Max Planck Institute of Immunobiology and Epigenetics

Publications

Publications

Grün Lab

Journal Article (54)

2024

Czech, M.; Schneider, S.; Peltokangas, N.; Khawanky, N. E.; Ghimire, S.; Andrieux, G.; Hülsdünker, J.; Krausz, M.; Proietti, M.; Braun, L. M. et al.; Rückert, T.; Langenbach, M.; Schmidt, D.; Martin, I.; Wenger, V.; de Vega, E.; Haring, E.; Pourjam, M.; Pfeifer, D.; Schmitt-Graeff, A.; Grimbacher, B.; Aumann, K.; Kircher, B.; Tilg, H.; Raffatellu, M.; Orberg, E. T.; Häcker, G.; Duyster, J.; Köhler, N.; Holler, E.; Nachbaur, D.; Boerries, M.; Gerner, R. R.; Grün, D.; Zeiser, R.: Lipocalin-2 expression identifies an intestinal regulatory neutrophil population during acute graft-versus-host disease. Science translational medicine: integrating medicine and science / American Association for the Advancement of Science 16, eadi1501 (2024)

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2022

Hess, I.; Sagar; Meara, C. O.; Grün, D.; Schorpp, M.; Boehm, T.: Stage-specific and cell type-specific requirements of ikzf1 during haematopoietic differentiation in zebrafish. Scientific Reports 12, 21401 (2022)

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publisher-version

Hochrein, S. M.; Wu, H.; Eckstein, M.; Arrigoni, L.; Herman, J. S.; Schumacher, F.; Gerecke, C.; Rosenfeldt, M.; Grün, D.; Kleuser, B. et al.; Gasteiger, G.; Kastenmüller, W.; Ghesquière, B.; den Bossche, J. V.; Abel, E. D.; Vaeth, M.: The glucose transporter GLUT3 controls T helper 17 cell responses through glycolytic-epigenetic reprogramming. Cell Metabolism 34, pp. 516 - 532 (2022)

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publisher-version

Kabat, A. M.; Hackl, A.; Sanin, D. E.; Zeis, P.; Grzes, K. M.; Baixauli, F.; Kyle, R.; Caputa, G.; Edwards-Hicks, J.; Villa, M. et al.; Rana, N.; Curtis, J. D.; Castoldi, A.; Cupovic, J.; Dreesen, L.; Sibilia, M.; Pospisilik, J. A.; Urban Jr, J. F.; Grün, D.; Pearce, E. L.; Pearce, E. J.: Resident T_H2 cells orchestrate adipose tissue remodeling at a site adjacent to infection. Science Immunology 7, eadd3263 (2022)

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publisher-version

Nusser, A.; Sagar; Swann, J.; Krauth, B.; Diekhoff, D.; Calderon, L.; Happe, C.; Grün, D.; Boehm, T.: Developmental dynamics of two bipotent thymic epithelial progenitor types. Nature 606, pp. 165 - 171 (2022)

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publisher-version

Zhang, Y. W.; Mess, J.; Aizarani, N.; Mishra, P.; Johnson, C.; Romero-Mulero, M. C.; Rettkowski, J.; Schönberger, K.; Obier, N.; Jäcklein, K. et al.; Woessner, N. M.; Lalioti, M.-E.; Velasco-Hernandez, T.; Sikora, K.; Wäsch, R.; Lehnertz, B.; Sauvageau, G.; Manke, T.; Menendez, P.; Walter, S. G.; Minguet, S.; Laurenti, E.; Günther, S.; Grün, D.; Cabezas-Wallscheid, N.: Hyaluronic acid–GPRC5C signalling promotes dormancy in haematopoietic stem cells. Nature Cell Biology 24, pp. 1038 - 1048 (2022)

