Research articles
158. Groth CB, Maric J, Lázaro IG, Hofman T, Zhang Z, Ni Y, Keller F, Seufert I, Hofmann M, Neumann-Haefelin C, Sticht C, Rippe K, Urban S, Cerwenka A (2023) Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity. Front Immunol 14, 1287367. doi: 10.3389/fimmu.2023.1287367 | Abstract | Reprint | Article metrics
157. Seufert I, Sant P, Bauer K, Syed AP, Rippe K*, Mallm JP* (2023) Enhancing sensitivity and versatility of Tn5 based single cell omics. Front Epigenet Epigenom 1, 1245879. *corresponding authors. doi: 10.3389/freae.2023.1245879 | Abstract | Reprint | Article metrics
156. Schuster LC, Syed AP, Tirier SM, Steiger S, Seufert I, Becker H, Duque-Afonso J, Ma T, Ogawa S, Mallm JP, Lübbert M, Rippe K. Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia. Blood Adv 7, 7079-7083. doi: 10.1182/bloodadvances.2022009096 | Abstract | Reprint | Article metrics
155. Piroeva KV, McDonald C, Xanthopoulos C, Fox C, Clarkson CT, Mallm J-P, Vainshtein Y, Ruje L, Klett LC, Stilgenbauer S, Mertens D, Kostareli E*, Rippe K*, Teif VB* (2023) Nucleosome repositioning in chronic lymphocytic leukaemia. Genome Res 33, 1649-1661. *corresponding authors. doi: 10.1101/gr.277298.122 | Abstract | Reprint | Article metrics
154. John L, Poos AM, Brobeil A, Schinke C, Huhn S, Prokoph N, Lutz R, Wagner B, Zangari M, Tirier SM, Mallm JP, Schumacher S, Vonficht D, Sole-Boldo L, Quick S, Steiger S, Przybilla MJ, Bauer K, Baumann A, Hemmer S, Rehnitz C, Luckerath C, Sachpekidis C, Mechtersheimer G, Haberkorn U, Dimitrakopoulou-Strauss A, Reichert P, Barlogie B, Muller-Tidow C, Goldschmidt H, Hillengass J, Rasche L, Haas SF, van Rhee F, Rippe K, Raab MS, Sauer S, Weinhold N (2023) Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level. Nat Commun 14, 5011. doi: 10.1038/s41467-023-40584-4 | Abstract | Reprint | Article metrics
153. Poos AM, Prokoph N, Przybilla MJ, Mallm J-P, Steiger S, Seufert I, John L, Tirier SM, Bauer K, Baumann A, Munawar U, Rasche L, Kortuem M, Giesen N, Huhn S, Reichert P, Mueller-Tidow C, Goldschmidt H, Stegle O, Raab MS, Rippe K*, Weinhold N* (2023) Resolving therapy resistance mechanisms in multiple myeloma by multi-omics subclone analysis. Blood 142, 1633-1646. *corresponding authors. doi: 10.1182/blood.2023019758 | Abstract | Reprint | Article metrics
152. Kotsiliti E, Leone V, Schuehle S, Govaere O, Li H, Wolf MJ, Horvatic H, Bierwirth S, Hundertmark J, Inverso D, Zizmare L, Sarusi-Portuguez A, Gupta R, O'Connor T, Giannou AD, Shiri AM, Schlesinger Y, Beccaria MG, Rennert C, Pfister D, Ollinger R, Gadjalova I, Ramadori P, Rahbari M, Rahbari N, Healy M, Fernandez-Vaquero M, Yahoo N, Janzen J, Singh I, Fan C, Liu X, Rau M, Feuchtenberger M, Schwaneck E, Wallace SJ, Cockell S, Wilson-Kanamori J, Ramachandran P, Kho C, Kendall TJ, Leblond AL, Keppler SJ, Bielecki P, Steiger K, Hofmann M, Rippe K, Zitzlesberger H, Weber A, Malek N, Ludde T, Vucur M, Augustin HG, Flavell R, Parnas O, Rad R, Pabst O, Henderson NC, Huber S, Macpherson A, Knolle P, Claasen M, Geier A, Trautwein C, Unger K, Elinav E, Waisman A, Abdullah Z, Haller D, Tacke F, Anstee QM, Heikenwalder M (2023) Intestinal B-cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcR signalling. J Hepatol 79, 296-313. doi: 10.1016/j.jhep.2023.04.037 | Abstract | Reprint | Article metrics
151. Friedrich MJ, Neri P, Kehl N, Michel J, Steiger S, Kilian M, Leblay N, Maity R, Sankowski R, Lee H, Barakat E, Ahn S, Weinhold N, Rippe K, Bunse L, Platten M, Müller-Tidow C, Goldschmidt H, Raab MS, Bahlis NJ (2023) The preexisting T Cell landscape determines response to T cell-engagers therapy. Cancer Cell 41, 711-725 e6. doi: 10.1016/j.ccell.2023.02.008 | Abstract | Reprint | Article metrics
150. Muckenhuber M, Seufert I, Müller-Ott K, Mallm JP, Klett LC, Knotz C, Hechler J, Kepper N, Erdel F, Rippe K (2023) Epigenetic signals that direct cell type specific interferon beta response in mouse cells (2023) Life Sci Alliance 6, e202201823. doi: 10.26508/lsa.202201823 | Abstract | Reprint | Article metrics
