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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. and Milek, M. and Beule, D. and Kluge, J. and Florian, S. and Sers, C. and Horst, D. and Morkel, M. and Bischoff, P.
Cellular Oncology 1 February 2024 (In Press)

2023

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J. and Theisen, S. and Dartsch, J. and Fritsche-Guenther, R. and Kirchner, M. and Obermayer, B. and Bauer, A. and Kahlert, A.K. and Rothe, M. and Beule, D. and Heuser, A. and Mertins, P. and Kirwan, J.A. and Berndt, N. and MacRae, C.A. and 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. and Chopra, A. and Weiner, J. and Beule, D. and 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. and Opitz, R. and Jyrch, S. and Megges, M. and Weiner, J. and Beule, D. and 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. and Heils, L. and Moos, V. and Weiß, F. and Krug, S.M. and Weiner, J. and Beule, D. and Gerhard, R. and 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. and Noerenberg, D. and Hennch, C. and Yoshida, K. and Hablesreiter, R. and Nimo, J. and Sasca, D. and Kirchner, M. and Mansouri, L. and Inoue, Y. and Wiegand, L. and Staiger, A.M. and Casadei, B. and Korkolopoulou, P. and Weiner, J. and Lopez-Guillermo, A. and Warth, A. and Schneider, T. and Nagy, Á. and Klapper, W. and Hummel, M. and Kanellis, G. and Anagnostopoulos, I. and Mertins, P. and Bullinger, L. and Rosenquist, R. and Vassilakopoulos, T.P. and Ott, G. and Ogawa, S. and Damm, F.
Leukemia 37 (11): 2237-2249. November 2023

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

Extracellular matrix remodeling in atopic dermatitis harnesses the onset of an asthmatic phenotype and is a potential contributor to the atopic march.
Graff, P. and Woerz, D. and Wilzopolski, J. and Voss, A. and Sarrazin, J. and Blimkie, T.M. and Weiner, J. and Kershaw, O. and Panwar, P. and Hackett, T. and Lau, S. and Brömme, D. and Beule, D. and Lee, Y.A. and Hancock, R.E.W. and Gruber, A.D. and Bäumer, W. and Hedtrich, S.
Journal of Investigative Dermatology 13 October 2023 (In Press)

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E. and Planas-Fèlix, M. and Burkert, M. and Puiggròs, M. and Toedling, J. and Thiessen, N. and Blanc, E. and Szymansky, A. and Hertwig, F. and Ishaque, N. and Beule, D. and Torrents, D. and Eggert, A. and Koche, R.P. and Schwarz, R.F. and Haase, K. and 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. and Postmus, D. and Stenzel, S. and Weiner, J. and Jansen, J. and Zapatero-Belinchón, F.J. and Olmer, R. and Richter, A. and Heinze, J. and Heinemann, N. and Mühlemann, B. and Schroeder, S. and Jones, T.C. and Müller, M.A. and Drosten, C. and Pich, A. and Thiel, V. and Martin, U. and Niemeyer, D. and Gerold, G. and 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. and Ginggen, K. and Ivanov, A. and Buckinx, A. and Lalive, A.L. and Tchenio, A. and Benson, S. and Vendrell, M. and D'Alessandro, A. and Beule, D. and Pellerin, L. and 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. and Benary, M. and Horak, P. and Lamping, M. and Stintzing, S. and Tinhofer, I. and Leyvraz, S. and Schäfer, R. and Klauschen, F. and Keller, U. and Stenzinger, A. and Fröhling, S. and Kurzrock, R. and Keilholz, U. and Rieke, D.T. and Jelas, I.
European Journal of Cancer 190 : 112925. September 2023

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

SODAR: managing multiomics study data and metadata.
Nieminen, M. and Stolpe, O. and Kuhring, M. and Weiner, J. and Pett, P. and 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. and Haenig, C. and Neuendorf, N. and Blanc, E. and Ivanov, A. and Kirchner, M. and Schleumann, P. and Bayraktaroğlu, I. and Richter, M. and Molenda, C.M. and Sporbert, A. and Zenkner, M. and Schnoegl, S. and Suenkel, C. and Schneider, L.S. and Rybak-Wolf, A. and Kochnowsky, B. and Byrne, L.M. and Wild, E.J. and Nielsen, J.E. and Dittmar, G. and Peters, O. and 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. and Weiner, J. and Bredow, J. and Zeitz, U. and Grittner, U. and Boschmann, M. and Dickmann, S. and Stobäus, N. and Schwartzenberg, R.J. and Brachs, M. and Spranger, J. and Mai, K.
Clinical Nutrition 42 (4): 559-567. April 2023

