Publications

Preprints:

  1. Stefan Peidli* , Tessa D. Green*, Ciyue Shen, Torsten Gross, Joseph Min, Jake P. Taylor-King, Debora S. Marks, Augustin Luna, Nils Blüthgen*, Chris Sander*. scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data, bioRxiv 2022.08.20.504663, doi: 10.1101/2022.08.20.504663
  2. Matthias M. Fischer, Nils Blüthgen. On tumoural growth and treatment under cellular dedifferentiation, bioRxiv 2022.05.10.491343; doi: 10.1101/2022.05.10.491343
  3. 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: 10.1101/2022.05.16.492138
  4. Sell, T.; Klotz, C.; Fischer, M. M; Astaburuaga-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  10.1101/2022.04.07.487491
  5. Maria Stella de Biase, Florian Massip, Tzu-Ting Wei, Federico M. Giorgi, Rory Stark, Amanda Stone, Amy Gladwell, Martin O’Reilly, Ines de Santiago, Kerstin Meyer, Florian Markowetz, Bruce A J Ponder, Robert C Rintoul, Roland F Schwarz. Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk. medRxiv 2021.11.24.21266740; doi: https://doi.org/10.1101/2021.11.24.21266740

Peer-reviewed publications

*: equal contribution / joined first or corresponding authors

  1. Rumberger JL, Baumann E, Hirsch P, Janowczyk A, Zlobec I, Kainmueller D. Panoptic segmentation with highly imbalanced semantic labels, 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 2022, pp. 1-4, doi: 10.1109/ISBIC56247.2022.9854551.
  2. Fries JA*, Seelam N*, Altay G*, Weber L*, Kang M*, Datta D*, Su R*, Garda S*, Wang B, Ott S, Samwald M, Kusa W (2022). Dataset Debt in Biomedical Language Modeling. Workshop on Challenges & Perspectives in Creating Large Language Models 2022 (accepted).
  3. Grabe, S., Mahammadov, E., Olmo, M. D., Herzel, H. (2022). Synergies of Multiple Zeitgebers Tune Entrainment. Frontiers in Network Physiology, 1.
  4. Keunecke C, Kulbe H, Dreher F, Taube ET, Chekerov R, Horst D, Hummel M, Kessler T, Pietzner K, Kassuhn W, Heitz F, Muallem MZ, Lang SM, Vergote I, Dorigo O, Lammert H, du Bois A, Angelotti T, Fotopoulou C, Sehouli J, Braicu EI. Predictive biomarker for surgical outcome in patients with advanced primary high-grade serous ovarian cancer. Are we there yet? An analysis of the prospective biobank for ovarian cancer. Gynecol Oncol. 2022 Aug;166(2):334-343. doi: 10.1016/j.ygyno.2022.06.010.
  5. Fischer MM, Herzel H, Blüthgen N. Mathematical modelling identifies conditions for maintaining and escaping feedback control in the intestinal epithelium. Sci Rep. 2022 Apr 2;12(1):5569. doi: 10.1038/s41598-022-09202-z
  6. Garda S, Lenihan-Geels F, Proft S, Hochmuth S, Schülke M, Seelow D, Leser U. RegEl corpus: identifying DNA regulatory elements in the scientific literature. Database (Oxford). 2022 Jun 27;2022:baac043. doi: 10.1093/database/baac043
  7. 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, 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
  8. 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. Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single-cell transcriptomics. Mol Ther. 2022 May 4;30(5):1952-1965. doi: 10.1016/j.ymthe.2022.03.014
  9. Rau A, Janssen N, Kühl L, Sell T, Kalmykova S, Mürdter TE, Dahlke MH, Sers C, Morkel M, Schwab M, Kontermann RE, Olayioye MA. Triple Targeting of HER Receptors Overcomes Heregulin-mediated Resistance to EGFR Blockade in Colorectal Cancer. Mol Cancer Ther. 2022 May 4;21(5):799-809. doi: 10.1158/1535-7163.MCT-21-0818
  10. Simon T, Riemer P, Jarosch A, Detjen K, Di Domenico A, Bormann F, Menne A, Khouja S, Monjé N, Childs LH, Lenze D, Leser U, Rossner F, Morkel M, Blüthgen N, Pavel M, Horst D, Capper D, Marinoni I, Perren A, Mamlouk S, Sers C. DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors. Genome Med. 2022 Mar 1;14(1):24. doi: 10.1186/s13073-022-01018-w
  11. Georg P*, Astaburuaga-García R*, Bonaguro L*, Brumhard S, Michalick L, Lippert LJ, Kostevc T, Gäbel C, Schneider M, Streitz M, Demichev V, Gemünd I, Barone M, Tober-Lau P, Helbig ET, Hillus D, Petrov L, Stein J, Dey HP, Paclik D, Iwert C, Mülleder M, Aulakh SK, Djudjaj S, Bülow RD, Mei HE, Schulz AR, Thiel A, Hippenstiel S, Saliba AE, Eils R, Lehmann I, Mall MA, Stricker S, Röhmel J, Corman VM, 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 WM, Meisel C, Ralser M, Schultze JL, Aschenbrenner AC, Thibeault C, Kurth F, Sander LE*, Blüthgen N*, Sawitzki B*; PA-COVID-19 Study Group. Complement activation induces excessive T cell cytotoxicity in severe COVID-19. Cell. 2022 Feb 3;185(3):493-512.e25. doi: 10.1016/j.cell.2021.12.040
