Publications

Swanepoel , C. M.; Wang, G.; Zhang, L.; Brändl, B.; Bauer, H.; Tsaytler, P.; Müller, F.-J.; Herrmann, B. G.; Mueller, J. L.: Acquisition of ampliconic sequences marks a selfish mouse t-haplotype. Nature Communications 17, 21 (2025)

Wang, G.; Korody, M. L.; Brändl, B.; Hernandez-Toro, C. J.; Rohrandt, C.; Hong, K.; Pang, A. W. C.; Lee, J.; Migliorelli, G.; Stanke, M. et al.; Ford, S. M.; Pollmann, I.; Houck, M. L.; Lewin, H. A.; Lear, T. L.; Ryder, O. A.; Meissner, A.; Loring, J. F.; Müller, F.-J.: Genomic map of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni). Proceedings of the National Academy of Sciences of the United States of America 122 (20) (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)

Evers , M.; Brändl, B.; Rohrandt, C.; Kubelt-Kwamin, C.; Müller, F.-J.; Danso, D.; Maicher , A.; Wang, G.; Friedrichsen , S.; Kolkenbrock, S.: Rapid intraoperative amplicon sequencing of CNS tumor markers. Computational and Structural Biotechnology Journal 26, pp. 51 - 57 (2024)

Maier, H. B.; Neyazi, A.; Bundies, G. L.; Meyer-Bockenkamp, F.; Bleich, S.; Pathak, H.; Ziert, Y.; Neuhaus, B.; Müller, F.-J.; Pollmann, I. e. a. et al.; Frieling, H.: Validation of the predictive value of BDNF -87 methylation for antidepressant treatment success in severely depressed patients-a randomized rater-blinded trial. Trials 25 (1), Article 247 (2024)

Bastian, L.; Beder, T.; Barz, M. J.; Bendig, S.; Bartsch, L.; Walter, W.; Wolgast , N.; Brändl, B.; Rohrandt, C.; Hansen, B.-T. et al.; Hartmann, A. M.; Iben, K.; das Gupta, D.; Denker, M.; Zimmermann , J.; Wittig, M.; Chitadze, G.; Neumann, M.; Schneller, F.; Fiedler, W.; Steffen, B.; Stelljes, M.; Faul, C.; Schwartz, S.; Müller, F.-J.; Cario, G.; Harder, L.; Haferlach, C.; Pfeifer, H.; Gökbuget, N.; Brüggemann, M.; Baldus, C. D.: Developmental trajectories and cooperating genomic events define molecular subtypes of BCR::ABL1-positive ALL. Blood 143 (14), pp. 1391 - 1398 (2024)

Kanczok, J.; Jauch-Chara, K.; Müller, F.-J.: Imagery rescripting and cognitive restructuring for inpatients with moderate and severe depression - a controlled pilot study. BMC Psychiatry 24 (1), Article 194 (2024)

Ilik, I. A.; Glažar, P.; Tse, K.; Brändl, B.; Meierhofer, D.; Müller, F.-J.; Smith, Z. D.; Aktas, T.: Autonomous transposons tune their sequences to ensure somatic suppression. Nature 626 (8001), pp. 1116 - 1124 (2024)

Afflerbach, A.-K.; Rohrandt, C.; Brändl, B.; Sönksen, M.; Hench, J.; Frank, S.; Börnigen, D.; Alawi, M.; Mynarek, M.; Winkler, B. et al.; Ricklefs, F.; Synowitz, M.; Dührsen, L.; Rutkowski, S.; Wefers, A. K.; Müller, F.-J.; Schoof, M.; Schüller, U.: Classification of Brain Tumors by Nanopore Sequencing of Cell-Free DNA from Cerebrospinal Fluid. Clinical Chemistry 70 (1), pp. 250 - 260 (2024)

Weigert, R.; Hetzel, S.; Bailly, N.; Haggerty, C.; Ilik, I. A.; Kwong Yung, P. Y.; Navarro, C.; Bolondi, A.; Sampath Kumar, A.; Anania, C. et al.; Brändl, B.; Meierhofer, D.; Lupiáñez, D. G.; Müller, F.-J.; Aktas, T.; Elsässer, S. J.; Kretzmer, H.; Smith, Z. D.; Meissner, A.: Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nature Cell Biology 25 (4), pp. 579 - 591 (2023)

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)

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 (6), pp. 981 - 995 (2022)

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 28 (7), pp. 594 - 603 (2021)

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)

Gießelmann, P.; Brändl, B.; Raimondeau, E.; Bowen, R.; Rohrandt, C.; Tandon, R.; Kretzmer, H.; Assum, G.; Galonska, C.; Siebert, R. et al.; Ammerpohl, O.; Heron, A.; Schneider, S. A.; Ladewig, J.; Koch, P.; Schuldt, B. M.; Graham, J. E.; Meissner, A.; Müller, F.-J.: Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing. Nature Biotechnology 37 (12), pp. 1478 - 1481 (2019)

Giesselmann, P.; Hetzel, S.; Müller, F.-J.; Meissner, A.; Kretzmer, H.: Nanopype: A modular and scalable nanopore data processing pipeline. Bioinformatics 35 (22), pp. 4770 - 4772 (2019)

Krols, M.; Asselbergh, B.; De Rycke, R.; De Winter, V.; Seyer, A.; Müller, F.-J.; Kurth, I.; Bultynck, G.; Timmerman, V.; Janssens, S.: Sensory neuropathy-causing mutations in ATL3 affect ER-mitochondria contact sites and impair axonal mitochondrial distribution. Human Molecular Genetics 28 (4), pp. 615 - 627 (2019)

Neureiter, A.; Brändl, B.; Hiber, M.; Tandon, R.; Müller, F.-J.; Steenpass, L.: Generation of an iPSC line of a patient with Angelman syndrome due to an imprinting defect. Stem Cell Research 33, pp. 20 - 24 (2018)

Tandon, R.; Brändl, B.; Baryshnikova, N.; Landshammer, A.; Steenpaß, L.; Keminer, O.; Pless, O.; Müller, F.-J.: Generation of two human isogenic iPSC lines from fetal dermal fibroblasts. Stem Cell Research 33, pp. 120 - 124 (2018)

Allison, T. F.; Andrews, P. W.; Avior, Y.; Barbaric, I.; Benvenisty, N.; Bock, C.; Brehm, J.; Bruestle, O.; Damjanov, I.; Elefanty, A. et al.; Felkner, D.; Gokhale, P. J.; Halbritter, F.; Healy, L. E.; Hu, T. X.; Knowles, B. B.; Loring, J. F.; Ludwig, T. E.; Mayberry, R.; Micallef, S.; Mohamed, J. S.; Müller, F.-J.; Mummery, C. L.; Nakatsuji, N.; Ng, E. S.; Oh, S. K. W.; O'Shea, O.; Pera, M. F.; Reubinoff, B.; Robson, P.; Rossant, J.; Schuldt, B. M.; Solter, D.; Sourris, K.; Stacey, G.; Stanley, E. G.; Suemori, H.; Takahashi, K.; Yamanaka, S.: Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells. Nature Communications 9 (1), 1925 (2018)