Mouse models of human multiple myeloma subgroups.
Winkler, W. and Farré Díaz, C. and Blanc, E. and Napieczynska, H. and Langner, P. and Werner, M. and Walter, B. and Wollert-Wulf, B. and Yasuda, T. and Heuser, A. and Beule, D. and Mathas, S. and Anagnostopoulos, I. and Rosenwald, A. and 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. and Blumenau, S. and Holtgrewe, M. and Paquette, K. and Westra, K. and Alonso, I. and Macario, M.d.C. and Morgadinho, A.S. and Velon, A.G. and Santo, G. and Santana, I. and Mönkäre, S. and Kuuluvainen, L. and Schleutker, J. and Pöyhönen, M. and Myllykangas, L. and Pavlovic, A. and Kostic, V. and Dobricic, V. and Lohmann, E. and Hanagasi, H. and Santos, M. and Guven, G. and Bilgic, B. and Bras, J. and Beule, D. and Dirnagl, U. and 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. and Pascual-Reguant, A. and Koehler, R. and Liebeskind, J. and Liebheit, A. and Bauherr, S. and Philipsen, L. and Dittmayer, C. and Laue, M. and von Manitius, R. and Elezkurtaj, S. and Durek, P. and Heinrich, F. and Heinz, G.A. and Guerra, G.M. and Obermayer, B. and Meinhardt, J. and Ihlow, J. and Radke, J. and Heppner, F.L. and Enghard, P. and Stockmann, H. and Aschman, T. and Schneider, J. and Corman, V.M. and Sander, L.E. and Mashreghi, M.F. and Conrad, T. and Hocke, A.C. and Niesner, R.A. and 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. and Keilholz, L. and Conrad, T. and Frentsch, M. and Blau, I.W. and Vuong, L. and Lesch, S. and Movasshagi, K. and Tietze-Stolley, C. and Loyal, L. and Henze, L. and Penack, O. and Stervbo, U. and Babel, N. and Haas, S. and Beule, D. and Bullinger, L. and Wittenbecher, Friedrich 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. and Eede, P. and Ivanov, A. and Sterczyk, N. and Schneeberger, S. and Borodina, T. and Sauer, S. and 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. and Weinhold, L. and Schmidt, A. and Holtgrewe, M. and Juranek, S.A. and Siewert, A. and Scheer, A.B. and Thieme, F. and Mangold, E. and Ishorst, N. and Brand, F.U. and Welzenbach, J. and Beule, D. and Paeschke, K. and Krawitz, P.M. and Ludwig, K.U.
Human Genetics and Genomics Advances 4 (1): 100166. 12 January 2023

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J. and Theisen, S. and Dartsch, J. and Fritsche-Guenther, R. and Kirchner, M. and Obermayer, B. and Bauer, A. and Kahlert, A.K. and Rothe, M. and Beule, D. and Heuser, A. and Mertins, P. and Kirwan, J.A. and Berndt, N. and MacRae, C.A. and Hubner, N. and Klaassen, S.
bioRxiv : 2023.01.10.523243. 10 January 2023

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

2022

State-of-the-art analytical methods of viral infections in human lung organoids.
Baumgardt, M. and Hülsemann, M. and Löwa, A. and Fatykhova, D. and Hoffmann, K. and Kessler, M. and Mieth, M. and Hellwig, K. and Frey, D. and Langenhagen, A. and Voss, A. and Obermayer, B. and Wyler, E. and Dökel, S. and Gruber, A.D. and Tölch, U. and Hippenstiel, S. and 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. and Obermayer, B. and Sugulle, M. and Herse, F. and Kräker, K. and Haase, N. and Langmia, I.M. and Müller, D.N. and Staff, A.C. and Beule, D. and Dechend, R.
International Journal of Molecular Sciences 23 (23): 15388. 6 December 2022