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publisher-version

2021

Clapes, T.; Polyzou, A.; Prater, P.; Sagar; Morales-Hernández, A.; Ferrarini, M. G.; Kehrer, N.; Lefkopoulos, S.; Bergo, V.; Hummel, B. et al.; Obier, N.; Maticzka, D.; Bridgeman, A.; Herman, J. S.; Ilik, I.; Klaeylé, L.; Rehwinkel, J.; McKinney-Freeman, S.; Backofen, R.; Akhtar, A.; Cabezas-Wallscheid, N.; Sawarkar, R.; Rebollo, R.; Grün, D.; Trompouki, E.: Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nature Cell Biology 23, pp. 704 - 717 (2021)

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publisher-version

publisher-version

Friedrich, C.; Taggenbrock, R. L. R. E.; Doucet-Ladevèze, R.; Golda, G.; Moenius, R.; Arampatzi, P.; Kragten, N. A. M.; Kreymborg, K.; de Agüero, M. G.; Kastenmüller, W. et al.; Saliba, A.-E.; Grün, D.; van Gisbergen, K. P. J. M.; Gasteiger, G.: Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues. Nature Immunology 22, pp. 1256 - 1267 (2021)

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publisher-version

Hensel, N.; Gu, Z.; Sagar, S.; Wieland, D.; Jechow, K.; Kemming, J.; Llewellyn-Lacey, S.; Gostick, E.; Sogukpinar, O.; Emmerich, F. et al.; Price, D. A.; Bengsch, B.; Boettler, T.; Neumann-Haefelin, C.; Eils, R.; Conrad, C.; Bartenschlager, R.; Grün, D.; Ishaque, N.; Thimme, R.; Hofmann, M.: Memory-like HCV-specific CD8⁺ T cells retain a molecular scar after cure of chronic HCV infection. Nature Immunology 22, pp. 229 - 239 (2021)

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Probst, S.; Sagar; Tosic, J.; Schwan, C.; Grün, D.; Arnold, S. J.: Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation. Development 148, dev193789 (2021)

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2020

Derecka, M.; Herman, J. S.; Cauchy, P.; Ramamoorthy, S.; Lupar, E.; Grün, D.; Grosschedl, R.: EBF1-deficient bone marrow stroma elicits persistent changes in HSC potential. Nature 21, pp. 261 - 273 (2020)

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Grün, D.: Revealing dynamics of gene expression variability in cell state space. Nature methods 17, pp. 45 - 49 (2020)

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Mereu, E.; Lafzi, A.; Moutinho, C.; Ziegenhain, C.; MacCarthy, D. J.; Alvarez, A.; Batlle, E.; Sagar, S.; Grün, D.; Lau, J. K. et al.; Boutet, S. C.; Sanada, C.; Ooi, A.; Jones, R. C.; Kaihara, K.; Brampton, C.; Talaga, Y.; Sasagawa, Y.; Tanaka, K.; Hayashi, T.; Nikaido, I.; Fischer, C.; Sauer, S.; Trefzer, T.; Conrad, C.; Adiconis, X.; Nguyen, L. T.; Regev, A.; Levin, J. Z.; Parekh, S.; Janjic, A.; Wange, L. E.; Bagnoli, J. W.; Enard, W.; Gut, M.; Sandberg, R.; Gut, I.; Stegle, O.; Heyn, H.: Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nature Biotechnology 38, pp. 747 - 755 (2020)

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Olah, M.; Menon, V.; Habib, N.; Taga, M. F.; Ma, Y.; Yung, C. J.; Cimpean, M.; Khairallah, A.; Coronas-Samano, G.; Sankowski, R. et al.; Grün, D.; Kroshilina, A. A.; Dionne, D.; Sarkis, R. A.; Cosgrove, G. R.; Helgager, J.; Golden, J. A.; Pennell, P. B.; Prinz, M.; Vonsattel, J. P. G.; Teich, A. F.; Schneider, J. A.; Bennett, D. A.; Regev, A.; Elyaman, W.; Bradshaw, E. M.; Jager, P. L. D.: Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer's disease. Nature Communications 11, pp. 1 - 18 (2020)

