Publications of Thomas Manke

Akol, I.; Izzo, A.; Gather, F.; Strack, S.; Heidrich, S.; hAilín, D. Ó.; Villarreal, A.; Hacker, C.; Rauleac, T.; Bella, C. et al.; Fischer, A.; Manke, T.; Vogel, T.: Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome. Proceedings of the National Academy of Sciences of the United States of America 120, e2122467120 (2023)

Lenaerts, A.; Kucinski, I.; Deboutte, W.; Derecka, M.; Cauchy, P.; Manke, T.; Göttgens, B.; Grosschedl, R.: EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors. Journal of Experimental Medicine 219, e20212437 (2022)

Ferrari, F.; Arrigoni, L.; Franz, H.; Izzo, A.; Butenko, L.; Trompouki, E.; Vogel, T.; Manke, T.: DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility. Nature Communications 11, p. 5200 (2020)

Wolff, J.; Bhardwaj, V.; Nothjunge, S.; Richard, G.; Renschler, G.; Gilsbach, R.; Manke, T.; Backofen, R.; Ramirez, F.; Grüning, B. A.: Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Research (London) 48, pp. W117 - W184 (2020)

Lopez-Delisle, L.; Rabbani, L.; Wolff, J.; Bhardwaj, V.; Backofen, R.; Grüning, B.; Ramírez, F.; Manke, T.: pyGenomeTracks: reproducible plots for multivariate genomic datasets. Bioinformatics 692, pp. 1 - 2 (2020)

Bhardwaj, V.; Semplicio, G.; Erdogdu, N. U.; Manke, T.; Akhtar, A.: MapCap allows high-resolution detection and differential expression analysis of transcription start sites. Nature Communications 10, p. 3219 (2019)

Panhale, A.; Richter , F. M.; Ramírez, F.; Shvedunova, M.; Manke, T.; Mittler, G.; Akhtar, A.: CAPRI enables comparison of evolutionary conserved RNA interacting regions. Nature Communications 10, 2682 (2019) (2019)

Ramisch, A.; Heinrich, V.; Glaser, L. V.; Fuchs, A.; Yang, X.; Benner, P.; Schöpflin, R.; Li, N.; Kinkley, S.; Römer-Hillmann, A. et al.; Longinotto, J.; Heyne, S.; Czepukojc, B.; Kessler, S. M.; Kiemer, A. K.; Cadenas, C.; Arrigoni, L.; Gasparoni, N.; Manke, T.; Pap, T.; Pospisilik, A.; Hengstler, J.; Walter, J.; Meijsing, S. H.; Chung, H.-R.; Vingron, M.: CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biology: Biology for the Post-Genomic Era 20, p. 227 (2019)

Ramirez, F.; Bhardwaj, V.; Arrigoni, L.; Lam, K. C.; Grüning, B. A.; Villaveces, J.; Habermann, B.; Akhtar, A.; Manke, T.: High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications 9, p. 189 (2018)

Arrigoni, L.; Al-Hasani, H.; Ramírez, F.; Panzeri, I.; Ryan, D. P.; Santacruz, D.; Kress, N.; Pospisilik, J. A.; Bönisch, U.; Manke, T.: RELACS nuclei barcoding enables high-throughput ChIP-seq. Communications Biology 214 (2018)

Aktas, T.; Ilik, I. A.; Maticzka, D.; Bhardwaj, V.; Rodrigues , C. P.; Mittler, G.; Manke, T.; Backofen, R.; Akhtar, A.: DHX9 Suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature 544, pp. 115 - 119 (2017)

Sheikh, B.N.; Bechtel-Walz, W.; Lucci, J.; Karpuik, O.; Hild, I.; Hartleben, B.; Vornweg, J.; Helmstädter, M.; Sahyoun, A.H.; Bhardwaj, V. et al.; Stehle, T.; Diehl, S.; Kretz, O.; Voss, A.K.; Thomas, T.; Manke, T.; Huber, T.B.; Akhtar, A.: MOF maintains transcriptional programs regulating cellular stress response. Oncogene 35, pp. 2698 - 2710 (2016)

Arrigoni, L.; Richter, A. S.; Betancourt, E.; Bruder, K.; Diehl, S.; Manke, T.; Bönisch, U.: Standardizing chromatin research: a simple and universal emthod for ChIP-seq. Nucleic Acids Research (London) 44, p. e67 (2016)

Chlamydas, S.; Holz, H.; Samata, M.; Chelmicki, T.; Georgiev, P.; Pelechano, V.; Dündar, F.; Dasmeh, P.; Mittler, G.; Tavares Cadete, F. et al.; Ramirez, F.; Conrad, T.; Wei, W.; Raja, S.; Manke, T.; Luscombe, N. M.; Steinmetz, L. M.; Akhtar, A.: Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation. Nature Structural and Molecular Biology 23, pp. 580 - 589 (2016)

Ramirez, F.; Lingg, T.; Toscano, S.; Lam, K.-C.; Georgiev, P.; Chung, H.-R.; Lajoie, B. R.; de Wit, E.; Zhan, Y.; de laat, W. et al.; Dekker, J.; Manke, T.; Akhtar, A.: High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Molecular Cell 60, pp. 146 - 162 (2015)

Bu, H.; Narisu, N.; Schlick, B.; Rainer, J.; Manke, T.; Schäfer, G.; Pasqualini, L.; Chines, P.; Schweiger, M. R.; Fuchsberger, C. et al.; Klocker , H.: Putatative Prostate Cancer Risk SNP in an Androgen Receptor-binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites. Human Mutations 37, pp. 52 - 64 (2015)

