Publications

Knisbacher, B. A.; Lin, Z.; Hahn, C. K.; Nadeu, F.; Duran-Ferrer, M.; Stevenson, K. E.; Tausch, E.; Delgado, J.; Barbera-Mourelle, A.; Taylor-Weiner, A. et al.; Bousquets-Muñoz, P.; Diaz-Navarro, A.; Dunford, A.; Anand, S.; Kretzmer, H.; Gutierrez-Abril, J.; López-Tamargo, S.; Fernandes, S. M.; Sun, C.; Sivina, M.; Rassenti, L. Z.; Schneider, C.; Li, S.; Parida, L.; Meissner, A.; Aguet , F.; Burger, J. A.; Wiestner, A.; Kipps, T. J.; Brown, J. R.; Hallek, M.; Stewart, C.; Neuberg, D. S.; Martín-Subero , J. I.; Puente, X. S.; Stilgenbauer, S.; Wu, C. J.; Campo, E.; Getz, G.: Molecular map of chronic lymphocytic leukemia and its impact on outcome. Nature Genetics (2022)

Wilder , A. P.; Dudchenko , O.; Curry , C.; Korody , M.; Turbek , S. P.; Daly, M.; Misuraca , A.; Wang, G.; Khan , R.; Weisz, D. et al.; Fronczek, J.; Lieberman Aiden , E.; Houck , M. L.; Shier , D. M.; Ryder , O. A.; Steiner , C. C.: A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population. Genome Biology and Evolution 14 (8), evac122 (2022)

Asimi, V.; Sampath Kumar, A.; Niskanen, H.; Riemenschneider, C.; Hetzel, S.; Naderi, J.; Fasching, N.; Popitsch, N.; Du, M.; Kretzmer, H. et al.; Smith, Z. D.; Weigert, R.; Walther, M.; Mamde, S.; Meierhofer, D.; Wittler, L.; Buschow, R.; Timmermann, B.; Cisse, I. I.; Ameres, S. L.; Meissner, A.; Hnisz, D.: Hijacking of transcriptional condensates by endogenous retroviruses. Nature Genetics 54 (8), pp. 1238 - 1247 (2022)

Yuan, W.; Ma, S.; Brown, J. R.; Kim, K.; Murek, V.; Trastulla, L.; Meissner, A.; Lodato, S.; Shetty, A. S.; Levin, J. Z. et al.; Buenrostro, J. D.; Ziller, M. J.; Arlotta, P.: Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature Neuroscience 25 (8), pp. 1049 - 1058 (2022)

Mattei, A. L.; Bailly, N.; Meissner, A.: DNA methylation: a historical perspective. Trends in Genetics 38 (7), pp. 676 - 707 (2022)

Rosebrock, D.; Arora, S.; Mutukula, N.; Volkman, R.; Gralinska, E.; Balaskas, A.; Aragonés Hernández, A.; Buschow, R.; Brändl, B.; Müller, F.-J. et al.; Arndt, P. F.; Vingron, M.; Elkabetz, Y.: Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells. Nature Cell Biology 24, pp. 981 - 995 (2022)

Hetzel, S.; Mattei, A. L.; Kretzmer, H.; Qu, C.; Chen, X.; Fan, Y.; Wu, G.; Roberts, K. G.; Luger, S.; Litzow, M. et al.; Rowe, J.; Paietta, E.; Stock, W.; Mardis, E. R.; Wilson, R. K.; Downing, J. R.; Mullighan, C. G.; Meissner, A.: Acute lymphoblastic leukemia displays a distinct highly methylated genome. Nature Cancer 3 (6), pp. 768 - 782 (2022)

Hochmair, J.; Exner, C.; Franck, M.; Dominguez-Baquero, A.; Diez, L.; Brognaro, H.; Kraushar, M.; Mielke, T.; Radbruch, H.; Kaniyappan, S. et al.; Falke, S.; Mandelkow, E.; Betzel, C.; Wegmann, S.: Molecular crowding and RNA synergize to promote phase separation, microtubule interaction, and seeding of Tau condensates. The EMBO Journal 41 (11), e108882 (2022)

Pour, M.; Sampath Kumar, A.; Farag, N.; Bolondi, A.; Kretzmer, H.; Walther, M.; Wittler, L.; Meissner, A.; Nachman, I.: Emergence and patterning dynamics of mouse-definitive endoderm. iScience 25 (1), 103556 (2022)

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)

Ambrozkiewicz, M. C.; Borisova, E.; Newman, A. G.; Kraushar, M. L.; Schaub, T.; Dannenberg, R.; Brockmann, M.; Rosário, M.; Turko, P.; Jahn, O. et al.; Kaplan, D. R.; Iwawaki, T.; Spahn, C. M. T.; Rosenmund, C.; Tarabykin, V.: Ire1α-Regulated Rate of mRNA Translation is Required for Acquisition of Identity and Polarity in Upper Layer Cortical Neurons. bioRxiv (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)