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Ramamoorthy, S.; Kometani, K.; Herman, J. S.; Bayer, M.; Boller, S.; Edwards-Hicks, J.; Ramachandran, H.; Li, R.; Klein-Geltink, R.; Pearce, E. L. et al.; Grün, D.; Grosschedl, R.: EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression, and folate metabolism. Genes and Development 34, pp. 1503 - 1519 (2020)

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Rodrigues, C. P.; Herman, J. S.; Herquel, B.; Velsecchi Keller, C. I.; Stehle, T.; Grün, D.; Akhtar, A.: Temporal expression of MOF acetyltransferase primes transcription factor networks for erythroid fate. Science Advances 6, p. eaaz4815 (2020)

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Sagar , S.; Grün, D.: Deciphering Cell Fate Decision by Integrated Single-Cell Sequencing Analysis. Annual Review of Biomedical Data Science 39, pp. 1 - 22 (2020)

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Sagar, S.; Pokrovskii, M.; Herman, J. S.; Naik, S.; Sock, E.; Zeis, P.; Lausch, U.; Wegner, M.; Tanriver, Y.; Littman, D. R. et al.; Grün, D.: Deciphering the regulatory landscapte of fetal and adult γδ T-cell development at single-cell resolution. The EMBO Journal 39, e104159 (2020)

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Sheikh, B. N.; Guhathakurta, S.; Tsang, T. H.; Schwabenland, M.; Renschler, G. V.; Herquel, B.; Bhardwaj, V.; Holz, H.; Stehle, T.; Bondareva, O. et al.; Aizarni, N.; Mossad, O.; Kretz, O.; Reichardt, W.; Chatterjee, A.; Braun, L. J.; Thevenon, J.; Sartelet, H.; Blank, T.; Grün, D.; von Elverfeldt, D.; Huber, T. B.; Vestweber, D.; Avilov, S.; Prinz, M.; Büscher, J. M.; Akhtar, A.: Neural metabolic imbalance induced by MOF dysfunction triggers pericyte activation and breakdown of vasculature. Nature Cell Biology 22, pp. 828 - 841 (2020)

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Zeis, P.; Lian, M.; Fan, X.; Herman, J. S.; Hernandez, D. C.; Gentek, R.; Elias, S.; Symowski, C.; Knöpper, K.; Peltokangas, N. et al.; Friedrich, C.; Doucet-Ladeveze, R.; Kabat, A. M.; Locksley, R. M.; Voehringer, D.; Bajenoff, M.; Rudensky, A. Y.; Romagnani, C.; Grün, D.; Gasteiger, G.: In situ Maturation and Tissue Adaptation of Type 2 Innate Lymphoid Cell Progenitors. Immunity 53, pp. 775 - 792 (2020)

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2019

Aizarani, N.; Saviano, A.; Sagar, S.; Mailly , L.; Durand, S.; Herman, J. S.; Pessaux, P.; Baumert , T. F.; Grün, D.: A human liver cell atlas reveals heterogeneity and epithelial progenitors. Nature 572, pp. 199 - 204 (2019)

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Honkoop, H.; de Bakker, D. E.; Aharonov, A.; Kruse, F.; Shakked, A.; Nguyen, P. D.; de Heus, C.; Garric, L.; Muraro, M. J.; Shoffner, A. et al.; Tessadori, F.; Peterson, J. C.; Noort, W.; Bertozzi, A.; Weidinger, G.; Posthuma, G.; Grün, D.; van der Laarse, W. J.; Klumperman, J.; Jaspers, R. T.; Poss, K. D.; van Oudenaarden, A.; Tzahor, E.; Bakkers, J.: Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. eLife 8, p. e50163 (2019)

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Hummel, J. F.; Zeis, P.; Fixemer, J.; Konrad, P.; Schachtrup, C.; Arnold, S. J.; Grün, D.; Tanriver, Y.: Single-cell RNA-sequencing identifies the developmental trajectory of C-Myc-dependent NK1.1^-T-bet⁺. Mucosal immunology: official journal of the Society for Mucosal Immunology 13, pp. 257 - 270 (2019)

