Publications

Preprints

Matthias M. Fischer, Nils Blüthgen. On tumoural growth and treatment under cellular dedifferentiation bioRxiv 2022.05.10.491343; doi: https://doi.org/10.1101/2022.05.10.491343

Geraldine Nouailles, Julia M. Adler, Peter Pennitz, Stefan Peidli, Gustavo Teixeira Alves, Morris Baumgart, Judith Bushe, Anne Voss, Alina Langenhagen, Fabian Pott, Julia Kazmierski, Cengiz Goekeri, Szandor Simmons, Na Xing, Christine Langner, Ricardo Martin Vidal, Azza Abdelgawad, Susanne Herwig, Günter Cichon, Daniela Niemeyer, Christian Drosten, Christine Goffinet, Markus Landthaler, Nils Blüthgen, Haibo Wu, Martin Witzenrath, Achim D. Gruber, Samantha D. Praktiknjo, Nikolaus Osterrieder, Emanuel Wyler, Dusan Kunec, Jakob Trimpert. A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants. bioRxiv 2022.05.16.492138; doi: https://doi.org/10.1101/2022.05.16.492138

Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Andrew Janowczyk, Inti Zlobec, Dagmar Kainmueller Panoptic segmentation with highly imbalanced semantic labels, arXiv:2203.11692

Sell, T.; Klotz, C.; Fischer, M. MAstaburuaga-Garcia, R.; Krug, S.; Drost, J.; Clevers, H.; Morkel, M. and Blüthgen, N. Oncogenic signalling is coupled to colorectal cancer cell differentiation state. bioRxiv, 2022 http://dx.doi.org/10.1101/2022.04.07.487491

 

Journal Papers

2022

Grabe, S., Mahammadov, E., Olmo, M. D., & Herzel, H. (2022). Synergies of Multiple Zeitgebers Tune Entrainment. Frontiers in Network Physiology, 1.

J.A. Fries*, N. Seelam*, G. Altay*, L. Weber*, M. Kang*, D. Datta*, R. Su*, S. Garda*, B. Wang, S. Ott, M. Samwald, W. Kusa (2022). Dataset Debt in Biomedical Language Modeling. Workshop on Challenges & Perspectives in Creating Large Language Models 2022 (accepted). *:Equal contribution

Garda S., Lenihan-Geels F., Proft S., Hochmuth S., Schülke M., Seelow D., et al. RegEl corpus: Identifying DNA regulatory elements in the scientific literature. Database Oxf. 2022;in press.

Olmo MD, Grabe S, Herzel H. Mathematical Modeling in Circadian Rhythmicity. Methods Mol Biol. 2022;2482:55-80. doi: 10.1007/978-1-0716-2249-0_4

Wyler E, Adler JM, Eschke K, Teixeira Alves G, Peidli S, Pott F, Kazmierski J, Michalick L, Kershaw O, Bushe J, Andreotti S, Pennitz P, Abdelgawad A, Postmus D, Goffinet C, Kreye J, Reincke SM, Prüss H, Blüthgen N, Gruber AD, Kuebler WM, Witzenrath M, Landthaler M, Nouailles G, Trimpert J. Mol Ther. 2022 May 4;30(5):1952-1965. doi: 10.1016/j.ymthe.2022.03.014

Georg, P. *; Astaburuaga-Garcia, 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. *, Sawitzki, B. * Complement activation induces excessive T cell cytotoxicity in severe COVID-19. Cell, 185: 493-512, 2022. 

Fischer, M M; Herzel, H., Blüthgen, N. Mathematical modelling identifies conditions for maintaining and escaping feedback control in the intestinal epithelium. Scientific Reports, 12: 5569, 2022 

Bischoff, P; Trinks, A; Wiederspahn, J; Obermayer, B; Pett, JP; Jurmeister, P; Elsner, A; Dziodzio, T; Rückert, JC; Neudecker, J; Falk, C; Beule, D; Sers, C; Morkel, M; Horst, D; Klauschen, F and Blüthgen, N The single-cell transcriptional landscape of lung carcinoid tumors. Int J Cancer 2022 Jun 15;150(12):2058-2071. doi: 10.1002/ijc.33995

 

2021

Weber, L., Sänger, M., Garda, S., Barth, F., Alt, C. and Leser, U. (2021). Humboldt@DrugProt: Chemical-Protein Relation Extraction with Pretrained Transformers and Entity Descriptions. 7th International BioCreative Challenge Evaluation.