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M. and Pascual-Leone, B.M. and Löber, U. and Kuhring, M. and Zhang, B. and Bruening, U. and Fritsche-Guenther, R. and Krzanowski, M. and Vernengo, F.F. and Brumhard, S. and Röwekamp, I. and Bielecka, A.A. and Lesker, T.R. and Wyler, E. and Landthaler, M. and Mantei, A. and Meisel, C. and Caesar, S. and Thiebeault, C. and Corman, V. and Marko, L. and Suttorp, N. and Strowig, T. and Kurth, F. and Sander, L.E. and Li, Y. and Kirwan, J.A. and Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 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. and Obermayer, B. and Mache, C. and Fathykova, D. and Kessler, M. and Dökel, S. and Wyler, E. and Baumgardt, M. and Löwa, A. and Hoffmann, K. and Graff, P. and Schulze, J. and Mieth, M. and Hellwig, K. and Demir, Z. and Biere, B. and Brunotte, L. and Mecate-Zambrano, A. and Bushe, J. and Dohmen, M. and Hinze, C. and Elezkurtaj, S. and Tönnies, M. and Bauer, T.T. and Eggeling, S. and Tran, H.L. and Schneider, P. and Neudecker, J. and Rückert, J.C. and Schmidt-Ott, K.M. and Busch, J. and Klauschen, F. and Horst, D. and Radbruch, H. and Radke, J. and Heppner, F. and Corman, V.M. and Niemeyer, D. and Müller, M.A. and Goffinet, C. and Mothes, R. and Pascual-Reguant, A. and Hauser, A.E. and Beule, D. and Landthaler, M. and Ludwig, S. and Suttorp, N. and Witzenrath, M. and Gruber, A.D. and Drosten, C. and Sander, L.E. and Wolff, T. and 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. and Bartolomaeus, H. and Löber, U. and Behrens, F. and Bartolomaeus, T.U.P. and Anandakumar, H. and Wimmer, M. and Vu, D.L. and Kuhring, M. and Brüning, U. and Maifeld, A. and Geisberger, S. and Kempa, S. and Schumacher, F. and Kleuser, B. and Bufler, P. and Querfeld, U. and Kitschke, S. and Engler, D. and Kuhrt, L.D. and Drechsel, O. and Eckardt, K.U. and Forslund, S. and Thürmer, A. and McParland, V. and Kirwan, J. and 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. and Topczewska, P.M. and Jakob, M.O. and Yano, H. and Arifuzzaman, M. and Gao, X. and Boulekou, S. and Stokic-Trtica, V. and Leclère, P.S. and Preußer, A. and Rompe, Z.A. and Stamm, A. and Tsou, A.M. and Chu, C. and Heinrich, F.R. and Guerra, G.M. and Durek, P. and Ivanov, A. and Beule, D. and Helfrich, S. and Duerr, C.U. and Kühl, A.A. and Stehle, C. and Romagnani, C. and Mashreghi, M.F. and Diefenbach, A. and 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. and Bunse, M. and Joedicke, J.J. and Blanc, E. and Gudipati, V. and Moles, M.W. and Shiku, H. and Beule, D. and Huppa, J.B. and 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. and Lammoglia Cobo, M.F. and Stein, C.A. and Hsu, M.T. and Ben Hamza, A. and Penter, L. and Chen, X. and Buccitelli, C. and Popp, O. and Mertins, P. and Dietze, K. and Bullinger, L. and Moosmann, A. and Blanc, E. and Beule, D. and Gerbitz, A. and Strobel, J. and Hackstein, H. and Rahn, H.P. and Dornmair, K. and 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. and de Bortoli, T. and Horak, P. and Lamping, M. and Benary, M. and Jelas, I. and Rüter, G. and Berger, J. and Zettwitz, M. and Kagelmann, N. and Kind, A. and Fabian, F. and Beule, D. and Glimm, H. and Brors, B. and Stenzinger, A. and 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. and Mattei, D. and Radscheit, K. and Compagnion, A.C. and Pett, J.P. and Herzel, H.P. and Paolicelli, R.C. and Piwecka, M. and 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. and Kirsten, H. and Friedrich, V.D. and Wyler, E. and Goekeri, C. and Obermayer, B. and Heinz, G.A. and Mashreghi, M.F. and Büttner, M. and Trimpert, J. and Landthaler, M. and Suttorp, N. and Hocke, A.C. and Hippenstiel, S. and Tönnies, M. and Scholz, M. and Kuebler, W.M. and Witzenrath, M. and 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. and Kocks, C. and Leiz, J. and Karaiskos, N. and Boltengagen, A. and Cao, S. and Skopnik, C.M. and Klocke, J. and Hardenberg, J.H. and Stockmann, H. and Gotthardt, I. and Obermayer, B. and Haghverdi, L. and Wyler, E. and Landthaler, M. and Bachmann, S. and Hocke, A.C. and Corman, V. and Busch, J. and Schneider, W. and Himmerkus, N. and Bleich, M. and Eckardt, K.U. and Enghard, P. and 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. and Obermayer, B. and Weiner, J.M. and Zimmermann, K. and Anania, C. and Wagner, L.K. and Lyras, E.M. and Sapozhnikova, V. and Lara-Astiaso, D. and Prósper, F. and Lang, R. and Lupiáñez, D.G. and Beule, D. and Höpken, U.E. and Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
Hoffmann, K. and Obermayer, B. and Hönzke, K. and Fatykhova, D. and Demir, Z. and Löwa, A. and Teixeira Alves, L.G. and Wyler, E. and Lopez-Rodriguez, E. and Mieth, M. and Baumgardt, M. and Hoppe, J. and Firsching, T.C. and Tönnies, M. and Bauer, T.T. and Eggeling, S. and Tran, H.L. and Schneider, P. and Neudecker, J. and Rückert, J.C. and Gruber, A.D. and Ochs, M. and Landthaler, M. and Beule, D. and Suttorp, N. and Hippenstiel, S. and 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. and Koch, L. and Fischer-Zirnsak, B. and Horn, D. and Gehle, P. and Kornak, U. and 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. and Laser, K.T. and Klingel, K. and Dartsch, J. and Theisen, S. and Pickardt, T. and Holtgrewe, M. and Gärtner, A. and Berger, F. and Beule, D. and Milting, H. and Schubert, S. and 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. and Sterczyk, N. and Wendlinger, S. and Obermayer, B. and Schulz, J. and Farztdinov, V. and Mülleder, M. and Ralser, M. and Houtman, J. and Fleck, L. and Braeuning, C. and Sansevrino, R. and Hoffmann, C. and Milovanovic, D. and Sigrist, S.J. and Conrad, T. and Beule, D. and 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. and Trinks, A. and Wiederspahn, J. and Obermayer, B. and Pett, J.P. and Jurmeister, P. and Elsner, A. and Dziodzio, T. and Rückert, J.C. and Neudecker, J. and Falk, C. and Beule, D. and Sers, C. and Morkel, M. and Horst, D. and 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. and Suwalski, P. and Asgharian, H. and Du Zhipei, G. and Lin, H. and Weiner, J. and Holtgrewe, M. and Thibeault, C. and Müller, M. and Wang, X. and Karadeniz, Z. and Saccomanno, J. and Doehn, J.M. and Hübner, R.H. and Hinzmann, B. and Blüher, A. and Siemann, S. and Telman, D. and Suttorp, N. and Witzenrath, M. and Hippenstiel, S. and Skurk, C. and Poller, W. and Sander, L.E. and Beule, D. and Kurth, F. and Guettouche, T. and Landmesser, U. and Berka, J. and Luong, K. and Rubelt, F. and Heidecker, B.
EClinicalMedicine 48 : 101438. June 2022