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Jordão, M. J. C.; Sankowski, R.; Brendecke, S. M.; Sagar, S.; Locatelli, G.; Tai, Y.-H.; Tay, T. L.; Schramm, E.; Armbruster, S.; Hagemeyer, N. et al.; Groß, O.; Mai, D.; Çiçek, Ö.; Falk, T.; Kerschensteiner, M.; Grün, D.; Prinz, M.: Single-cell profiling identifies myeloid cell subsets with distinct fates during neuro inflammation. Science 363 (2019)

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Kolter, J.; Feuerstein, R.; Zeis, P.; Hagemeyer, N.; Paterson, N.; d’Errico, P.; Baasch, S.; Amann, L.; Masuda, T.; Lösslein, A. et al.; Gharun, K.; Meyer-Luehmann, M.; Waskow, C.; Franzke, C.-W.; Grün, D.; Lämmermann, T.; Prinz, M.; Henneke, P.: A Subset of Skin Macrophages Contributes to the Seruveillance and Regeneration of Local Nerves. Immunity 50, pp. 1482 - 1497 (2019)

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Masuda, T.; Sankowski, R.; Staszewski, O.; Böttcher, C.; Amann, L.; Sagar, S.; Scheiwe, C.; Nessler, S.; Kunz, P.; van Loo, G. et al.; Coenen, V. A.; Reinacher, P. C.; Michel, A.; Sure, U.; Gold, R.; Grün, D.; Priller, J.; Stadelmann, C.; Prinz, M.: Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature 566, pp. 388 - 392 (2019)

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Sankowski, R.; Böttcher, C.; Masuda, T.; Geirsdottir, L.; Sagar, S.; Sindram, E.; Seredenina, T.; Muhs, A.; Scheiwe, C.; Shah, M. J. et al.; Heiland, D. H.; Schnell, O.; Grün, D.; Priller, J.; Prinz, M.: Mapping microglia states in the human brain through the integration of high-dimensional techniques. Nature Neuroscience 22, pp. 2098 - 2110 (2019)

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Sheikh, B. N.; Bondareva, O.; Guhathakurta, S.; Tsang, T. H.; Sikora, K.; Aizarani, N.; Sagar, S.; Holz, H.; Grün, D.; Hein, L. et al.; Akhtar, A.: Systematic Identification of Cell-Cell Communication Networks in the Developing Brain. iScience 21, pp. 273 - 287 (2019)

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2018

Boisset, J.-C.; Vivie, J.; Grün, D.; Muraro, M. J.; Lyubimova, A.; van Oudenaarden, A.: Mapping the physical network of cellular interactions. Nature methods 15, pp. 547 - 553 (2018)

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Costa , F.; Grün, D.; Backofen, R.: GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge. Nature Communications 9, p. 3685 (2018)

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Felmlee, D. J.; Baumert, T. F.; Grün, D.: Zooming in on Liver Zonation. Hepatology 67, pp. 784 - 787 (2018)

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Grün, D.: Revealing routes of cellular differentiation by single-cell RNA-seq. Current Opinion in Systems Biology 11, pp. 9 - 17 (2018)

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Herman, J. S.; Sagar, S.; Grün, D.: FateID infers fate bias in multipotent progenitors from single-cell RNA-seq data. Nature methods 15, pp. 379 - 386 (2018)

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Lu, T. T.-H.; Heyne, S.; Dror, E.; Casas, E.; Leonhardt, L.; Boenke, T.; Yang, C.-H.; Sagar, S.; Arrigoni, L.; Dalgaard, K. et al.; Teperino, R.; Enders, L.; Selvaraj, M.; Ruf, M.; Raja, S. J.; Xie, H.; Boenisch, U.; Orkin, S. H.; Lynn, F. C.; Hoffman, B. G.; Grün, D.; Vavouri, T.; Lempradl, A. M.; Pospisilik, J. A.: The Polycomb-Dependent Epigenome Controls β Cell Cysfunction, Dedifferentiation, and Diabetes. Cell Metabolism 15, pp. 1294 - 1308 (2018)