  12. 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
  13. Rumberger JL, Yu X, Hirsch P, Dohmen M, Guarino VE, Mokarian A, Mais L, FunkeJ ,  Kainmüller D. How Shift Equivariance Impacts Metric Learning for Instance Segmentation. Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV), 2021, pp. 7128-7136
  14. 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*, 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
  15. 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
  16. 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
  17. Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J, Monin MB, Hoffmeister C, Schlabe S, De Domenico E, Reusch N, Händler K, Reynolds G, Blüthgen N, Hack G, Finnemann C, Nischalke HD, Strassburg CP, Stephenson E, Su Y, Gardner L, Yuan D, Chen D, Goldman J, Rosenstiel P, Schmidt SV, Latz E, Hrusovsky K, Ball AJ, Johnson JM, Koenig PA, Schmidt FI, Haniffa M, Heath JR, Kümmerer BM, Keitel V, Jensen B, Stubbemann P, Kurth F, Sander LE, Sawitzki B; Deutsche COVID-19 OMICS Initiative (DeCOI), Aschenbrenner AC, Schultze JL, 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
  18. 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 JH, Selbach M, Blüthgen N. Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance. PLoS Comput Biol. 2021 Nov 4;17(11):e1009515. doi: 10.1371/journal.pcbi.1009515
  19. 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
  20. Szymansky A*, Kruetzfeldt LM*, Heukamp LC, Hertwig F, Theissen J, Deubzer HE, Willing EM, Menon R, Fuchs S, Thole T, Schulte S, Schmelz K, Künkele A, Lang P, Fuchs J, Eggert A, Eckert C, Fischer M, Henssen AG, Rodriguez-Fos E, Schulte JH. Neuroblastoma Risk Assessment and Treatment Stratification with Hybrid Capture-Based Panel Sequencing. J Pers Med. 2021 Jul 22;11(8):691. doi: 10.3390/jpm11080691
  21. Reimann M, Schrezenmeier J, Richter-Pechanska P, Dolnik A, Hick TP, Schleich K, Cai X, Fan DNY, Lohneis P, Maßwig S, Denker S, Busse A, Knittel G, Flümann R, Childs D, Childs L, Gätjens-Sanchez AM, Bullinger L, Rosenwald A, Reinhardt HC, Schmitt CA. Adaptive T-cell immunity controls senescence-prone MyD88- or CARD11-mutant B-cell lymphomas. Blood. 2021 May 20;137(20):2785-2799. doi:10.1182/blood.2020005244
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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 BRAFV600E in Colorectal Cancer Cells. Cell Rep. 2020 Sep 22;32(12):108184. doi: 10.1016/j.celrep.2020.108184
  28. 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
  29. Kulbe H, Klein O, Wu Z, Taube ET, Kassuhn W, Horst D, Darb-Esfahani S, Jank P, Abobaker S, Ringel F, du Bois A, Heitz F, Sehouli J, Braicu EI. Discovery of Prognostic Markers for Early-Stage High-Grade Serous Ovarian Cancer by Maldi-Imaging. Cancers (Basel). 2020 Jul 22;12(8):2000. doi: 10.3390/cancers12082000
  30. Schleich K, Kase J, Dörr JR, Trescher S, Bhattacharya A, Yu Y, Wailes EM, Fan DNY, Lohneis P, Milanovic M, Lau A, Lenze D, Hummel M, Chapuy B, Leser U, Reimann M, Lee S, Schmitt CA. H3K9me3-mediated epigenetic regulation of senescence in mice predicts outcome of lymphoma patients. Nat Commun. 2020 Jul 20;11(1):3651. doi: 10.1038/s41467-020-17467-z
  31. Gross T, Blüthgen N. Identifiability and experimental design in perturbation studies. Bioinformatics. 2020 Jul 1;36(Suppl_1):i482-i489. doi: 10.1093/bioinformatics/btaa404
  32. 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
  33. 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
  34. 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
  35. 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, Blüthgen 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
  36. Rumberger JL, Mais L, Kainmueller D: Probabilistic deep learning for instance segmentation. 2020. European Conference on Computer Vision, 445-457
  37. 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
  38. 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
  39. 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
  40. Gross T, Wongchenko MJ, Yan Y, Blüthgen N. Robust network inference using response logic. Bioinformatics. 2019 Jul 15;35(14):i634-i642. doi: 10.1093/bioinformatics/btz32
  41. Trescher S, Leser U. Estimation of Transcription Factor Activity in Knockdown Studies. Sci Rep. 2019 Jul 3;9(1):9593. doi: 10.1038/s4159

 

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