Publications

Drewes, C.; López, C.; Okeke, N.; Jebaraj, B.; Wiegreffe, C.; Kraus, I. .; Hillebrecht, S.; Awada, A.; Bens, S.; Chteinberg, E. et al.; Eichhorst, B.; Datismann, S.; Dyer, M. J. S.; Fischer, A.; Fischer, K.; Glaser, S.; Hallek, M.; Kretzmer, H.; Mottok, A.; Pfaff, D.; Schnitzler, K.; Meier-Kolthoff, J. P.; Schlesner, M.; Schneider, C.; Britsch, S.; Ammerpohl, O.; Stilgenbauer, S.; Tausch, E.; Siebert, R.: The spectrum of immunoglobulin heavy chain enhancer hijacking in chronic lymphocytic leukemia. Leukemia (2026)

Tornisiello, R.; Kretzmer, H.: scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data. Bioinformatics Advances (2026)

Steiger, M.; Singh, N.; Tyers, A. M.; Kretzmer, H.; Valenzano, D. R.; Meissner, A.: The DNA methylation landscape of naturally short-lived killifish. Scientific Reports 16, 7173 (2026)

Heß, A.; Kovacsovics, A.; Bachinger, F.; Vallier, L.; Kretzmer, H.; Meissner, A.: Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation. Genome Biology 27, 59 (2026)

Heß, A.; Seelow, D.; Kretzmer, H.: DNAvi: integration, statistics, and visualization of cell-free DNA fragment traces. Bioinformatics (2026)

Drewes, C.; López, C.; Martinez‐Manjón, J. E.; Okeke, N.; Jebaraj, B.; Bens, S.; Brändl, B.; Dyer, M. J. S.; Eichhorst, B.; Fischer, A. et al.; Fischer, K.; Robrecht, S.; Hallek, M.; Glaser, S.; Hillebrecht, S.; Jayne, S.; Kretzmer, H.; Mottok, A.; Müller, F.; Schneider, C.; Ammerpohl, O.; del Val, C.; Stilgenbauer, S.; Tausch, E.; Siebert, R.: Chronic lymphocytic leukemia withIGH::BCL3‐translocation is characterized by a homogeneous and distinct genetic and epigenetic landscape. HemaSphere 10 (2026)

Lin, Y.-Y.; Breuer, K.; Weichenhan, D.; Lafrenz, P.; Sarnataro, A.; Wilk, A.; Chepeleva, M.; Mücke, O.; Schönung, M.; Petermann, F. et al.; Kensche, P. R.; Weiser, L.; Thommen, .; Giacomelli, G.; Nordstroem, K.; Gonzalez-Avalos, E.; Merkel, A.; Kretzmer, H.; Fischer, J.; Krämer, S.; Iskar, M.; Wolf, S.; Buchhalter, I.; Esteller, M.; Lawerenz, C.; Twardziok, S.; Zapatka, M.; Hovestadt, V.; Schlesner, M.; Schulz, M. H.; Hoffmann, S.; Gerhause, C.; Walter, J.; Hartmann, M.; Lipka, D. B.; Assenov, Y.; Bock, C.; Plass, C.; Toth, R.; Lutsik, P.: Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard. Nucleic Acids Research 53 (2025)

Guckelberger, P.; Haut, L.; Tornisiello, R.; Kretzmer, H.; Meissner, A.: HELLS is required for maintaining proper DNA modification at human satellite repeats. Genome Biology (26) (2025)

Hetzel, S.; Hodis , E.; Torlai Triglia, E.; Kovacsovics, A.; Steinmann , K.; Gnirke, A.; Cui, M.; McQuaid, D.; Weigert, R.; Pohl, G. et al.; Muzumdar, M. D.; Leyvraz, S.; Keilholz, U.; Yaspo, M.-L.; Regev, A.; Kretzmer, H.; Smith, Z.; Meissner, A.: Direct genetic transformation bypasses tumor-associated DNA methylation alterations. Genome Biology (26) (2025)

Chteinberg, E.; Kolarova, J.; Vogt, J.; Macamo, A.; Bormann, F.; Kretzmer, H.; Speel, E. J.; van den Oord, J.; Schneider, C.; Stilgenbauer, S. et al.; Becker, J. C.; Winnepenninckx, V.; Biessen, E.; Zenke, M.; Kurz, A. K.; Siebert, R.; Zur Hausen , A.: The significance of PAX5 in Merkel cell carcinoma. The Journal of Pathology: an Official Journal of the Pathological Society of Great Britain and Ireland 266 (1), pp. 81 - 94 (2025)

Glaser , S.; Fischer, A.; Martínez-Manjón, J. E.; López, C.; Kretzmer, H.; Burkhardt, B.; Hübschmann, D.; Hummel, M.; Klapper, W.; Kolarova, J. et al.; Kreuz, M.; Ott, G. e. a.: Subgrouping germinal center-derived B-cell lymphomas based on machine learning-deduced DNA methylation modules. Leukemia 39 (4), pp. 967 - 971 (2025)