Venn diagrams may indicate erroneous statistical reasoning in transcriptomics.
Weiner, J. and 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. and Willimsky, G. and Peuker, C.A. and Rhein, S. and Hansmann, L. and Blankenstein, T. and Blanc, E. and Beule, D. and Keller, U. and 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. and 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. and von Arx, A.S. and Cruz-Ochoa, N. and Dawson, K. and Ivanov, A. and Mueller, F.S. and Lin, H.Y. and Amport, R. and Mildenberger, W. and Mattei, D. and Beule, D. and Földy, C. and Greter, M. and Notter, T. and Meyer, U.
Science Advances 8 (9): eabi6672. 4 March 2022

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
Freitag, K. and Eede, P. and Ivanov, A. and Schneeberger, S. and Borodina, T. and Sauer, S. and Beule, D. and Heppner, F.
Research Square : rs.3.rs-1362379/v1. 28 February 2022

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P. and Astaburuaga-García, R. and Bonaguro, L. and Brumhard, S. and Michalick, L. and Lippert, L.J. and Kostevc, T. and Gäbel, C. and Schneider, M. and Streitz, M. and Demichev, V. and Gemünd, I. and Barone, M. and Tober-Lau, P. and Helbig, E.T. and Hillus, D. and Petrov, L. and Stein, J. and Dey, H.P. and Paclik, D. and Iwert, C. and Mülleder, M. and Aulakh, S.K. and Djudjaj, S. and Bülow, R.D. and Mei, H.E. and Schulz, A.R. and Thiel, A. and Hippenstiel, S. and Saliba, A.E. and Eils, R. and Lehmann, I. and Mall, M.A. and Stricker, S. and Röhmel, J. and Corman, V.M. and Beule, D. and Wyler, E. and Landthaler, M. and Obermayer, B. and von Stillfried, S. and Boor, P. and Demir, M. and Wesselmann, H. and Suttorp, N. and Uhrig, A. and Müller-Redetzky, H. and Nattermann, J. and Kuebler, W.M. and Meisel, C. and Ralser, M. and Schultze, J.L. and Aschenbrenner, A.C. and Thibeault, C. and Kurth, F. and Sander, L.E. and 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. and Holtgrewe, M. and Jäger, M. and Flöttman, R. and Mensah, M.A. and Spielmann, M. and Krawitz, P. and Horn, D. and Beule, D. and Mundlos, S.
European Journal of Human Genetics 30 (2): 178-186. February 2022

2021

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

The single-cell transcriptional landscape of lung carcinoid tumors.
Bischoff, P. and Trinks, A. and Wiederspahn, J. and Obermayer, B. and Pett, J.P. and Jurmeister, P. and Elsner, A. and Dziodzio, T. and Rückert, J.C. and Neudecker, J. and Falk, C. and Beule, D. and Sers, C. and Morkel, M. and Horst, D. and Klauschen, F. and Blüthgen, N.
bioRxiv : 2021.12.07.471416. 8 December 2021

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

Depletion of cardiac cardiolipin synthase alters systolic and diastolic function.
Smeir, E. and Leberer, S. and Blumrich, A. and Vogler, G. and Vasiliades, A. and Dresen, S. and Jaeger, C. and Gloaguen, Y. and Klose, C. and Beule, D. and Schulze, P.C. and Bodmer, R. and 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. and Klinger, B. and Mari, T. and Toedling, J. and Blanc, E. and Messerschmidt, C. and Nadler-Holly, M. and Ziehm, M. and Sieber, A. and Hertwig, F. and Beule, D. and Eggert, A. and Schulte, J.H. and 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. and Bischoff, P. and Peidli, S. and Sieber, A. and Trinks, A. and Lüthen, M. and Obermayer, B. and Blanc, E. and Ruchiy, Y. and Sell, T. and Mamlouk, S. and Arsie, R. and Wei, T.T. and Klotz-Noack, K. and Schwarz, R.F. and Sawitzki, B. and Kamphues, C. and Beule, D. and Landthaler, M. and Sers, C. and Horst, D. and Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