Weber, L., Garda, S., Münchmeyer, J. and Leser, U. (2021). Extend, don't rebuild: Phrasing conditional graph modification as autoregressive sequence labelling. EMNLP, Punta Cana, Dominican Republic.

Garda, S., Schwarz, J. M., Schuelke, M., Leser, U. and Seelow, D. (2021). Public data sources for regulatory genomic features. Medizinische Genetik

Kassuhn, W; Klein, O; Darb-Esfahani, S; Lammert, H; Handzik, S; Taube, ET; Schmitt, WD; Keunecke, C; Horst, D; Dreher, F; George, J; Bowtell, DD; Dorigo, O; Hummel, M; Sehouli, J; Blüthgen, N; Kulbe, H and Braicu, EI Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging. Cancers, 13: 1512, 2021

Josef Lorenz Rumberger, Xiaoyan Yu, Peter Hirsch, Melanie Dohmen, Vanessa Emanuela Guarino, Ashkan Mokarian, Lisa Mais, Jan Funke, Dagmar Kainmüller; How Shift Equivariance Impacts Metric Learning for Instance Segmentation. Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV), 2021, pp. 7128-7136

Schmelz K, Toedling J, Huska M, Cwikla MC, Kruetzfeldt LM, Proba J, Ambros PF, Ambros IM, Boral S, Lodrini M, Chen CY, Burkert M, Guergen D, Szymansky A, Astrahantseff K, Kuenkele A, Haase K, Fischer M, Deubzer HE, Hertwig F, Hundsdoerfer P, Henssen AG, Schwarz RF, Schulte JH, Eggert A. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions. Nat Commun. 2021 Nov 23;12(1):6804. doi: 10.1038/s41467-021-26870-z

Simon, T.; Riemer, P.; Detjen, K.; Di Domenico, A.; Bormann, F.; Menne, A.; Khouja, S.; Monj'e, N.; Childs, L. H.; Lenze, D.; Leser, U.; Jarosch, A.; Rossner, F.; Morkel, M.; Blüthgen, N.; Pavel, M.; Horst, D.; Capper, D.; Marinoni, I.; Perren, A.; Mamlouk, S. and Sers, C. DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs). Genome Med. 2022 Mar 1;14(1):24. https://dx.doi.org/10.1186/s13073-022-01018-w

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

Schmelz K, Toedling J, Huska M, Cwikla MC, Kruetzfeldt LM, Proba J, Ambros PF, Ambros IM, Boral S, Lodrini M, Chen CY, Burkert M, Guergen D, Szymansky A, Astrahantseff K, Kuenkele A, Haase K, Fischer M, Deubzer HE, Hertwig F, Hundsdoerfer P, Henssen AG, Schwarz RF, Schulte JH, Eggert A. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy- based neuroblastoma treatment decisions. Nat Commun. 2021 Nov 23;12(1):6804. doi: 10.1038/s41467-021-26870-z. PMID: 34815394; PMCID: PMC8611017.

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 TT, Klotz-Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N*, Morkel M*. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med. 2021 Oct 7;13(10):e14123. doi: 10.15252/emmm.202114123. Epub 2021 Aug 19. PMID: 34409732; PMCID: PMC8495451.