149. Rademacher A, Weinmann R, Erdel F, Rippe K (2023) Assessing the phase separation propensity of proteins in living cells through optodroplet formation. Meth Mol Biol 2563, 395-411. doi: 10.1007/978-1-0716-2663-4_20 | Abstract | Reprint | Article metrics
148. Kehl N, Kilian M, Michel J, Wagner TR, Uhrig S, Brobeil A, Sester LS, Blobner S, Steiger S, Hundemer M, Weinhold N, Rippe K, Fröhling S, Eichmüller SB, Bunse L, Müller-Tidow C, Goldschmidt H, Platten M, Raab MS, Friedrich MJ (2022). IgE type multiple myeloma exhibits hypermutated phenotype and tumor reactive T cells. J Immunother Cancer 10, e005815. doi: 10.1136/jitc-2022-005815 | Abstract | Reprint | Article metrics
147. Bogeska R, Mikecin AM, Kaschutnig P, Fawaz M, Buchler-Schaff M, Le D, Ganuza M, Vollmer A, Paffenholz SV, Asada N, Rodriguez-Correa E, Frauhammer F, Buettner F, Ball M, Knoch J, Stable S, Walter D, Petri A, Carreno-Gonzalez MJ, Wagner V, Brors B, Haas S, Lipka DB, Essers MAG, Weru V, Holland-Letz T, Mallm JP, Rippe K, Kramer S, Schlesner M, McKinney Freeman S, Florian MC, King KY, Frenette PS, Rieger MA, Milsom MD (2022) Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging. Cell Stem Cell 29, 1273-1284 e8. doi: 10.1016/j.stem.2022.06.012 | Abstract | Reprint | Article metrics
146. Trojanowski J, Frank L, Rademacher A, Mücke N, Grigaitis P, Rippe K (2022) Transcription activation is enhanced by multivalent interactions independent of phase separation. Mol Cell 82, 1878-1893. doi: 10.1016/j.molcel.2022.04.017 | Abstract | Reprint | Article metrics
145. Thorn GJ, Clarkson CT, Rademacher A, Mamayusupova H, Schotta G, Rippe K, Teif VB (2022). DNA sequence-dependent formation of heterochromatin nanodomains, Nat Commun 1861. doi: 10.1038/s41467-022-29360-y | Abstract | Reprint | Article metrics
144. Poos AM, Schröder C, Jaishankar N, Röll D, Oswald M, Meiners J, Braun D, Bauer C, Frank L, Gunkel M, Spilger R, Wollmann T, Polonski A, Makrypidi-Fraune G, Chung I, Stenzel A, Erfle H, Rohr K, Baniahmad A, Sauter G, Rippe K, Simon R, König R (2022) PITX1 regulates telomerase in prostate cancer with high prognostic power. Cancers 14, 1267. doi: 10.3390/cancers14051267 | Abstract | Reprint | Article metrics
143. Frank L, Rademacher A, Mücke N, Tirier SM, Koeleman E, Knotz C, Schumacher S, Stainczyk SA, Westermann F, Fröhling S, Chudasama P, Rippe K (2022) ALT-FISH quantifies alternative lengthening of telomeres activity by imaging of single-stranded repeats. Nucleic Acids Res 50, e61. doi: 10.1093/nar/gkac113 | Abstract | Reprint | Article metrics
142. Berlin C, Cottard F, Willmann D, Urban S, Tirier SM, Marx L, Rippe K, Schmitt M, Petrocelli V, Greten FR, Fichtner-Feigl S, Kesselring R, Metzger E, Schüle R (2022) KMT9 controls stemness and growth of colorectal cancer. Cancer Res 82, 210-220. doi: 10.1158/0008-5472.CAN-21-1261 | Abstract | Reprint | Article metrics
141. Hanna BS, Llao-Cid L, Iskar M, Roessner PM, Klett LC, Wong JKL, Paul Y, Ioannou N, Ozturk S, Mack N, Kalter V, Colomer D, Campo E, Bloehdorn J, Stilgenbauer S, Dietrich S, Schmidt M, Gabriel R, Rippe K, Feuerer M, Ramsay AG, Lichter P, Zapatka M, Seiffert M (2021) Interleukin-10 receptor signaling promotes the maintenance of a PD-1(int) TCF-1(+) CD8(+) T cell population that sustains anti-tumor immunity. Immunity 54, 2825-2841 e2810. doi: 10.1016/j.immuni.2021.11.004 | Abstract | Reprint | Article metrics
140. Tirier SM, Mallm J-P, Steiger S, Poos AM, Awwad M, Giesen N, Casiraghi N, Susak H, Bauer K, Baumann A, John L, Seckinger A, Hose D, Müller-Tidow C, Goldschmidt H, Stegle O, Hundemer M, Weinhold N, Raab MS, Rippe K (2021) Subclone specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single cell transcriptomics. Nat Commun 12, 6960. doi: 10.1038/s41467-021-26951-z | Abstract | Reprint | Article metrics
