Publications

Blanco, M. A.; Sykes, D. B.; Gu, L.; Wu, M.; Petroni, R.; Karnik, R.; Wawer, M.; Rico, J.; Li, H.; Jacobus, W. D. et al.; Jambhekar, A.; Cheloufi, S.; Meissner, A.; Hochedlinger, K.; Scadden, D. T.; Shi, Y.: Chromatin-state barriers enforce an irreversible mammalian cell fate decision. Cell Reports 37 (6), 109967 (2021)

Andergassen, D.; Smith, Z. D.; Kretzmer, H.; Rinn, J. L.; Meissner, A.: Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages. Developmental Cell 56 (21), e4, pp. 2995 - 3005 (2021)

Hetzel, S.; Gießelmann, P.; Reinert, K.; Meissner, A.; Kretzmer, H.: RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. Bioinformatics 37 (21), pp. 3934 - 3935 (2021)

Gu, H.; Raman, A. T.; Wang, X.; Gaiti, F.; Chaligne, R.; Mohammad, A. W.; Arczewska, A. A.; Smith, Z. D.; Landau, D. A.; Aryee, M. J. et al.; Meissner, A.; Gnirke, A.: Smart-RRBS for single-cell methylome and transcriptome analysis. Nature Protocols 16, pp. 4004 - 4030 (2021)

Yagi , M.; Ji, F.; Charlton, J.; Cristea, S.; Messemer, K.; Horwitz, N.; Di Stefano, B.; Tsopoulidis, N.; Hoetker, M. S.; Huebner, A. J. et al.; Bar-Nur, O.; Almada, A. E.; Yamamoto, M.; Patelunas, A.; Goldhamer, D. J.; Wagers, A. J.; Michor, F.; Meissner, A.; Sadreyev, R. I.; Hochedlinger, K.: Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes and Development 35 (17-18), pp. 1209 - 1228 (2021)

Huang, Y.-H.; Chen, C.-W.; Sundaramurthy, V.; Słabicki, M.; Hao, D.; Watson, C. J.; Tovy, A.; Reyes, J. M.; Dakhova, O.; Crovetti, B. R. et al.; Galonska, C.; Lee, M.; Brunetti, L.; Zhou, Y.; Tatton-Brown, K.; Huang, Y.; Cheng, X.; Meissner, A.; Valk, P. J. M.; Van Maldergem, L.; Sanders, M. A.; Blundell, J. R.; Li, W.; Ebert, B. L.; Goodell, M. A.: Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor. Cancer Discovery, CD-21-0560 (2021)

Wu, H.-J.; Landshammer, A.; Stamenova, E. K.; Bolondi, A.; Kretzmer, H.; Meissner, A.; Michor, F.: Topological isolation of developmental regulators in mammalian genomes. Nature Communications 12, 4897 (2021)

Bulut-Karslioglu, A.; Jin, H.; Kim, Y.-K.; Cho, B.; Guzman-Ayala, M.; Williamson, A. J. K.; Hejna, M.; Stötzel, M.; Whetton, A. D.; Song, J. S. et al.; Ramalho-Santos, M.: Chd1 protects genome integrity at promoters to sustain hypertranscription in embryonic stem cells. Nature Communications 12, 4859 (2021)

Haggerty, C.; Kretzmer, H.; Riemenschneider, C.; Sampath Kumar, A.; Mattei, A. L.; Bailly, N.; Gottfreund, J.; Giesselmann, P.; Weigert, R.; Brändl, B. et al.; Giehr, P.; Buschow, R.; Galonska, C.; von Meyenn, F.; Pappalardi, M. B.; McCabe, M. T.; Wittler, L.; Giesecke-Thiel, C.; Mielke, T.; Meierhofer, D.; Timmermann, B.; Müller, F.-J.; Walter, J.; Meissner, A.: Dnmt1 has de novo activity targeted to transposable elements. Nature Structural and Molecular Biology 2021 (2021)

Bolondi, A.; Haut, L.; Gassaloglu, S. I.; Burton, P.; Kretzmer, H.; Buschow, R.; Meissner, A.; Herrmann, B. G.; Veenvliet, J. V.: Generation of Mouse Pluripotent Stem Cell-derived Trunk-like Structures: An in vitro Model of Post-implantation Embryogenesis. Bio-protocol 11 (11), e4042 (2021)

Rossmann, M. P.; Hoi, K.; Chan, V.; Abraham, B. J.; Yang, S.; Mullahoo, J.; Papanastasiou, M.; Wang, Y.; Elia, I.; Perlin, J. R. et al.; Hagedorn, E. J.; Hetzel, S.; Weigert, R.; Vyas, S.; Nag, P. P.; Sullivan, L. B.; Warren, C. R.; Dorjsuren, B.; Custo Greig, E.; Adatto, I.; Cowan, C. A.; Schreiber, S. L.; Young, R. A.; Meissner, A.; Haigis, M. C.; Hekimi, S.; Carr, S. A.; Zon, L. I.: Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis. Science 372 (6543), pp. 716 - 721 (2021)