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

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.
Weiner, J. and Suwalski, P. and Holtgrewe, M. and Rakitko, A. and Thibeault, C. and Müller, M. and Patriki, D. and Quedenau, C. and Krüger, U. and Ilinsky, V. and Popov, I. and Balnis, J. and Jaitovich, A. and Helbig, E.T. and Lippert, L.J. and Stubbemann, P. and Real, L.M. and Macías, J. and Pineda, J.A. and Fernandez-Fuertes, M. and Wang, X. and Karadeniz, Z. and Saccomanno, J. and Doehn, J.M. and Hübner, R.H. and Hinzmann, B. and Salvo, M. and Blueher, A. and Siemann, S. and Jurisic, S. and Beer, J.H. and Rutishauser, J. and Wiggli, B. and Schmid, H. and Danninger, K. and Binder, R. and Corman, V.M. and Mühlemann, B. and Arjun Arkal, R. and Fragiadakis, G.K. and Mick, E. and Calfee, C.S. and Erle, D.J. and Hendrickson, C.M. and Kangelaris, K.N. and Krummel, M.F. and Woodruff, P.G. and Langelier, C.R. and Venkataramani, U. and García, F. and Zyla, J. and Drosten, C. and Braun, A. and Jones, T.C. and Suttorp, N. and Witzenrath, M. and Hippenstiel, S. and Zemojtel, T. and Skurk, C. and Wolfgang, P. and Borodina, T. and Ripke, S. and Sander, L.E. and Beule, D. and Landmesser, U. and Guettouche, T. and 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. and Siddiqui, J. and Rakijas, J. and Nicolay, B. and Lin, C. and Khan, E. and Patel, R. and Morris, R. and Wyler, E. and Boukhali, M. and Balasubramanyam, J. and Ranjith Kumar, R. and Van Rechem, C. and Vogel, C. and Elchuri, S.V. and Landthaler, M. and Obermayer, B. and Haas, W. and 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. and Wyler, E. and Pennitz, P. and Postmus, D. and Vladimirova, D. and Kazmierski, J. and Pott, F. and Dietert, K. and Muelleder, M. and Farztdinov, V. and Obermayer, B. and Wienhold, S.M. and Andreotti, S. and Hoefler, T. and Sawitzki, B. and Drosten, C. and Sander, L.E. and Suttorp, N. and Ralser, M. and Beule, D. and Gruber, A.D. and Goffinet, C. and Landthaler, M. and 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. and Holtgrewe, M. and Al-Wakeel-Marquard, N. and Opgen-Rhein, B. and Dartsch, J. and Herbst, C. and Beule, D. and Pickardt, T. and Klingel, K. and Messroghli, D. and Berger, F. and Schubert, S. and 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. and Foddis, M. and Blumenau, S. and Müller, S. and Kajetan, B. and Holtgrewe, M. and Kola, V. and 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. and Vallone, V.F. and Ivanov, A. and Peng, Y. and Körtvelyessy, P. and Nolte, L. and Huehnchen, P. and Beule, D. and Stachelscheid, H. and 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. and Heimann, A. and Obermayer, B. and Ciraolo, E. and Althoff, S. and Ruß, J. and Grunert, C. and Busse, A. and Bullinger, L. and Pezzutto, A. and Blankenstein, T. and Beule, D. and Na, I.K.
International Journal of Cancer 148 (12): 3097-3110. 15 June 2021

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M. and Klinger, B. and Mari, T. and Toedling, J. and Blanc, E. and Messerschmidt, C. and Nadler-Holly, M. and Ziehm, M. and Sieber, A. and Hertwig, F. and Beule, D. and Eggert, A. and Schulte, J.H. and Selbach, M. and Blüthgen, N.
bioRxiv : 2021.06.14.448322. 14 June 2021

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P. and Astaburuaga-García, R. and Bonaguro, L. and Brumhard, S. and Michalick, L. and Lippert, L.J. and Kostevc, T. and Gäbel, C. and Schneider, M. and Streitz, M. and Demichev, V. and Gemünd, I. and Barone, M. and Tober-Lau, P. and Helbig, E.T. and Stein, J. and Dey, H.P. and Paclik, D. and Mülleder, M. and Aulakh, S.K. and Mei, H.E. and Schulz, A.R. and Hippenstiel, S. and Corman, V.M. and Beule, D. and Wyler, E. and Landthaler, M. and Obermayer-Wasserscheid, B. and Boor, P. and Demir, M. and Wesselmann, H. and Suttorp, N. and Uhrig, A. and Müller-Redetzky, H. and Nattermann, J. and Kuebler, W.M. and Meisel, C. and Ralser, M. and Schultze, J.L. and Aschenbrenner, A.C. and Thibeault, C. and Kurth, F. and Sander, L.E. and Blüthgen, N. and Sawitzki, B.
medRxiv : 2021.06.08.21258481. 11 June 2021

YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer.
Quinn, H.M. and Vogel, R. and Popp, O. and Mertins, P. and Lan, L. and Messerschmidt, C. and Landshammer, A. and Lisek, K. and Château-Joubert, S. and Marangoni, E. and Koren, E. and 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. and Mösbauer, K. and Franke, V. and Diag, A. and Gottula, L.T. and Arsiè, R. and Klironomos, F. and Koppstein, D. and Hönzke, K. and Ayoub, S. and Buccitelli, C. and Hoffmann, K. and Richter, A. and Legnini, I. and Ivanov, A. and Mari, T. and Del Giudice, S. and Papies, J. and Praktiknjo, S. and Meyer, T.F. and Müller, M.A. and Niemeyer, D. and Hocke, A. and Selbach, M. and Akalin, A. and Rajewsky, N. and 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. and Foddis, M. and Blumenau, S. and Müller, S. and Bentele, K. and Holtgrewe, M. and Kun-Rodrigues, C. and Alonso, I. and do Carmo Macario, M. and Morgadinho, A.S. and Velon, A.G. and Santo, G. and Santana, I. and Mönkäre, S. and Kuuluvainen, L. and Schleutker, J. and Pöyhönen, M. and Myllykangas, L. and Senatore, A. and Berchtold, D. and Winek, K. and Meisel, A. and Pavlovic, A. and Kostic, V. and Dobricic, V. and Lohmann, E. and Hanagasi, H. and Guven, G. and Bilgic, B. and Bras, J. and Guerreiro, R. and Beule, D. and Dirnagl, U. and Sassi, C.
Scientific Reports 11 (1): 6072. 16 March 2021

