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Journal Article (31)

2019

MPG.PuRe

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publisher-version

Journal Article
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)
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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, p. 2682 (2019)
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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)
2018

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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) 46, pp. W11 - W16 (2018)
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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)
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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)
2017

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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)
2016

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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)
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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)
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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)
2015

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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)
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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)
2014

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Bulut-Karslioglu, A.; De La Rosa-Valázquez, 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)
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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)
MPG.PuRe

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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)
2013

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

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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)
2012

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Bulut-Karslioglu, A.; Perrera, V.; Scaranaro, M.; de la Rosa-Velazquez, I. A.; van de Nobelin, 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 & Molecular Biology 19, pp. 1023 - 1030 (2012)
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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)
2011

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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)
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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)
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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)
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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)
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Thomas-Chollier, M.; Hufton, A.; Heinig, M.; O'Keeffe, S.; El Masri, N.; Roider, H. G.; Manke, T.; Vingron, M.: Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nature Protocols 6, pp. 1860 - 1869 (2011)
2010

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Warnatz, H.-J.; Querfurth, R.; Guerasimova, A.; Cheng, X.; Haas, S. A.; Hufton, A. L.; Manke, T.; Vanhecke, D.; Nietfeld, W.; Vingron, M. et al.; Janitz, M.; Lehrach, H.; Yaspo, M.-L.: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Research 38, pp. 6112 - 6123 (2010)
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Hov, J. R.; Keitel, V.; Laerdahl, J. K.; Spomer, L.; Ellinghaus, E.; Elsharawy, A.; Melum, E.; Boberg, K. M.; Manke, T.; Balschun, T. et al.; Schramm, C.; Bergquist, A.; Weismüller, T.; Gotthardt, D.; Rust, C.; Henckaerts, L.; Onnie, C. M.; Weersma, R. K.; Sterneck, M.; Teufel, A.; Runz, H.; Stiehl, A.; Ponsioen, C. Y.; Wijmenga, C.; Vatn, M. H.; Stokkers, P. C. F.; Vermeire, S.; Mathew, C. G.; Lie, B. A.; Beuers, U.; Manns, M. P.; Schreiber, S.; Schrumpf, E.; Häussinger, D.; Franke, A.; Karlsen, T. H.: Mutational Characterization of the Bile Acid Receptor TGR5 in Primary Sclerosing Cholangitis. PLoS ONE 5, p. e12403 - e12403 (2010)
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Schaefer, A.; Richter, G. M.; Nothnagel, M.; Manke, T.; Dommisch, H.; Jacobs, G.; Arlt, A.; Rosenstiel, P.; Noack, B.; Groessner-Schreiber, B. et al.; Søren, J.; Loos, B. G.; Schreiber, S.: A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis. Human Molecular Genetics 29, pp. 553 - 562 (2010)