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Roovers, E. F.; Kaaij, L. J.T.; Redl, S.; Bronkhorst, A. W.; Wiebrands, K.; de Domingues, A. M. J.; Huang, H.-Y.; Han, C.-T.; Riemer, S.; Dosch, R. et al.; Salvenmoser, W.; Grün, D.; Butter, F.; van Oudenaarden, A.; Ketting, R. F.: Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification. Developmental Cell 46, pp. 285 - 301 (2018)

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Sagar, S.; Hermann, J. S.; Pospisilik, J. A.; Grün, D.: High-Throughput Single-Cell RNA Sequencing and Data Analaysis. Methods in Molecular Biology 1766, pp. 257 - 283 (2018)

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Tay, T. L.; Sagar, S.; Dautzenberg, J.; Grün, D.; Prinz, M.: Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration. Acta Neuropathologica Communications 6, p. 87 (2018)

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2017

Tay, T. L.; Mai, D.; Dautzenberg, J.; Fernández-Klett, F.; Lin, G.; Sagar, S.; Datta, M.; Drougard, A.; Stempfl, T.; Ardura-Fabregat, A. et al.; Staszewski, O.; Margineanu, A.; Sporbert, A.; Steinmetz, L. M.; Pospisilik, J. A.; Jung, S.; Priller, J.; Grün, D.; Ronneberger, O.; Prinz, M.: A new fate mapping system reveals context-dependent random or clonal expansion of microglia. Nature Neuroscience 20, pp. 793 - 803 (2017)

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2016

Grün, D.; Muraro, M. J.; Boisset, J.-C.; Wiebrands, K.; Lyubimova, A.; Dharmadhikari, G.; van den Born, M.; Jansen, E.; Clevers, H.; de Koning, E. J.P. et al.; van Oudenaarden, A.: De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data. Cell Stem Cell 19, pp. 266 - 277 (2016)

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Herrtwich, L.; Nanda, I.; Evangelou, K.; Nikolova, T.; Horn, V.; Sagar, S.; Erny, D.; Stefanowski, J.; Rogell, L.; Klein, C. et al.; Gharun, K.; Follo, M.; Seidl, M.; Kremer, B.; Münke, N.; Senges, J.; Fliegauf, M.; Aschman, T.; Pfeifer, D.; Sarrazin, S.; Sieweke, M. H.; Wagner, D.; Dierks, C.; Haaf, T.; Ness, T.; Zaiss, M. M.; Voll, R. E.; Deshmukh, S. D.; Prinz, M.; Goldmann, T.; Hölscher, C.; Hauser, A. E.; Lopez-Contreras, A. J.; Grün, D.; Gorgoulis, V.; Diefenbach, A.; Henneke, P.; Triantafyllopoulou, A.: DNA Damage Signaling Instructs Polypoid Macrophage Fate in Granulomas. Cell 167, pp. 1264 - 1280 (2016)

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Muraro, M. J.; Dharmadhikari, G.; Grün, D.; Groen, N.; Dielen, T.; Jansen, E.; van Gurp, L.; Engelse, M. A.; Carlotti, F.; de Koning, E. J.P. et al.; van Oudenaarden, A.: A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3, pp. 385 - 394 (2016)

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Wu, C.-C.; Kruse, F.; Vasudevarao, M. D.; Junker, J. P.; Zebrowski, D. C.; Fischer, K.; Noël, E. S.; Grün, D.; Berezikov, E.; Engel, F. B. et al.; van Oudenaarden, A.; Weidinger, G.; Bakkers, J.: Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration. Developmental Cell 36, pp. 36 - 49 (2016)

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2015

Grün, D.; Lyubimova, A.; Kester, L.; Wiebrands, K.; Basak, O.; Sasaki, N.; Clevers, H.; van Oudenaarden, A.: Single-cell mRNA sequencing reveales rare intestinal cell types. Nature 525, pp. 251 - 255 (2015)