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

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

2020

Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2.
Nouailles, G. and Wyler, E. and Pennitz, P. and Postmus, D. and Vladimirova, D. and Kazmierski, J. and Pott, F. and Dietert, K. and Mülleder, M. and Farztdinov, V. and Obermayer, B. and Wienhold, S.M. and Andreotti, S. and Höfler, T. and Sawitzki, B. and Drosten, C. and Sander, L.E. and Suttorp, N. and Ralser, M. and Beule, D. and Gruber, A.D. and Goffinet, C. and Landthaler, M. and Trimpert, J. and Witzenrath, M.
bioRxiv : 2020.12.18.423524. 19 December 2020

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma.
Bischoff, P. and Trinks, A. and Obermayer, B. and Pett, J.P. and Lehmann, A. and Jurmeister, P. and Elsner, A. and Dziodzio, T. and Rückert, J.C. and Neudecker, J. and Falk, C. and Beule, D. and Sers, C. and Morkel, M. and Horst, D. and Blüthgen, N. and Klauschen, F.
bioRxiv : 2020.12.11.419606. 11 December 2020

SODAR Core: a Django-based framework for scientific data management and analysis web apps.
Nieminen, M. and Stolpe, O. and Schumann, F. and 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. and Ivanov, A. and van Oostrum, M. and Pantelyushin, S. and Richetto, J. and Mueller, F. and Beffinger, M. and Schellhammer, L. and Vom Berg, J. and Wollscheid, B. and Beule, D. and 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. and Sprüssel, A. and Linke, R.B. and Astrahantseff, K. and Grimaldi, M. and Schmelz, K. and Toedling, J. and Schulte, J.H. and Fischer, M. and Messerschmidt, C. and Beule, D. and Keilholz, U. and Eggert, A. and 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. and Obermayer, B. and Klinghammer, K. and Ochsenreither, S. and Treue, D. and Stenzinger, A. and Glimm, H. and Fröhling, S. and Kindler, T. and Brandts, C.H. and Schulze-Osthoff, K. and Weichert, W. and Tinhofer, I. and Klauschen, F. and Keilholz, U. and Beule, D. and Rieke, D.T.
International Journal of Cancer 147 (8): 2293-2302. 15 October 2020

Deep learning assisted peak curation for large scale LC-MS Metabolomics.
Gloaguen, Y. and Kirwan, J. and Beule, D.
bioRxiv : 2020.08.09.242727. 10 August 2020

Concepts and software package for efficient quality control in targeted metabolomics studies - MeTaQuaC.
Kuhring, M. and Eisenberger, A. and Schmidt, V. and Kränkel, N. and Leistner, D.M. and 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. and Stolpe, O. and Nieminen, M. and Mundlos, S. and Knaus, A. and Kornak, U. and Seelow, D. and Segebrecht, L. and Spielmann, M. and Fischer-Zirnsak, B. and Boschann, F. and Scholl, U. and 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. and Fischer, A. and Goetzke, C.C. and Neumaier, H.L. and Sauter, M. and Kespohl, M. and Müller, A.M. and Meckes, C. and Salbach, C. and Schenk, M. and Heuser, A. and Landmesser, U. and Weiner, J. and Meder, B. and Lehmann, L. and Kratzer, A. and Klingel, K. and Katus, H.A. and Kaya, Z. and Beling, A.
Circulation 141 (23): 1885-1902. 9 June 2020

YAP and β-catenin co-operate to drive oncogenesis in basal breast cancer.
Quinn, H. and Koren, E. and Vogel, R. and Popp, O. and Mertins, P. and Messerschmidt, C. and Marangoni, E. and 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. and Bux, M. and Brandt, J. and Messerschmidt, C. and Reinert, K. and Beule, D. and Leser, U.
arXiv : 2006.03104. 4 June 2020

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

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations.
Mattei, D. and Ivanov, A. and van Oostrum, M. and Pantelyushin, S. and Richetto, J. and Mueller, F. and Beffinger, M. M. and Schellhammer, L. and vom Berg, J. and Wollscheid, B. and Beule, D. and Paolicelli, R.C. and Meyer, U.
bioRxiv : 2020.05.14.095422. 16 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. and Kleo, K. and Oker, E. and Tomaszewski, N. and Messerschmidt, C. and López, C. and Wagener, R. and Oehl-Huber, K. and Dettmer, K. and Schoeler, A. and Lenze, D. and Oefner, P.J. and Beule, D. and Siebert, R. and Capper, D. and Dimitrova, L. and Hummel, M.
BMC Cancer 20 (1): 427. 14 May 2020

