich, F., Heinz, G.A., Guerra, G.M., Obermayer, B., Meinhardt, J., Ihlow, J., Radke, J., Heppner, F.L., Enghard, P., Stockmann, H., Aschman, T., Schneider, J., Corman, V.M., Sander, L.E., Mashreghi, M.F., Conrad, T., Hocke, A.C., Niesner, R.A., Radbruch, H. and Hauser, A.E.
Nature Communications 14 (1): 791. 11 February 2023

Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.
Obermayer, B., Keilholz, L., Conrad, T., Frentsch, M., Blau, I.W., Vuong, L., Lesch, S., Movasshagi, K., Tietze-Stolley, C., Loyal, L., Henze, L., Penack, O., Stervbo, U., Babel, N., Haas, S., Beule, D., Bullinger, L., Wittenbecher, F. and Na, I.K.
Frontiers in Immunology 14 : 1114368. 10 February 2023

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
Freitag, K., Eede, P., Ivanov, A., Sterczyk, N., Schneeberger, S., Borodina, T., Sauer, S., Beule, D. and Heppner, F.L.
Communications Biology 6 (1): 40. 13 January 2023

Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations.
Zieger, H.K., Weinhold, L., Schmidt, A., Holtgrewe, M., Juranek, S.A., Siewert, A., Scheer, A.B., Thieme, F., Mangold, E., Ishorst, N., Brand, F.U., Welzenbach, J., Beule, D., Paeschke, K., Krawitz, P.M. and Ludwig, K.U.
Human Genetics and Genomics Advances 4 (1): 100166. 12 January 2023

Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutated salivary duct carcinoma.
Rieke, D.T., Schröder, S., Schafhausen, P., Blanc, E., Zuljan, E., von der Emde, B., Beule, D., Keller, U., Keilholz, U. and Klinghammer, K.
Frontiers in Oncology 13 : 1107134. 2023

State-of-the-art analytical methods of viral infections in human lung organoids.
Baumgardt, M., Hülsemann, M., Löwa, A., Fatykhova, D., Hoffmann, K., Kessler, M., Mieth, M., Hellwig, K., Frey, D., Langenhagen, A., Voss, A., Obermayer, B., Wyler, E., Dökel, S., Gruber, A.D., Tölch, U., Hippenstiel, S., Hocke, A.C. and Hönzke, K.
PLoS ONE 17 (12): e0276115. 20 December 2022

Placental transcriptome profiling in subtypes of diabetic pregnancies is strongly confounded by fetal sex.
Kedziora, S.M., Obermayer, B., Sugulle, M., Herse, F., Kräker, K., Haase, N., Langmia, I.M., Müller, D.N., Staff, A.C., Beule, D. and Dechend, R.
International Journal of Molecular Sciences 23 (23): 15388. 6 December 2022

Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
Hönzke, K., Obermayer, B., Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E., Baumgardt, M., Löwa, A., Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M., Hinze, C., Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M., Busch, J., Klauschen, F., Horst, D., Radbruch, H., Radke, J., Heppner, F., Corman, V.M., Niemeyer, D., Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D., Landthaler, M., Ludwig, S., Suttorp, N., Witzenrath, M., Gruber, A.D., Drosten, C., Sander, L.E., Wolff, T., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 60 (6): 2102725. 1 December 2022

Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
Holle, J., Bartolomaeus, H., Löber, U., Behrens, F., Bartolomaeus, T.U.P., Anandakumar, H., Wimmer, M., Vu, D.L., Kuhring, M., Brüning, U., Maifeld, A., Geisberger, S., Kempa, S., Schumacher, F., Kleuser, B., Bufler, P., Querfeld, U., Kitschke, S., Engler, D., Kuhrt, L.D., Drechsel, O., Eckardt, K.U., Forslund, S., Thürmer, A., McParland, V., Kirwan, J., Wilck, N. and Mueller, D.
Journal of the American Society of Nephrology 33 (12): 2259-2275. December 2022

Non-redundant functions of group 2 innate lymphoid cells.
Jarick, K.J., Topczewska, P.M., Jakob, M.O., Yano, H., Arifuzzaman, M., Gao, X., Boulekou, S., Stokic-Trtica, V., Leclère, P.S., Preußer, A., Rompe, Z.A., Stamm, A., Tsou, A.M., Chu, C., Heinrich, F.R., Guerra, G.M., Durek, P., Ivanov, A., Beule, D., Helfrich, S., Duerr, C.U., Kühl, A.A., Stehle, C., Romagnani, C., Mashreghi, M.F., Diefenbach, A., Artis, D. and Klose, C.S.N.
Nature 611 (7937): 794-800. 24 November 2022

EBAG9-silencing exerts an immune checkpoint function without aggravating adverse effects.
Wirges, A., Bunse, M., Joedicke, J.J., Blanc, E., Gudipati, V., Moles, M.W., Shiku, H., Beule, D., Huppa, J.B., Höpken, U.E. and Rehm, A.
Molecular Therapy 30 (11): 3358-3378. 2 November 2022