Krämer, B.; Knoll, R.; Bonaguro, L.; ToVinh, M.; Raabe, J.; Astaburuaga-García, R.; Schulte-Schrepping, J.; Kaiser, K. M.; Rieke, G. J.; Bischoff, J.; Monin, M. B.; Hoffmeister, C.; Schlabe, S.; De Domenico, E.; Reusch, N.; Händler, K.; Reynolds, G.; Blüthgen, N.; Hack, G.; Finnemann, C.; Nischalke, H. D.; Strassburg, C. P.; Stephenson, E.; Su, Y.; Gardner, L.; Yuan, D.; Chen, D.; Goldman, J.; Rosenstiel, P.; Schmidt, S. V.; Latz, E.; Hrusovsky, K.; Ball, A. J.; Johnson, J. M.; Koenig, P. A.; Schmidt, F. I.; Haniffa, M.; Heath, J. R.; Kümmerer, B. M.; Keitel, V.; Jensen, B.; Stubbemann, P.; Kurth, F.; Sander, L. E.; Sawitzki, B.; Aschenbrenner, A. C.; Schultze, J. L. and Nattermann, J. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity, online ahead of print, 2021 Krämer, B.; Knoll, R.; Bonaguro, L.; ToVinh, M.; Raabe, J.; Astaburuaga-García, R.; Schulte-Schrepping, J.; Kaiser, K. M.; Rieke, G. J.; Bischoff, J.; Monin, M. B.; Hoffmeister, C.; Schlabe, S.; De Domenico, E.; Reusch, N.; Händler, K.; Reynolds, G.; Blüthgen, N.; Hack, G.; Finnemann, C.; Nischalke, H. D.; Strassburg, C. P.; Stephenson, E.; Su, Y.; Gardner, L.; Yuan, D.; Chen, D.; Goldman, J.; Rosenstiel, P.; Schmidt, S. V.; Latz, E.; Hrusovsky, K.; Ball, A. J.; Johnson, J. M.; Koenig, P. A.; Schmidt, F. I.; Haniffa, M.; Heath, J. R.; Kümmerer, B. M.; Keitel, V.; Jensen, B.; Stubbemann, P.; Kurth, F.; Sander, L. E.; Sawitzki, B.; Aschenbrenner, A. C.; Schultze, J. L. and Nattermann, J. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity,  2021 Nov 9;54(11):2650-2669.e14. doi: 10.1016/j.immuni.2021.09.002

Bischoff, P; Trinks, A; Obermayer, B; Pett, JP; Wiederspahn, J; Uhlitz, F; Liang, X; Lehmann, A; Jurmeister, P; Elsner, A; Dziodzio, T; Rückert, JC; Neudecker, J; Falk, C; Beule, D; Sers, C; Morkel, M; Horst, D; Blüthgen, N * and Klauschen, F * Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma. Oncogene,  2021 Dec;40(50):6748-6758. doi: 10.1038/s41388-021-02054-3.

Burt P, Grabe S, Madeti C, Upadhyay A, Merrow M, Roenneberg T, Herzel H, Schmal C. Principles underlying the complex dynamics of temperature entrainment by a circadian clock. iScience. 2021 Oct 30;24(11):103370. doi: 10.1016/j.isci.2021.103370. PMID: 34816105; PMCID: PMC8593569.

Quinn HM, Vogel R, Popp O, Mertins P, Lan L, Messerschmidt C, Landshammer A, Lisek K, Château-Joubert S, Marangoni E, Koren E, Fuchs Y, Birchmeier W. YAP and β-Catenin Cooperate to Drive Oncogenesis in Basal Breast Cancer. Cancer Res. 2021 Apr 15;81(8):2116-2127. doi: 10.1158/0008-5472.CAN-20-2801. Epub 2021 Feb11. PMID: 33574090.

Messerschmidt C, Foddis M, Blumenau S, Müller S, Bentele K, Holtgrewe M, Kun-Rodrigues C, Alonso I, do Carmo Macario M, Morgadinho AS, Velon AG, 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, Sassi C. PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice. Sci Rep. 2021 Mar 16;11(1):6072. doi: 10.1038/s41598-021-84919-x. PMID: 33727568; PMCID:PMC7966789.

 

2020

Klotz-Noack K, Klinger B, Rivera M, Bublitz N, Uhlitz F, Riemer P, Lüthen M, Sell T, Kasack K, Gastl B, Ispasanie SSS, Simon T, Janssen N, Schwab M, Zuber J, Horst D, Blüthgen N, Schäfer R, Morkel M, Sers C. SFPQ Depletion Is Synthetically Lethal with BRAF<sup>V600E</sup> in Colorectal Cancer Cells. Cell Rep. 2020 Sep 22;32(12):108184. doi: 10.1016/j.celrep.2020.108184. PMID: 32966782.

Rumberger, J.L., Mais, L., Kainmueller, D. (2020). Probabilistic Deep Learning for Instance Segmentation. In: Bartoli, A., Fusiello, A. (eds) Computer Vision – ECCV 2020 Workshops. ECCV 2020. Lecture Notes in Computer Science(), vol 12535. Springer, Cham. https://doi.org/10.1007/978-3-030-66415-2_29

Mamlouk S, Simon T, Tomás L, Wedge DC, Arnold A, Menne A, Horst D, Capper D, Morkel M, Posada D, Sers C, Bläker H. Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression. BMC Biol. 2020 Sep 7;18(1):116. doi: 10.1186/s12915-020-00844-x. PMID: 32895052; PMCID: PMC7487684.