Pan, H.; Renaud, L.; Chaligne, R.; Bloehdorn, J.; Tausch, E.; Mertens, D.; Fink, A. M.; Fischer, K.; Zhang, C.; Betel, D. et al.; Gnirke, A.; Imielinski, M.; Moreaux, J.; Hallek, M.; Meissner, A.; Stilgenbauer, S.; Wu, C. J.; Elemento, O.; Landau, D. A.: Discovery of candidate DNA methylation cancer driver genes. Cancer Discovery 2021, 20-1334 (2021)

Hübschmann, D.; Kleinheinz, K.; Wagener, R.; Bernhart, S. H.; López, C.; Toprak, U. H.; Sungalee, S.; Ishaque, N.; Kretzmer, H.; Kreuz, M. et al.; Waszak, S. M.; Paramasivam, N.; Ammerpohl, O.; Aukema, S. M.; Beekman, R.; Bergmann, A. K.; Bieg, M.; Binder, H.; Borkhardt, A.; Borst, C.; Brors, B.; Bruns, P.; de Santa Pau, E. C.; Claviez, A.; Doose, G.; Haake, A.; Karsch, D.; Haas, S.; Hansmann, M.-L.; Hoell, J. I.; Hovestadt, V.; Huang, B.; Hummel, M.; Jäger-Schmidt, C.; Kerssemakers, J. N. A.; Korbel, J. O.; Kube, D.; Lawerenz, C.; Lenze, D.; Martens, J. H. A.; Ott, G.; Radlwimmer, B.; Reisinger, E.; Richter, J.; Rico, D.; Rosenstiel, P.; Rosenwald, A.; Schillhabel, M.; Stilgenbauer, S.; Stadler, P. F.; Martín-Subero, J. I.; Szczepanowski, M.; Warsow, G.; Weniger, M. A.; Zapatka, M.; Valencia, A.; Stunnenberg, H. G.; Lichter, P.; Möller, P.; Loeffler, M.; Eils, R.; Klapper, W.; Hoffmann, S.; Trümper, L.; ICGC MMML-Seq consortium; ICGC DE-Mining consortium; BLUEPRINT consortium; Küppers, R.; Schlesner, M.; Siebert, R.: Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia: the Journal of Normal and Malignant Hemopoiese ; Official Journal of the Leukemia Research Fund U.K. 2021 (2021)

Veenvliet, J. V.; Bolondi, A.; Kretzmer, H.; Haut, L.; Scholze-Wittler, M.; Schifferl, D.; Koch, F.; Guignard, L.; Sampath Kumar, A.; Pustet, M. et al.; Heimann, S.; Buschow, R.; Wittler, L.; Timmermann, B.; Meissner, A.; Herrmann, B. G.: Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites. Science 370 (6522), eaba4937 (2020)

Kretzmer, H.; Biran, A.; Purroy, N.; Lemvigh, C. K.; Clement, K.; Gruber, M.; Gu, H.; Rassenti, L.; Mohammad, A. W.; Lesnick, C. et al.; Slager, S. L.; Braggio, E.; Shanafelt, T. D.; Kay, N. E.; Fernandes, S. M.; Brown, J. R.; Wang, L.; Li, S.; Livak, K. J.; Neuberg, D. S.; Klages, S.; Timmermann, B.; Kipps, T. J.; Campo, E.; Gnirke, A.; Wu, C. J.; Meissner, A.: Pre-neoplastic alterations define CLL DNA methylome and persist through disease progression and therapy. Blood Cancer Discovery 2 (1), 2:1–16 (2020)

Riege, K.; Kretzmer, H.; Sahm, A.; McDade, S. S.; Hoffmann, S.; Fischer, M.: Dissecting the DNA binding landscape and gene regulatory network of p63 and p53. eLife 9, e63266 (2020)

Grosswendt, S.; Kretzmer, H.; Smith, Z. D.; Sampath Kumar, A.; Hetzel, S.; Wittler, L.; Klages, S.; Timmermann, B.; Mukherji, S.; Meissner, A.: Epigenetic regulator function through mouse gastrulation. Nature 584, pp. 102 - 108 (2020)

Charlton, J.; Jung, E. J.; Mattei, A. L.; Bailly, N.; Liao, J.; Martin, E. J.; Gießelmann, P.; Brändl, B.; Stamenova, E. K.; Müller, F.-J. et al.; Kiskinis, E.; Gnirke, A.; Smith, Z. D.; Meissner, A.: TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers. Nature Genetics 52 (8), pp. 819 - 827 (2020)

The ENCODE Project Consortium; Snyder, M. P.; Gingeras, T. R.; Moore, J. E.; Weng, Z.; Gerstein, M. B.; Ren, B.; Hardison, R. C.; Stamatoyannopoulos, J. A.; Graveley, B. R. et al.; Feingold, E. A.; Pazin, M. J.; Pagan, M.; Gilchrist, D. A.; Hitz, B. C.; Cherry, J. M.; Bernstein, B. E.; Mendenhall, E. M.; Zerbino, D. R.; Frankish, A.; Flicek, P.; Myers , R. M.; Meissner, A.: Perspectives on ENCODE. Nature 583, pp. 693 - 698 (2020)

Yagi, M.; Kabata, M.; Tanaka, A.; Ukai, T.; Ohta, S.; Nakabayashi, K.; Shimizu, M.; Hata, K.; Meissner, A.; Yamamoto, T. et al.; Yamada, Y.: Identification of distinct loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development. Nature Communications 11, 3199 (2020)