Immune phenotypes and target antigens of clonally expanded bone marrow T cells in treatment-naïve multiple myeloma.
Welters, C., Lammoglia Cobo, M.F., Stein, C.A., Hsu, M.T., Ben Hamza, A., Penter, L., Chen, X., Buccitelli, C., Popp, O., Mertins, P., Dietze, K., Bullinger, L., Moosmann, A., Blanc, E., Beule, D., Gerbitz, A., Strobel, J., Hackstein, H., Rahn, H.P., Dornmair, K., Blankenstein, T. and Hansmann, L.
Cancer Immunology Research 10 (11): 1407-1419. 1 November 2022

Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.
Rieke, D.T., de Bortoli, T., Horak, P., Lamping, M., Benary, M., Jelas, I., Rüter, G., Berger, J., Zettwitz, M., Kagelmann, N., Kind, A., Fabian, F., Beule, D., Glimm, H., Brors, B., Stenzinger, A., Fröhling, S. and Keilholz, U.
BMC Medicine 20 (1): 367. 24 October 2022

Analyses of circRNA expression throughout the light-dark cycle reveal a strong regulation of (Cdr1as), associated with light entrainment in the SCN.
Ivanov, A., Mattei, D., Radscheit, K., Compagnion, A.C., Pett, J.P., Herzel, H.P., Paolicelli, R.C., Piwecka, M., Meyer, U. and Beule, D.
International Journal of Molecular Sciences 23 (20): 12347. October 2022

A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.
Pennitz, P., Kirsten, H., Friedrich, V.D., Wyler, E., Goekeri, C., Obermayer, B., Heinz, G.A., Mashreghi, M.F., Büttner, M., Trimpert, J., Landthaler, M., Suttorp, N., Hocke, A.C., Hippenstiel, S., Tönnies, M., Scholz, M., Kuebler, W.M., Witzenrath, M., Hoenzke, K. and Nouailles, G.
European Respiratory Review 31 (165): 220056. 30 September 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C., Kocks, C., Leiz, J., Karaiskos, N., Boltengagen, A., Cao, S., Skopnik, C.M., Klocke, J., Hardenberg, J.H., Stockmann, H., Gotthardt, I., Obermayer, B., Haghverdi, L., Wyler, E., Landthaler, M., Bachmann, S., Hocke, A.C., Corman, V., Busch, J., Schneider, W., Himmerkus, N., Bleich, M., Eckardt, K.U., Enghard, P., Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D., Obermayer, B., Weiner, J.M., Zimmermann, K., Anania, C., Wagner, L.K., Lyras, E.M., Sapozhnikova, V., Lara-Astiaso, D., Prósper, F., Lang, R., Lupiáñez, D.G., Beule, D., Höpken, U.E., Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
Hoffmann, K., Obermayer, B., Hönzke, K., Fatykhova, D., Demir, Z., Löwa, A., Teixeira Alves, L.G., Wyler, E., Lopez-Rodriguez, E., Mieth, M., Baumgardt, M., Hoppe, J., Firsching, T.C., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Gruber, A.D., Ochs, M., Landthaler, M., Beule, D., Suttorp, N., Hippenstiel, S., Hocke, A.C. and Kessler, M.
Communications Biology 5 (1): 875. 25 August 2022

ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise.
May, V., Koch, L., Fischer-Zirnsak, B., Horn, D., Gehle, P., Kornak, U., Beule, D. and Holtgrewe, M.
Bioinformatics 38 (16): 3871-3876. 15 August 2022

Pathogenic variants in cardiomyopathy disorder genes underlie pediatric myocarditis - Further impact of heterozygous immune disorder gene variants?
Seidel, F., Laser, K.T., Klingel, K., Dartsch, J., Theisen, S., Pickardt, T., Holtgrewe, M., Gärtner, A., Berger, F., Beule, D., Milting, H., Schubert, S., Klaassen, S. and Kühnisch, J.
Journal of Cardiovascular Development and Disease 9 (7): 216. 5 July 2022

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
Freitag, K., Sterczyk, N., Wendlinger, S., Obermayer, B., Schulz, J., Farztdinov, V., Mülleder, M., Ralser, M., Houtman, J., Fleck, L., Braeuning, C., Sansevrino, R., Hoffmann, C., Milovanovic, D., Sigrist, S.J., Conrad, T., Beule, D., Heppner, F.L. and Jendrach, M.
Journal of Neuroinflammation 19 (1): 172. 2 July 2022

The single-cell transcriptional landscape of lung carcinoid tumors.
Bischoff, P., Trinks, A., Wiederspahn, J., Obermayer, B., Pett, J.P., Jurmeister, P., Elsner, A., Dziodzio, T., Rückert, J.C., Neudecker, J., Falk, C., Beule, D., Sers, C., Morkel, M., Horst, D., Klauschen, F. and Blüthgen, N.
International Journal of Cancer 150 (12): 2058-2071. 15 June 2022

Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19.
Dannebaum, R., Suwalski, P., Asgharian, H., Du Zhipei, G., Lin, H., Weiner, J., Holtgrewe, M., Thibeault, C., Müller, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.M., Hübner, R.H., Hinzmann, B., Blüher, A., Siemann, S., Telman, D., Suttorp, N., Witzenrath, M., Hippenstiel, S., Skurk, C., Poller, W., Sander, L.E., Beule, D., Kurth, F., Guettouche, T., Landmesser, U., Berka, J., Luong, K., Rubelt, F. and Heidecker, B.
EClinicalMedicine 48 : 101438. June 2022

Venn diagrams may indicate erroneous statistical reasoning in transcriptomics.
Weiner, J., Obermayer, B. and Beule, D.
Frontiers in Genetics 13 : 818683. 14 April 2022

Isolation of neoantigen-specific human T cell receptors from different human and murine repertoires.
Grunert, C., Willimsky, G., Peuker, C.A., Rhein, S., Hansmann, L., Blankenstein, T., Blanc, E., Beule, D., Keller, U., Pezzutto, A. and Busse, A.
Cancers 14 (7): 1842. 6 April 2022

Deep learning-assisted peak curation for large-scale LC-MS metabolomics.
Gloaguen, Y., Kirwan, J.A. and Beule, D.
Analytical Chemistry 94 (12): 4930-4937. 29 March 2022

Adolescence is a sensitive period for prefrontal microglia to act on cognitive development.
Schalbetter, S.M., von Arx, A.S., Cruz-Ochoa, N., Dawson, K., Ivanov, A., Mueller, F.S., Lin, H.Y., Amport, R., Mildenberger, W., Mattei, D., Beule, D., Földy, C., Greter, M., Notter, T. and Meyer, U.
Science Advances 8 (9): eabi6672. 4 March 2022

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P., Astaburuaga-García, R., Bonaguro, L., Brumhard, S., Michalick, L., Lippert, L.J., Kostevc, T., Gäbel, C., Schneider, M., Streitz, M., Demichev, V., Gemünd, I., Barone, M., Tober-Lau, P., Helbig, E.T., Hillus, D., Petrov, L., Stein, J., Dey, H.P., Paclik, D., Iwert, C., Mülleder, M., Aulakh, S.K., Djudjaj, S., Bülow, R.D., Mei, H.E., Schulz, A.R., Thiel, A., Hippenstiel, S., Saliba, A.E., Eils, R., Lehmann, I., Mall, M.A., Stricker, S., Röhmel, J., Corman, V.M., Beule, D., Wyler, E., Landthaler, M., Obermayer, B., von Stillfried, S., Boor, P., Demir, M., Wesselmann, H., Suttorp, N., Uhrig, A., Müller-Redetzky, H., Nattermann, J., Kuebler, W.M., Meisel, C., Ralser, M., Schultze, J.L., Aschenbrenner, A.C., Thibeault, C., Kurth, F., Sander, L.E., Blüthgen, N. and Sawitzki, B.
Cell 185 (3): 493-512. 3 February 2022

Combining callers improves the detection of copy number variants from whole-genome sequencing.
Coutelier, M., Holtgrewe, M., Jäger, M., Flöttman, R., Mensah, M.A., Spielmann, M., Krawitz, P., Horn, D., Beule, D. and Mundlos, S.
European Journal of Human Genetics 30 (2): 178-186. February 2022

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma.
Bischoff, P., Trinks, A., Obermayer, B., Pett, J.P., Wiederspahn, J., Uhlitz, F., Liang, X., Lehmann, A., Jurmeister, P., Elsner, A., Dziodzio, T., Rückert, J.C., Neudecker, J., Falk, C., Beule, D., Sers, C., Morkel, M., Horst, D., Blüthgen, N. and Klauschen, F.
Oncogene 40 : 6748–6758. 16 December 2021

Depletion of cardiac cardiolipin synthase alters systolic and diastolic function.
Smeir, E., Leberer, S., Blumrich, A., Vogler, G., Vasiliades, A., Dresen, S., Jaeger, C., Gloaguen, Y., Klose, C., Beule, D., Schulze, P.C., Bodmer, R., Foryst-Ludwig, A. and Kintscher, U.
iScience 24 (11): 103314. 19 November 2021

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M., Klinger, B., Mari, T., Toedling, J., Blanc, E., Messerschmidt, C., Nadler-Holly, M., Ziehm, M., Sieber, A., Hertwig, F., Beule, D., Eggert, A., Schulte, J.H., Selbach, M. and Blüthgen, N.
PLoS Computational Biology 17 (11): e1009515. 4 November 2021

Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
Uhlitz, F., Bischoff, P., Peidli, S., Sieber, A., Trinks, A., Lüthen, M., Obermayer, B., Blanc, E., Ruchiy, Y., Sell, T., Mamlouk, S., Arsie, R., Wei, T.T., Klotz-Noack, K., Schwarz, R.F., Sawitzki, B., Kamphues, C., Beule, D., Landthaler, M., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.
Weiner, J., Suwalski, P., Holtgrewe, M., Rakitko, A., Thibeault, C., Müller, M., Patriki, D., Quedenau, C., Krüger, U., Ilinsky, V., Popov, I., Balnis, J., Jaitovich, A., Helbig, E.T., Lippert, L.J., Stubbemann, P., Real, L.M., Macías, J., Pineda, J.A., Fernandez-Fuertes, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.M., Hübner, R.H., Hinzmann, B., Salvo, M., Blueher, A., Siemann, S., Jurisic, S., Beer, J.H., Rutishauser, J., Wiggli, B., Schmid, H., Danninger, K., Binder, R., Corman, V.M., Mühlemann, B., Arjun Arkal, R., Fragiadakis, G.K., Mick, E., Calfee, C.S., Erle, D.J., Hendrickson, C.M., Kangelaris, K.N., Krummel, M.F., Woodruff, P.G., Langelier, C.R., Venkataramani, U., García, F., Zyla, J., Drosten, C., Braun, A., Jones, T.C., Suttorp, N., Witzenrath, M., Hippenstiel, S., Zemojtel, T., Skurk, C., Wolfgang, P., Borodina, T., Ripke, S., Sander, L.E., Beule, D., Landmesser, U., Guettouche, T., Kurth, F. and Heidecker, B.
EClinicalMedicine 40 : 101099. October 2021

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.
Rajasekaran, S., Siddiqui, J., Rakijas, J., Nicolay, B., Lin, C., Khan, E., Patel, R., Morris, R., Wyler, E., Boukhali, M., Balasubramanyam, J., Ranjith Kumar, R., Van Rechem, C., Vogel, C., Elchuri, S.V., Landthaler, M., Obermayer, B., Haas, W., Dyson, N. and Miles, W.
Communications Biology 4 (1): 977. 17 August 2021

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.
Nouailles, G., Wyler, E., Pennitz, P., Postmus, D., Vladimirova, D., Kazmierski, J., Pott, F., Dietert, K., Muelleder, M., Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L.E., Suttorp, N., Ralser, M., Beule, D., Gruber, A.D., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Nature Communications 12 (1): 4869. 11 August 2021

Pathogenic variants associated with dilated cardiomyopathy predict outcome in pediatric myocarditis.
Seidel, F., Holtgrewe, M., Al-Wakeel-Marquard, N., Opgen-Rhein, B., Dartsch, J., Herbst, C., Beule, D., Pickardt, T., Klingel, K., Messroghli, D., Berger, F., Schubert, S., Kühnisch, J. and Klaassen, S.
Circulation Genomic and Precision Medicine 14 (4): e003250. 4 August 2021

Shared and oppositely regulated transcriptomic signatures in Huntington's disease and brain ischemia confirm known and unveil novel potential neuroprotective genes.
Yildirim, F., Foddis, M., Blumenau, S., Müller, S., Kajetan, B., Holtgrewe, M., Kola, V., Beule, D. and Sassi, C.
Neurobiology of Aging 104 : 122.e1-122.e17. August 2021

Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
Schinke, C., Vallone, V.F., Ivanov, A., Peng, Y., Körtvelyessy, P., Nolte, L., Huehnchen, P., Beule, D., Stachelscheid, H., Boehmerle, W. and Endres, M.
Neurobiology of Disease 155 : 105391. July 2021

Long-term in vitro expansion ensures increased yield of central memory T cells as perspective for manufacturing challenges.
Herda, S., Heimann, A., Obermayer, B., Ciraolo, E., Althoff, S., Ruß, J., Grunert, C., Busse, A., Bullinger, L., Pezzutto, A., Blankenstein, T., Beule, D. and Na, I.K.
International Journal of Cancer 148 (12): 3097-3110. 15 June 2021

YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer.
Quinn, H.M., Vogel, R., Popp, O., Mertins, P., Lan, L., Messerschmidt, C., Landshammer, A., Lisek, K., Château-Joubert, S., Marangoni, E., Koren, E., Fuchs, Y. and Birchmeier, W.
Cancer Research 81 (8): 2116-2127. April 2021

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice.
Messerschmidt, C., Foddis, M., Blumenau, S., Müller, S., Bentele, K., Holtgrewe, M., Kun-Rodrigues, C., Alonso, I., do Carmo Macario, M., Morgadinho, A.S., Velon, A.G., Santo, G., Santana, I., Mönkäre, S., Kuuluvainen, L., Schleutker, J., Pöyhönen, M., Myllykangas, L., Senatore, A., Berchtold, D., Winek, K., Meisel, A., Pavlovic, A., Kostic, V., Dobricic, V., Lohmann, E., Hanagasi, H., Guven, G., Bilgic, B., Bras, J., Guerreiro, R., Beule, D., Dirnagl, U. and Sassi, C.
Scientific Reports 11 (1): 6072. 16 March 2021

Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L., Krupp, F., Harnett, D., Turko, P., Ambrozkiewicz, M.C., Sprink, T., Imami, K., Günnigmann, M., Zinnall, U., Vieira-Vieira, C.H., Schaub, T., Münster-Wandowski, A., Bürger, J., Borisova, E., Yamamoto, H., Rasin, M.R., Ohler, U., Beule, D., Mielke, T., Tarabykin, V., Landthaler, M., Kramer, G., Vida, I., Selbach, M. and Spahn, C.M.T.
Molecular Cell 81 (2): 304-322. 21 January 2021

SODAR Core: a Django-based framework for scientific data management and analysis web apps.
Nieminen, M., Stolpe, O., Schumann, F., Holtgrewe, M. and Beule, D.
Journal of Open Source Software 5 (55): 1584. 15 November 2020

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations.
Mattei, D., Ivanov, A., van Oostrum, M., Pantelyushin, S., Richetto, J., Mueller, F., Beffinger, M., Schellhammer, L., Vom Berg, J., Wollscheid, B., Beule, D., Paolicelli, R.C. and Meyer, U.
International Journal of Molecular Sciences 21 (21): 7944. 1 November 2020

Multiplexed quantification of four neuroblastoma DNA targets in a single droplet digital PCR reaction.
Peitz, C., Sprüssel, A., Linke, R.B., Astrahantseff, K., Grimaldi, M., Schmelz, K., Toedling, J., Schulte, J.H., Fischer, M., Messerschmidt, C., Beule, D., Keilholz, U., Eggert, A., Deubzer, H.E. and Lodrini, M.
Journal of Molecular Diagnostics 22 (11): 1309-1323. November 2020

Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC.
Messerschmidt, C., Obermayer, B., Klinghammer, K., Ochsenreither, S., Treue, D., Stenzinger, A., Glimm, H., Fröhling, S., Kindler, T., Brandts, C.H., Schulze-Osthoff, K., Weichert, W., Tinhofer, I., Klauschen, F., Keilholz, U., Beule, D. and Rieke, D.T.
International Journal of Cancer 147 (8): 2293-2302. 15 October 2020

Concepts and software package for efficient quality control in targeted metabolomics studies - MeTaQuaC.
Kuhring, M., Eisenberger, A., Schmidt, V., Kränkel, N., Leistner, D.M., Kirwan, J. and Beule, D.
Analytical Chemistry 92 (15): 10241-10245. 4 August 2020

VarFish: comprehensive DNA variant analysis for diagnostics and research.
Holtgrewe, M., Stolpe, O., Nieminen, M., Mundlos, S., Knaus, A., Kornak, U., Seelow, D., Segebrecht, L., Spielmann, M., Fischer-Zirnsak, B., Boschann, F., Scholl, U., Ehmke, N. and Beule, D.
Nucleic Acids Research 48 (W1): W162-W169. 2 July 2020

Heart-specific immune responses in an animal model of autoimmune-related myocarditis mitigated by an immunoproteasome inhibitor and genetic ablation.
Bockstahler, M., Fischer, A., Goetzke, C.C., Neumaier, H.L., Sauter, M., Kespohl, M., Müller, A.M., Meckes, C., Salbach, C., Schenk, M., Heuser, A., Landmesser, U., Weiner, J., Meder, B., Lehmann, L., Kratzer, A., Klingel, K., Katus, H.A., Kaya, Z. and Beling, A.
Circulation 141 (23): 1885-1902. 9 June 2020

Progression-dependent altered metabolism in osteosarcoma resulting in different nutrient source dependencies.
Fritsche-Guenther, R., Gloaguen, Y., Kirchner, M., Mertins, P., Tunn, P.U. and Kirwan, J.A.
Cancers 12 (6): 1371. 27 May 2020

Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model.
Akpa, C.A., Kleo, K., Oker, E., Tomaszewski, N., Messerschmidt, C., López, C., Wagener, R., Oehl-Huber, K., Dettmer, K., Schoeler, A., Lenze, D., Oefner, P.J., Beule, D., Siebert, R., Capper, D., Dimitrova, L. and Hummel, M.
BMC Cancer 20 (1): 427. 14 May 2020

Investigating APOE, APP-Aβ metabolism genes and Alzheimer's disease GWAS hits in brain small vessel ischemic disease.
Blumenau, S., Foddis, M., Müller, S., Holtgrewe, M., Bentele, K., Berchtold, D., Beule, D., Dirnagl, U. and Sassi, C.
Scientific Reports 10 (1): 7103. 28 April 2020

Digestiflow: from BCL to FASTQ with ease.
Holtgrewe, M., Messerschmidt, C., Nieminen, M. and Beule, D.
Bioinformatics 36 (6): 1983-1985. 15 March 2020

Paroxysmal tonic upgaze: a heterogeneous clinical condition responsive to carbonic anhydrase inhibition.
Quade, A., Thiel, A., Kurth, I., Holtgrewe, M., Elbracht, M., Beule, D., Eggermann, K., Scholl, U.I. and Häusler, M.
European Journal of Paediatric Neurology 25 : 181-186. March 2020