Brändl, B.; Steiger, M.; Kubelt, C.; Rohrandt, C.; Zhu, Z.; Evers, M.; Wang, G.; Schuldt, B.; Afflerbach, A.-K.; Wong, D. et al.; Lum, A.; Halldorsson, S.; Djirackor, L.; Leske, H.; Magadeeva, S.; Smicius, R.; Quedenau, C.; Schmidt, N. O.; Schüller, U.; Vik-Mo, E. O.; Proescholdt, M.; Riemenschneider, M. J.; Zadeh, G.; Ammerpohl, O.; Yip, S.; Synowitz, M.; van Bömmel, A.; Kretzmer, H.; Müller, F.-J.: Rapid brain tumor classification from sparse epigenomic data. Nature Medicine 31 (3), pp. 840 - 848 (2025)

Glaser, S.; Wagener, R.; Kretzmer, H.; López, C.; Baptista, M. J.; Bens, S.; Bernhart, S.; Bhatia, K.; Borkhardt, A.; Elgaafary, S. et al.; Hoffmann, S.; Hübschmann, D.; Hummel, M.; Klapper, W.; Kolarova, J.; Kreuz, M.; Lazzi, S.; Löffler, M.; Navarro, J. T.; Neequaye, J.; Onyango, N.; Onyuma, T.; Ott, G.; Radlwimmer, B.; Rohde, M.; Rosenwald, A.; Rosolowski, M.; Schlesner, M.; Szczepanowski, M.; Tapia, G.; Wößmann, W.; Küppers, R.; Trümper, L.; Leoncini, L.; Lichter, P.; del Val, C.; Ammerpohl, O.; Burkhardt, B.; Mbulaiteye, S. M.; Siebert, R.: Subtyping Burkitt Lymphoma by DNA Methylation. Genes, Chromosomes and Cancer 64 (2025)

Taguchi, A.; Magalhães, A. P.; Bolondi, A.; Lee, M.-K.; Kretzmer, H.; Wittler, L.; Hnisz, D.; Meissner, A.: Single-cell activation screen identifies hepatic maturation regulators with zonal resolution. Developmental Cell (2025)

Glaser, S.; Kretzmer, H.; Kolassa, I. T.; Schlesner, M.; Fischer, A.; Fenske, I.; Siebert, R.; Ammerpohl , O.: Navigating Illumina DNA methylation data: biology versus technical artefacts. NAR: genomics and bioinformatics 6 (4), Article lqae181 (2024)

Stötzel, M.; Cheng, C.-Y.; Ilik, I. A.; Sampath Kumar, A.; Akbari-Omgba, P.; van der Weijden, V. A.; Zhang, Y.; Vingron, M.; Meissner, A.; Aktas, T. et al.; Kretzmer, H.; Bulut-Karslioglu, A.: TET activity safeguards pluripotency throughout embryonic dormancy. Nature Structural & Molecular Biology 31 (10), pp. 1625 - 1639 (2024)

Fleischmann, L. S.; Nemes, K.; Glaser, S.; Kouroukli, A. G.; Boros , M.; Bens, S.; Dahlum, S.; Kretzmer, H.; Oyen, F.; Gerss, J. et al.; Hasselblatt, M.; Frühwald, M. C.; Siebert, R.: Constitutional mosaicism of pathogenic variants in SMARCB1 in a subset of patients with sporadic rhabdoid tumors. Neuro-Oncology: official journal of the World Federation of Neuro-Oncology, Article noae188 (2024)

Roessner, P. M.; Seufert, I.; Chapaprieta, V.; Jayabalan, R.; Briesch, H.; Massoni-Badosa, R.; Boskovic, P.; Benckendorff, J. ....; Kretzmer, H.; Naake, T. e. a.: T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia. Blood 144 (5), pp. 510 - 524 (2024)

Bolondi, A.; Law, B. K.; Kretzmer, H.; Gassaloglu, S. I.; Buschow, R.; Riemenschneider, C.; Yang, D.; Walther, M.; Veenvliet, J. V.; Meissner, A. et al.; Smith, Z. D.; Chan, M. M.: Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 59 (12), pp. 1489 - 1505 (2024)

Sato, N. S.; Rosa , V. S.; Makhlouf, A.; Kretzmer, H.; Sampath Kumar, A.; Grosswendt, S.; Mattei, A. L.; Courbot, O.; Wolf, S.; Boulanger, J. et al.; Langevin, F.; Wiacek, M.; Karpinski, D.; Elosegui-Artola, A.; Meissner, A.; Zernicka-Goetz , M.; Shahbazi, M. N.: Basal delamination during mouse gastrulation primes pluripotent cells for differentiation. Developmental Cell 59 (10), pp. 1252 - 1268 (2024)