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention.
Wyler, E. and Mösbauer, K. and Franke, V. and Diag, A. and Gottula, L.T. and Arsie, R. and Klironomos, F. and Koppstein, D. and Ayoub, S. and Buccitelli, C. and Richter, A. and Legnini, I. and Ivanov, A. and Mari, T. and Del Giudice, S. and Papies, J.P. and Müller, M.A. and Niemeyer, D. and Selbach, M. and Akalin, A. and Rajewsky, N. and Drosten, C. and Landthaler, M.
bioRxiv : 2020.05.05.079194. 5 May 2020

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

Digestiflow: from BCL to FASTQ with ease.
Holtgrewe, M. and Messerschmidt, C. and 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. and Thiel, A. and Kurth, I. and Holtgrewe, M. and Elbracht, M. and Beule, D. and Eggermann, K. and 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. and Benary, M. and Leyvraz, S. and Messerschmidt, C. and Blanc, E. and Kessler, T. and Schütte, M. and Lenze, D. and Jöhrens, K. and Burock, S. and Klinghammer, K. and Ochsenreither, S. and Sers, C. and Schäfer, R. and Tinhofer, I. and Beule, D. and Klauschen, F. and Yaspo, M.L. and 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. and Obermayer, B. and Zhu, Q. and Fang, L. and Liu, H. and Quinn, H. and Stoeckius, M. and Kocks, C. and 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. and Holtgrewe, M. and Nieminen, M. and 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. and Toedling, J. and Sprüssel, A. and Pfeil, S. and Savelyeva, L. and Capper, D. and Messerschmidt, C. and Beule, D. and Groeneveld-Krentz, S. and Eckert, C. and Gambara, G. and Henssen, A.G. and Finkler, S. and Schulte, J.H. and Sieber, A. and Bluethgen, N. and Regenbrecht, C.R.A. and Künkele, A. and Lodrini, M. and Eggert, A. and Deubzer, H.E.
International Journal of Cancer 146 (4): 1031-1041. 15 February 2020

The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L. and Krupp, F. and Turko, P. and Ambrozkiewicz, M.C. and Sprink, T. and Imami, K. and Vieira-Vieira, C.H. and Schaub, T. and Harnett, D. and Münster-Wandowski, A. and Bürger, J. and Zinnall, U. and Borisova, E. and Yamamoto, H. and Rasin, M.R. and Beule, D. and Landthaler, M. and Mielke, T. and Tarabykin, V. and Vida, I. and Selbach, M. and Spahn, C.M.T.
bioRxiv : 2020.02.08.939488. 10 February 2020

An exploratory investigation of brain collateral circulation plasticity after cerebral ischemia in two experimental C57BL/6 mouse models.
Foddis, M. and Winek, K. and Bentele, K. and Mueller, S. and Blumenau, S. and Reichhart N, N. and Crespo-Garcia, S. and Harnett, D. and Ivanov, A. and Meisel, A. and Joussen, A. and Strauss, O. and Beule, D. and 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. and Walenda, G. and Messerschmidt, C. and Obermayer, B. and Peitzsch, M. and Wallace, P. and Bahethi, R. and Yoo, T. and Choi, M. and Schrade, P. and Bachmann, S. and Liebisch, G. and Eisenhofer, G. and Beule, D. and Scholl, U.
Endocrine Connections 9 (2): 122-134. February 2020

VarFish - Collaborative and comprehensive variant analysis for diagnosis and research.
Holtgrewe, M. and Stolpe, O. and Nieminen, M. and Mundlos, S. and Knaus, A. and Kornak, U. and Seelow, D. and Segebrecht, L. and Spielmann, M. and Fischer-Zirnsak, B. and Boschann, F. and Scholl, U. and 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. and Bischoff, P. and Sieber, A. and Obermayer, B. and Blanc, E. and Lüthen, M. and Sawitzki, B. and Kamphues, C. and Beule, D. and Sers, C. and Horst, D. and Blüthgen, N. and Morkel, M.
bioRxiv : 2020.01.10.901579. 11 January 2020

Concepts and software package for efficient quality control in targeted metabolomics studies - MeTaQuaC.
Kuhring, M. and Eisenberger, A. and Schmidt, V. and Kränkel, N. and Leistner, D.M. and Kirwan, J. and Beule, D.
bioRxiv : 2020.01.10.901710. 11 January 2020

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

2019

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. and Bauer, A. and Gloaguen, Y. and 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. and Efe, I.E. and Guneykaya, D. and Ivanov, A. and Huang, Y. and Orlowski, E. and Krüger, C. and Deisz, R.A. and Markovic, D. and Flüh, C. and Newman, A.G. and Schneider, U.C. and Beule, D. and Wolf, S.A. and Dzaye, O. and Gutmann, D.H. and Semtner, M. and 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. and Herbst, C. and Al-Wakeel-Marquard, N. and Dartsch, J. and Holtgrewe, M. and Baban, A. and Mearini, G. and Hardt, J. and Kolokotronis, K. and Gerull, B. and Carrier, L. and Beule, D. and Schubert, S. and Messroghli, D. and Degener, F. and Berger, F. and Klaassen, S.
Clinical Genetics 96 (6): 549-559. December 2019