Bulut-Karslioglu, A.; De la Rosa-Velazquez, I. A.; Ramirez, F.; Barenboim, M.; Onishi-Seebacher, M.; Arand, J.; Galán, C.; Winter, G. E.; Engist, B.; Gerle, B. et al.; O'Sullivan, R. J.; Martens, J. H. A.; Walter, J.; Manke, T.; Lachner, M.; Jenuwein, T.: Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells. Molecular Cell 55, pp. 277 - 290 (2014)

Chelmicki, T.; Dündar, F.; Turley, M. J.; Khanam, T.; Aktas, T.; Ramírez, F.; Gendrel, A.-V.; Wright, P. R.; Videm, P.; Backofen, R. et al.; Heard, E.; Manke, T.; Akhtar, A.: MOF-associated complexes ensure stem cell identity and Xist repression. eLife 3, p. e02024 (2014)

Ramírez, F.; Dündar, F.; Diehl, S.; Grüning, B. A.; Manke, T.: deep Tools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Research 42, pp. W187 - W191 (2014)

Izzo, A.; Kamieniarz-Gdula, K.; Ramirez, F.; Noureen, N.; Kind, J.; Manke, T.; van Steensel, B.; Schneider, R.: The Genome Landscape of the Somatic Linker Histone Subtypes H1.1 to H1.5 in Human Cells. Cell Reports 3, pp. 2142 - 2154 (2013)

Barenboim, M.; Manke, T.: ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. Bioinformatics 29, pp. 2197 - 2198 (2013)

Bu, H.; Schweiger, M. R.; Manke, T.; Wunderlich, A.; Timmerman, B.; Kerick, M.; Pasqualini, L.; Shehu, E.; Fuchsberger, C.; Cato, A. C. B. et al.; Klocker, H.: Anterior gradient 2 and 3 - two prototype androgen-responsive genes transcriptionally upregulated by androgens and by oestrogens in prostate cancer cells. FEBS Journal 280, pp. 1249 - 1266 (2013)

Fejer, G.; Wegner, M. D.; Györy, I.; Cohen, I.; Engelhard, P.; Voronov, E.; Manke, T.; Ruzsics, Z.; Dölken, L.; Prazeres da Costa, O. et al.; Branzk, N.; Huber, M.; Prasse, A.; Schneider, R.; Apte, R. N.; Galanos, C.; Freudenberg, M. A.: Nontransformed, GM-CSF-dependent macrophage lines are a unique model to study tissue macrophage functions. Proceedings of the National Academy of Sciences Uzs.A. 110, pp. E-2191 - E-2198 (2013)

Schaefer, A. S.; Bochenek, G.; Manke, T.; Nothnagel, M.; Graetz, C.; Thien, A.; Jockel-Schneider, Y.; Harks, I.; Staufenbiel, I.; Wijmenga, C. et al.; Eberhard, J.; Guzeldemir-Akcakanat, E.; Cine, N.; Folwaczny, M.; Noack, B.; Meyle, J.; Eickholz, P.; Trombelli, L.; Scapoli, C.; Nohutcu, R.; Bruckmann, C.; Doerfer, C.; Jepsen, S.; Loos, B. G.; Schreiber, S.: Validation of reported genetic risk factors for periodontitis in a large-scale replication study. Journal of Clinical Periodontology 40, pp. 563 - 572 (2013)

Bulut-Karslioglu, A.; Perrera, V.; Scaranaro, M.; de la Rosa-Velazquez, I. A.; van de Nobelen, S.; Shukeir, N.; Popow, J.; Gerle, B.; Opravil, S.; Pagani, M. et al.; Meidhof, S.; Brabletz, T.; Manke, T.; Lachner, M.; Jenuwein, T.: A transcription factor-based mechanism for mouse heterochromatin formation. Nature Structural and Molecular Biology 19, pp. 1023 - 1030 (2012)

Lam, K. C.; Mühlpfordt, F.; Vaquerizas, J. M.; Raja, S. J.; Holz, H.; Luscombe, N. M.; Manke, T.; Akhtar, A.: The NSL Complex Regulates Housekeeping Genes in Drosophila. PLoS Genetics 8, p. e1002736 - e1002736 (2012)

Warnatz, H.-J.; Schmidt, D.; Manke, T.; Piccini, I.; Sultan, M.; Borodina, T.; Balzereit, D.; Wruck, W.; Soldatov, A.; Vingron, M. et al.; Lehrach, M.; Yaspo, M.-L.: The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle. The Journal of Biological Chemistry 286, pp. 23521 - 23532 (2011)

Billmann-Born, S.; Till, A.; Arlt, A.; Lipinski, S.; Sina, C.; Latiano, A.; Annese, V.; Häsler, R.; Kerick, M.; Manke, T. et al.; Seegert, D.; Hanidu, A.; Schäfer, H.; van Heel, D.; Li, J.; Schreiber, S.; Rosenstiel, P.: Genome-Wide Expression Profiling Identifies an Impairment of Negative Feedback Signals in the Crohn's Disease-Associated NOD2 Variant L1007fsinsC. The Journal of Immunology 186, pp. 4027 - 4038 (2011)

Olszak, A. M.; van Essen, D.; Pereira, A.; Diehl, S.; Manke, T.; Maiato, H.; Saccani, S.; Heun, P.: Heterochromatin boundaries are hotspots for de novo kinetochore formation. Nature Cell Biology 13, pp. 799 - 808 (2011)

Ott, C. E.; Grünhagen, J.; Jäger, M.; Horbelt, D.; Schwill, S.; Kallenbach, K.; Guo, G.; Manke, T.; Mundlos, S.; Robinson, P. N.: MicroRNAs Differentially Expressed in Postnatal Aortic Development Downregulate Elastin via 3' UTR and Coding-Sequence Binding Sites. Plosone 6, pp. e16250 - e12650 (2011)