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2014

Grün, D.; Kester, L.; van Oudenaarden, &. A.: Validation of noise models for single-cell transcriptomics enables genome-wiede quentification of stochastic gene expression. Nature methods 11, pp. 637 - 640 (2014)

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Grün, D.; Kirchner, M.; Thierfelder, N.; Stoeckius, M.; Selbach, M.; Rajewsky, N.: Conservation of mRNA and protein expression during development of C.elegans. Cell Reports 6, pp. 565 - 577 (2014)

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Stoeckius, M.; Grün, D.; Kirchner, M.; Ayoub, S.; Torti, F.; Piano, F.; Herzog, M.; Selbach, M.; Rajewsky, N.: Global characterization of the oocyte‐to‐embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism. EMBO Journal 33, pp. 1751 - 1766 (2014)

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Stoeckius, M.; Grün, D.; Rajewsky, N.: Paternal RNA contributions of C.elegans zygote. EMBO Journal 33, pp. 1740 - 1750 (2014)

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2013

Kim, D. h.; Grün, D.; van Oudenaarden, A.: Dampening of expression oscillation by synchronous regulation of a microRNA and its target. Nature Genetics 45, pp. 1337 - 1344 (2013)

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2012

Önal, P.; Grün, D.; Adamidi, C.; Rybak, A.; Solana, J.; Mastrobuoni, G.; Wang, Y.; Rahn, H.; Chen, W.; Kempa, S. et al.; Ziebold, U.; Rajewsky, N.: Molecular determinants of pluripotency are deeply conserved between mammalian and planarian stem cells. EMBO Journal 31, pp. 2755 - 2769 (2012)

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2011

Adamidi, C.; Wang, Y.; Grün, D.; Mastrobuoni, G.; You, X.; Tolle, D.; Dodt, M.; Mackowiak, S. D.; Gogol-Doering, A.; Oenal, P. et al.; Rybak, A.; Ross, E.; Alvarado, A. S.; Kempa, S.; Dieterich, C.; Rajewsky, N.; Chen, W.: De novo assembly and vailidation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 21, pp. 1193 - 1120 (2011)

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Jungkamp, A.-C.; Stoeckius, M.; Mecenas, D.; Grün, D.; Mastrobuoni, G.; Kempa, S.; Rajewsky, N.: In vivo and treanscritopme-wide identification of RNA-binding protein target sites. Molecular Cell 44, pp. 828 - 840 (2011)

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2006

Lall, S.; Grün, D.; Krek, A.; Chen, K.; Wang, Y.-L.; Dewey, C. N.; Sood, P.; Colombo, T.; Bray, N.; MacMenamin, P. et al.; Kao, H.-L.; Gunsalus, K. C.; Pachter, L.; Piano, F.; Rajewsky, N.: A genome-wide map of conserved microRNA targets in C.elegans. Current Biology 16, pp. 460 - 471 (2006)

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2005

Grün, D.; Wang, Y.-L.; Langenberger, D.; Gunsalus, K. C.; Rajewsky, N.: microRNA target prediction across seven Drosophila species and comparison to mammalian targets. PLoS Computational Biology 1, p. e13 (2005)

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Krek, A.; Grün, D.; Poy, M. N.; Wolf, R.; Rosenberg, L.; Epstein, E. J.; MacMenamin, P.; da Piedade, I.; Gunsalus, K. C.; &, M. S. et al.; Rajewsky, N.: Combinatorial microRNA target predictions. Nature Genetics 37, pp. 495 - 500 (2005)

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Book Chapter (2)

2019

Sagar, S.; Grün, D.: Lineage Inference and Stem Cell Identity prediction Using Single-Cell RNA-Sequencing Data. In: Methods in Molecular Biology, pp. 227 - 301. Humana Press, Clifton, N.J. (2019)

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2008

Grün, D.; Rajewsky, N.: Computional prediction of microRNA targets in vertebrates, fruitflies and nematodes. In: MicroRNAs: From Basic Science to Disease Biology, pp. 172 - 186. Cambridge University Press (2008)

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