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

SigsPack, a package for cancer mutational signatures.
Schumann, F. and Blanc, E. and Messerschmidt, C. and Blankenstein, T. and 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. and Gloaguen, Y. and Opialla, T. and Blanc, E. and Sicard, E. and Royer, A.L. and Le Bizec, B. and Durand, S. and Migné, C. and Pétéra, M. and Pujos-Guillot, E. and Giacomoni, F. and Guitton, Y. and Beule, D. and Kirwan, J.
Metabolites 9 (9): 171. 21 August 2019

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

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

WiPP: workflow for improved peak picking for gas chromatography-mass spectrometry (GC-MS) data.
Borgsmüller, N. and Gloaguen, Y. and Opialla, T. and Blanc, E. and Sicard, E. and Royer, A.L. and Le Bizec, B. and Durand, S. and Migné, C. and Pétéra, M. and Pujos-Guillot, E. and Giacomoni, F. and Guitton, Y. and Beule, D. and Kirwan, J.
bioRxiv : 713925. 24 July 2019

Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC.
Messerschmidt, C. and Obermayer, B. and Klinghammer, K. and Ochsenreither, S. and Treue, D. and Stenzinger, A. and Glimm, H. and Fröhling, S. and Kindler, T. and Brandts, C.H. and Schulze-Osthoff, K. and Weichert, W. and Tinhofer, I. and Klauschen, F. and Keilholz, U. and Beule, D. and Rieke, D.T.
bioRxiv : 586396. 28 March 2019

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

2018

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

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

Parasitic nematodes exert antimicrobial activity and benefit from microbiota-driven support for host immune regulation.
Rausch, S. and Midha, A. and Kuhring, M. and Affinass, N. and Radonic, A. and Kühl, A.A. and Bleich, A. and 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. and Ivanov, A. and Perez Hernandez, D. and Haage, V. and Wojtas, B. and Meyer, N. and Maricos, M. and Jordan, P. and Buonfiglioli, A. and Gielniewski, B. and Ochocka, N. and Cömert, C. and Friedrich, C. and Suarez Artiles, L. and Kaminska, B. and Mertins, P. and Beule, D. and 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. and Kuhring, M. and Radonic, A. and Midha, A. and Renard, B.Y. and Hartmann, S.
Frontiers in Immunology 9 : 1868. 15 August 2018

Identification and ranking of recurrent neo-epitopes in cancer.
Blanc, E. and Holtgrewe, M. and Dhamodaran, A. and Messerschmidt, C. and Willimsky, G. and Blankenstein, T. and Beule, D.
bioRxiv : 389437. 10 August 2018

MetExplore: collaborative edition and exploration of metabolic networks.
Cottret, L. and Frainay, C. and Chazalviel, M. and Cabanettes, F. and Gloaguen, Y. and Camenen, E. and Merlet, B. and Heux, S. and Portais, J.C. and Poupin, N. and 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. and Foryst-Ludwig, A. and Bentele, K. and Blumrich, A. and Smeir, E. and Ban, Z. and Brix, S. and Grune, J. and Beyhoff, N. and Klopfleisch, R. and Dunst, S. and Surma, M.A. and Klose, C. and Rothe, M. and Heinzel, F.R. and Krannich, A. and Kershaw, E.E. and Beule, D. and Schulze, P.C. and Marx, N. and Kintscher, U.
PLoS Genetics 14 (1): e1007171. 10 January 2018

2017

HLA-MA: simple yet powerful matching of samples using HLA typing results.
Messerschmidt, C. and 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. and Doldan-Martelli, V. and Klinger, B. and Cokelaer, T. and Sieber, A. and Kogera, F. and Dorel, M. and Garnett, M.J. and 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. and Ivanov, A. and Ferrai, C. and Jordan, P. and Guneykaya, D. and Buonfiglioli, A. and Schaafsma, W. and Przanowski, P. and Deuther-Conrad, W. and Brust, P. and Hesse, S. and Patt, M. and Sabri, O. and Ross, T.L. and Eggen, B.J.L. and Boddeke, E.W.G.M. and Kaminska, B. and Beule, D. and Pombo, A. and 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. and Friese, C. and Arina, A. and Idel, C. and Briesemeister, D. and Rothe, M. and Ivanov, A. and Szymborska, A. and Patone, G. and Kunz, S. and Sommermeyer, D. and Engels, B. and Leisegang, M. and Textor, A. and Fehling, H.J. and Fruttiger, M. and Lohoff, M. and Herrmann, A. and Yu, H. and Weichselbaum, R. and Uckert, W. and Hübner, N. and Gerhardt, H. and Beule, D. and 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. and Childs, L.H. and Aust, D. and Heim, D. and Melching, F. and Oliveira, C. and Wolf, T. and Durek, P. and Schumacher, D. and Blaeker, H. and von Winterfeld, M. and Gastl, B. and Moehr, K. and Menne, A. and Zeugner, S. and Redmer, T. and Lenze, D. and Tierling, S. and Moebs, M. and Weichert, W. and Folprecht, G. and Blanc, E. and Beule, D. and Schaefer, R. and Morkel, M. and Klauschen, F. and Leser, U. and Sers, C.
Nature Communications 8 : 14093. 25 January 2017

2016

HLA-MA: Simple yet powerful matching of samples using HLA typing results.
Messerschmidt, C. and Holtgrewe, M. and Beule, D.
bioRxiv : 066548. 24 August 2016

This list was generated on Fri Mar 29 02:24:24 2024 CET.
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