Support of a molecular tumour board by an evidence-based decision management system for precision oncology.
Lamping, M., Benary, M., Leyvraz, S., Messerschmidt, C., Blanc, E., Kessler, T., Schütte, M., Lenze, D., Jöhrens, K., Burock, S., Klinghammer, K., Ochsenreither, S., Sers, C., Schäfer, R., Tinhofer, I., Beule, D., Klauschen, F., Yaspo, M.L., Keilholz, U. and Rieke, D.T.
European Journal of Cancer 127 : 41-51. March 2020

Tracing tumorigenesis in a solid tumor model at single-cell resolution.
Praktiknjo, S.D., Obermayer, B., Zhu, Q., Fang, L., Liu, H., Quinn, H., Stoeckius, M., Kocks, C., Birchmeier, W. and Rajewsky, N.
Nature Communications 11 (1): 991. 20 February 2020

SCelVis: exploratory single cell data analysis on the desktop and in the cloud.
Obermayer, B., Holtgrewe, M., Nieminen, M., Messerschmidt, C. and Beule, D.
PeerJ 8 : e8607. 19 February 2020

Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model.
Thole, T.M., Toedling, J., Sprüssel, A., Pfeil, S., Savelyeva, L., Capper, D., Messerschmidt, C., Beule, D., Groeneveld-Krentz, S., Eckert, C., Gambara, G., Henssen, A.G., Finkler, S., Schulte, J.H., Sieber, A., Bluethgen, N., Regenbrecht, C.R.A., Künkele, A., Lodrini, M., Eggert, A. and Deubzer, H.E.
International Journal of Cancer 146 (4): 1031-1041. 15 February 2020

An exploratory investigation of brain collateral circulation plasticity after cerebral ischemia in two experimental C57BL/6 mouse models.
Foddis, M., Winek, K., Bentele, K., Mueller, S., Blumenau, S., Reichhart N, N., Crespo-Garcia, S., Harnett, D., Ivanov, A., Meisel, A., Joussen, A., Strauss, O., Beule, D., Dirnagl, U. and Sassi, C.
Journal of Cerebral Blood Flow and Metabolism 40 (2): 276-287. 1 February 2020

Generation and characterization of a mitotane-resistant adrenocortical cell line.
Seidel, E., Walenda, G., Messerschmidt, C., Obermayer, B., Peitzsch, M., Wallace, P., Bahethi, R., Yoo, T., Choi, M., Schrade, P., Bachmann, S., Liebisch, G., Eisenhofer, G., Beule, D. and Scholl, U.
Endocrine Connections 9 (2): 122-134. February 2020

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche, R.P., Rodriguez-Fos, E., Helmsauer, K., Burkert, M., MacArthur, I.C., Maag, J., Chamorro, R., Munoz-Perez, N., Puiggròs, M., Dorado Garcia, H., Bei, Y., Röefzaad, C., Bardinet, V., Szymansky, A., Winkler, A., Thole, T., Timme, N., Kasack, K., Fuchs, S., Klironomos, F., Thiessen, N., Blanc, E., Schmelz, K., Künkele, A., Hundsdörfer, P., Rosswog, C., Theissen, J., Beule, D., Deubzer, H., Sauer, S., Toedling, J., Fischer, M., Hertwig, F., Schwarz, R.F., Eggert, A., Torrents, D., Schulte, J.H. and Henssen, A.G.
Nature Genetics 52 (1): 29-34. January 2020

Modified protocol of harvesting, extraction, and normalization approaches for gas chromatography mass spectrometry-based metabolomics analysis of adherent cells grown under high fetal calf serum conditions.
Fritsche-Guenther, R., Bauer, A., Gloaguen, Y., Lorenz, M. and Kirwan, J.A.
Metabolites 10 (1): 2. 18 December 2019

let-7 microRNAs regulate microglial function and suppress glioma growth through Toll-like receptor 7.
Buonfiglioli, A., Efe, I.E., Guneykaya, D., Ivanov, A., Huang, Y., Orlowski, E., Krüger, C., Deisz, R.A., Markovic, D., Flüh, C., Newman, A.G., Schneider, U.C., Beule, D., Wolf, S.A., Dzaye, O., Gutmann, D.H., Semtner, M., Kettenmann, H. and Lehnardt, S.
Cell Reports 29 (11): 3460-3471. 10 December 2019

Targeted panel sequencing in pediatric primary cardiomyopathy supports a critical role of TNNI3.
Kühnisch, J., Herbst, C., Al-Wakeel-Marquard, N., Dartsch, J., Holtgrewe, M., Baban, A., Mearini, G., Hardt, J., Kolokotronis, K., Gerull, B., Carrier, L., Beule, D., Schubert, S., Messroghli, D., Degener, F., Berger, F. and Klaassen, S.
Clinical Genetics 96 (6): 549-559. December 2019