Kassuhn W, Klein O, Darb-Esfahani S, Lammert H, Handzik S, Taube ET, Schmitt WD, Keunecke C, Horst D, Dreher F, George J, Bowtell DD, Dorigo O, Hummel M, Sehouli J, Blüthgen N, Kulbe H, Braicu EI. Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging. Cancers (Basel). 2021 Mar 25;13(7):1512. doi: 10.3390/cancers13071512. PMID: 33806030; PMCID: PMC8036744.

Rumberger, J.L., Mais, L., Kainmüller, D. Probabilistic Deep Learning for Instance Segmentation, Bio Image Computing Workshop within ECCV2020, https://arxiv.org/abs/2008.10678

Gross, T. and Blüthgen, N., Identifiability and experimental design in perturbation studies. Bioinformatics 2020, https://dx.doi.org/10.1093/bioinformatics/btaa404

Messerschmidt C, Obermayer B, Klinghammer K, Ochsenreither S, Treue D, Stenzinger A, Glimm H, Fröhling S, Kindler T, Brandts CH, Schulze-Osthoff K, Weichert W, Tinhofer I, Klauschen F, Keilholz U, Beule D, Rieke DT. Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC. Int J Cancer. 2020 Oct 15;147(8):2293-2302. doi: 10.1002/ijc.33123. Epub 2020 Jun 18. PMID: 32468570.

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, Scholl UI. Generation and characterization of a mitotane-resistant adrenocortical cell line. Endocr Connect. 2020 Feb;9(2):122-134. doi:10.1530/EC-19-0510. PMID: 31910152; PMCID: PMC6993260.

Thole TM, Toedling J, Sprüssel A, Pfeil S, Savelyeva L, Capper D, Messerschmidt C, Beule D, Groeneveld-Krentz S, Eckert C, Gambara G, Henssen AG, Finkler S, Schulte JH, Sieber A, Bluethgen N, Regenbrecht CRA, Künkele A, Lodrini M, Eggert A, Deubzer HE. Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model. Int J Cancer. 2020 Feb 15;146(4):1031-1041. doi: 10.1002/ijc.32572. Epub 2019 Aug 1. PMID: 31304977.

Blanc E, Holtgrewe M, Dhamodaran A, Messerschmidt C, Willimsky G, Blankenstein T, Beule D. Identification and ranking of recurrent neo-epitopes in cancer. BMC Med Genomics. 2019 Nov 27;12(1):171. doi: 10.1186/s12920-019-0611-7. PMID: 31775766; PMCID: PMC6882202.
Obermayer B, Holtgrewe M, Nieminen M, Messerschmidt C, Beule D. SCelVis: exploratory single cell data analysis on the desktop and in the cloud. PeerJ. 2020 Feb 19;8:e8607. doi: 10.7717/peerj.8607. PMID: 32117635; PMCID: PMC7035868.

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 ML, Keilholz U, Rieke DT. Support of a molecular tumour board by an evidence-based decision management system for precision oncology. Eur J Cancer. 2020 Mar;127:41-51. doi: 10.1016/j.ejca.2019.12.017. Epub 2020 Jan 23. PMID: 31982633.

Peitz C, Sprüssel A, Linke RB, Astrahantseff K, Grimaldi M, Schmelz K, Toedling J, Schulte JH, Fischer M, Messerschmidt C, Beule D, Keilholz U, Eggert A, Deubzer HE, Lodrini M. Multiplexed Quantification of Four Neuroblastoma DNA Targets in a Single Droplet Digital PCR Reaction. J Mol Diagn. 2020 Nov;22(11):1309-1323. doi: 10.1016/j.jmoldx.2020.07.006. Epub 2020 Aug 26. PMID:32858250.

Akpa CA, Kleo K, Oker E, Tomaszewski N, Messerschmidt C, López C, Wagener R, Oehl-Huber K, Dettmer K, Schoeler A, Lenze D, Oefner PJ, Beule D, Siebert R, Capper D, Dimitrova L, Hummel M. Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model. BMC Cancer. 2020 May 14;20(1):427. doi: 10.1186/s12885-020-06937-8. PMID: 32408898; PMCID: PMC7227222

 

2019

Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D. SigsPack, a package for cancer mutational signatures. BMC Bioinformatics. 2019 Sep 2;20(1):450. doi: 10.1186/s12859-019-3043-7. PMID: 31477009; PMCID: PMC6720940.

 

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