Identification and ranking of recurrent neo-epitopes in cancer.
Blanc, E., Holtgrewe, M., Dhamodaran, A., Messerschmidt, C., Willimsky, G., Blankenstein, T. and Beule, D.
BMC Medical Genomics 12 : 171. 27 November 2019

SigsPack, a package for cancer mutational signatures.
Schumann, F., Blanc, E., Messerschmidt, C., Blankenstein, T., Busse, A. and Beule, D.
BMC Bioinformatics 20 (1): 450. 2 September 2019

WiPP: workflow for improved peak picking for gas chromatography-mass spectrometry (GC-MS) data.
Borgsmüller, N., Gloaguen, Y., Opialla, T., Blanc, E., Sicard, E., Royer, A.L., Le Bizec, B., Durand, S., Migné, C., Pétéra, M., Pujos-Guillot, E., Giacomoni, F., Guitton, Y., Beule, D. and Kirwan, J.
Metabolites 9 (9): 171. 21 August 2019

AltamISA: a Python API for ISA-Tab files.
Kuhring, M., Nieminen, M., Kirwan, J., Beule, D. and Holtgrewe, M.
Journal of Open Source Software 4 (40): 1610. 20 August 2019

The anti-amyloid compound DO1 decreases plaque pathology and neuroinflammation-related expression changes in 5xFAD transgenic mice.
Boeddrich, A., Babila, J.T., Wiglenda, T., Diez, L., Jacob, M., Nietfeld, W., Huska, M.R., Haenig, C., Groenke, N., Buntru, A., Blanc, E., Meier, J.C., Vannoni, E., Erck, C., Friedrich, B., Martens, H., Neuendorf, N., Schnoegl, S., Wolfer, D.P., Loos, M., Beule, D., Andrade-Navarro, M.A. and Wanker, E.E.
Cell Chemical Biology 26 (1): 109-120. 17 January 2019

Multisite de novo mutations in human offspring after paternal exposure to ionizing radiation.
Holtgrewe, M., Knaus, A., Hildebrand, G., Pantel, J.T., de los Santos, M.R., Neveling, K., Goldmann, J., Schubach, M., Jäger, M., Coutelier, M., Mundlos, S., Beule, D., Sperling, K. and Krawitz, P.M.
Scientific Reports 8 (1): 14611. 2 October 2018

Parasitic nematodes exert antimicrobial activity and benefit from microbiota-driven support for host immune regulation.
Rausch, S., Midha, A., Kuhring, M., Affinass, N., Radonic, A., Kühl, A.A., Bleich, A., Renard, B.Y. and Hartmann, S.
Frontiers in Immunology 9 : 2282. October 2018

Transcriptional and translational differences of microglia from male and female brains.
Guneykaya, D., Ivanov, A., Perez Hernandez, D., Haage, V., Wojtas, B., Meyer, N., Maricos, M., Jordan, P., Buonfiglioli, A., Gielniewski, B., Ochocka, N., Cömert, C., Friedrich, C., Suarez Artiles, L., Kaminska, B., Mertins, P., Beule, D., Kettenmann, H. and Wolf, S.A.
Cell Reports 24 (10): 2773-2783. 4 September 2018

Silent witness: dual-species transcriptomics reveals epithelial immunological quiescence to helminth larval encounter and fostered larval development.
Ebner, F., Kuhring, M., Radonic, A., Midha, A., Renard, B.Y. and Hartmann, S.
Frontiers in Immunology 9 : 1868. 15 August 2018

MetExplore: collaborative edition and exploration of metabolic networks.
Cottret, L., Frainay, C., Chazalviel, M., Cabanettes, F., Gloaguen, Y., Camenen, E., Merlet, B., Heux, S., Portais, J.C., Poupin, N., Vinson, F. and Jourdan, F.
Nucleic Acids Research 46 (W1): W495-W502. 2 July 2018

Adipose tissue ATGL modifies the cardiac lipidome in pressure-overload-induced left ventricular failure.
Salatzki, J., Foryst-Ludwig, A., Bentele, K., Blumrich, A., Smeir, E., Ban, Z., Brix, S., Grune, J., Beyhoff, N., Klopfleisch, R., Dunst, S., Surma, M.A., Klose, C., Rothe, M., Heinzel, F.R., Krannich, A., Kershaw, E.E., Beule, D., Schulze, P.C., Marx, N. and Kintscher, U.
PLoS Genetics 14 (1): e1007171. 10 January 2018

HLA-MA: simple yet powerful matching of samples using HLA typing results.
Messerschmidt, C., Holtgrewe, M. and Beule, D.
Bioinformatics 33 (14): 2241-2242. 15 July 2017

Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models.
Eduati, F., Doldan-Martelli, V., Klinger, B., Cokelaer, T., Sieber, A., Kogera, F., Dorel, M., Garnett, M.J., Blüthgen, N. and Saez-Rodriguez, J.
Cancer Research 77 (12): 3364-3375. 15 June 2017

Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment.
Mattei, D., Ivanov, A., Ferrai, C., Jordan, P., Guneykaya, D., Buonfiglioli, A., Schaafsma, W., Przanowski, P., Deuther-Conrad, W., Brust, P., Hesse, S., Patt, M., Sabri, O., Ross, T.L., Eggen, B.J.L., Boddeke, E.W.G.M., Kaminska, B., Beule, D., Pombo, A., Kettenmann, H. and Wolf, S.A.
Translational Psychiatry 7 (5): e1120. 9 May 2017

Tumour ischaemia by interferon-γ resembles physiological blood vessel regression.
Kammertoens, T., Friese, C., Arina, A., Idel, C., Briesemeister, D., Rothe, M., Ivanov, A., Szymborska, A., Patone, G., Kunz, S., Sommermeyer, D., Engels, B., Leisegang, M., Textor, A., Fehling, H.J., Fruttiger, M., Lohoff, M., Herrmann, A., Yu, H., Weichselbaum, R., Uckert, W., Hübner, N., Gerhardt, H., Beule, D., Schreiber, H. and Blankenstein, T.
Nature 545 (7652): 98-102. 4 May 2017

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer.
Mamlouk, S., Childs, L.H., Aust, D., Heim, D., Melching, F., Oliveira, C., Wolf, T., Durek, P., Schumacher, D., Blaeker, H., von Winterfeld, M., Gastl, B., Moehr, K., Menne, A., Zeugner, S., Redmer, T., Lenze, D., Tierling, S., Moebs, M., Weichert, W., Folprecht, G., Blanc, E., Beule, D., Schaefer, R., Morkel, M., Klauschen, F., Leser, U. and Sers, C.
Nature Communications 8 : 14093. 25 January 2017

Preprint

Cytokines as potential novel therapeutic targets in severe inflammatory cardiomyopathy.
Suwalski, P., Golpour, A., Weiner, J., Musigk, N., Balzer, F., Giesa, N., Amr, A., Trebing, J., Sedaghat, F., Meder, B., Beule, D., Landmesser, U. and Heidecker, B.
bioRxiv : 2023.07.27.23293253. 4 August 2023

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M., Pascual-Leone, B.M., Löber, U., Kuhring, M., Zhang, B., Bruening, U., Fritsche-Guenther, R., Krzanowski, M., Vernengo, F.F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thiebeault, C., Corman, V., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
Freitag, K., Eede, P., Ivanov, A., Schneeberger, S., Borodina, T., Sauer, S., Beule, D. and Heppner, F.L.
bioRxiv : 2021.08.02.454573v1. 28 November 2021

Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19.
Nouailles, Geraldine, Wyler, E., Pennitz, P., Postmus, D., Vladrimirova, D., Kazmierski, J., Pott, F., Dietert, K., Mülleder, M.l, Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L., Suttorp, N., Ralser, M., Beule, D., Gruber, A., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Research Square : rs-148392/v1. 28 January 2021

YAP and β-catenin co-operate to drive oncogenesis in basal breast cancer.
Quinn, H., Koren, E., Vogel, R., Popp, O., Mertins, P., Messerschmidt, C., Marangoni, E., Fuchs, Y. and Birchmeier, W.
bioRxiv : 2020.06.05.115881. 6 June 2020

Portability of scientific workflows in NGS data analysis: a case study.
Schiefer, C., Bux, M., Brandt, J., Messerschmidt, C., Reinert, K., Beule, D. and Leser, U.
arXiv : 2006.03104. 4 June 2020

VarFish - Collaborative and comprehensive variant analysis for diagnosis and research.
Holtgrewe, M., Stolpe, O., Nieminen, M., Mundlos, S., Knaus, A., Kornak, U., Seelow, D., Segebrecht, L., Spielmann, M., Fischer-Zirnsak, B., Boschann, F., Scholl, U., Ehmke, N. and Beule, D.
bioRxiv : 2020.01.27.921965. 31 January 2020

A census of cell types and paracrine interactions in colorectal cancer.
Uhlitz, F., Bischoff, P., Sieber, A., Obermayer, B., Blanc, E., Lüthen, M., Sawitzki, B., Kamphues, C., Beule, D., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
bioRxiv : 2020.01.10.901579. 11 January 2020

SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud.
Obermayer, B., Holtgrewe, M., Nieminen, M., Messerschmidt, C. and Beule, D.
bioRxiv : 713008. 24 July 2019

Emergence of robust nucleosome patterns from an interplay of positioning mechanisms.
Nuebler, J., Wolff, M., Obermayer, B., Mobius, W. and Gerland, U.
bioRxiv : 431445. 1 October 2018

Other

Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
Schinke, C., Fernandez Vallone, V., Ivanov, A., Peng, Y., Körtvelyessy, P., Nolte, L., Huehnchen, P., Beule, D., Stachelscheid, H., Boehmerle, W. and Endres, M.
Elsevier. October 2021