139. Faure-Dupuy S, Riedl T, Rolland M, Hizir Z, Reisinger F, Neuhaus K, Schuehle S, Remouchamps C, Gillet N, Schönung M, Stadler M, Wettengel J, Barnault R, Parent R, Schuster LC, Farhat R, Prokosch S, Leuchtenberger C, Öllinger R, Engleitner T, Rippe K, Rad R, Unger K, Tscharahganeh D, Lipka DB, Protzer U, Durantel D, Lucifora J, Dejardin E, Heikenwalder M (2021) Control of APOBEC3B induction and cccDNA decay by NF-κB and miR-138-5p. JHEP Reports 3, 100354. doi: 10.1016/j.jhepr.2021.100354 | Abstract | Reprint | Article metrics
138. Frank L, Weinmann R, Erdel F, Trojanowski J, Rippe K (2021) Transcriptional activation of heterochromatin by recruitment of dCas9 activators. Meth Mol Biol 2351, 307-320. doi: 10.1007/978-1-0716-1597-3_17 | Abstract | Reprint | Article metrics
137. Hartlieb SA, Sieverling L, Nadler-Holly M, Ziehm M, Toprak UH, Herrmann C, Ishaque N, Okonechnikov K, Gartlgruber M, Park YG, Wecht EM, Savelyeva L, Henrich KO, Rosswog C, Fischer M, Hero B, Jones DTW, Pfaff E, Witt O, Pfister SM, Volckmann R, Koster J, Kiesel K, Rippe K, Taschner-Mandl S, Ambros P, Brors B, Selbach M, Feuerbach L, Westermann F (2021) Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nat Commun 12, 1269. doi: 10.1038/s41467-021-21247-8 | Abstract | Reprint | Article metrics
136. Mallm J-P, Bundschuh C, Kim H, Weidner N, Steiger S, Lander I, Börner K, Bauer K, Hübschmann D, Benes V, Rausch T, Trevisan Doimo de Azevedo N, Telzerow A, Jost KL, Parthé S, Schnitzler P, Boutros M, Müller B, Bartenschlager R, Kräusslich H-G, Rippe K (2021) Local emergence and decline of a SARS-CoV-2 variant with mutations L452R and N501Y in the spike protein. medRxiv 2021.04.27.21254849. doi: 10.1101/2021.04.27.21254849 | Preprint | Article metrics
135. Roider T, Seufert J, Uvarovskii A, Frauhammer F, Bordas M, Abedpour N, Stolarczyk M, Mallm, JP, Herbst S, Bruch P, Balke-Want H, Hundemer M, Rippe K, Goeppert B, Seiffert M, Brors B, Mechtersheimer G, Zenz T, Peifer M, Chapuy B, Schlesner M, Müller-Tidow C, Fröhling S, Huber W, Anders S, Dietrich S (2020). Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels. Nat Cell Biol 22, 896-906. doi: 10.1038/s41556-020-0532-x | Abstract | Reprint (19.9 MB) | Article metrics
134. Rademacher A, Erdel F, Trojanowski J, Rippe K (2020) Tracing reversible light-induced chromatin binding with near-infrared fluorescent proteins. Meth Mol Biol 2173, 171-188. doi: 10.1007/978-1-0716-0755-8_12 | Abstract | Reprint (0.8 MB) | Article metrics
133. Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F (2020). Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol 3, 188. doi: 10.1038/s42003-020-0922-4 | Abstract | Reprint (11.9 MB) | Article metrics
132. Wierzbinska JA, Toth R, Ishaque N, Rippe K, Mallm JP, Klett LC, Mertens D, Zenz T, Hielscher T, Seifert M, Küppers R, Assenov Y, Lutsik P, Stilgenbauer S, Roessner PM, Seiffert M, Byrd J, Oakes CC, Plass C, Lipka DB (2020) Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL. Genome Med 12, 29. doi: 10.1186/s13073-020-00724-7 | Abstract | Reprint (5.0 MB) | Article metrics
131. Erdel F, Rademacher A, Vlijm R, Tünnermann J, Schweigert E, Frank L, Yserantant K, Hummert J, Bauer C, Schumacher S, Weinmann R, Alwash AA, Normand C, Herten D-P, Engelhardt J, Rippe K (2020) Mouse heterochromatin adopts digital compaction states without showing hallmarks of HP1-driven liquid-liquid phase separation. Mol Cell 78, 236-249.e7. doi: 10.1016/j.molcel.2020.02.005 | Abstract | Reprint (6.2 MB) | Article metrics | Comment
130. Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortes-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L, PCAWG Consortium (2020) Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 11, 733. doi: 10.1038/s41467-019-13824-9 | Abstract | Reprint (2.2 MB) | Article metrics
129. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020) Pan-cancer analysis of whole genomes. Nature 578, 82-93. doi: 10.1038/s41586-020-1969-6 | Abstract | Reprint (23.6 MB) | Article metrics
128. Mallm JP, Windisch P, Biran A, Schumacher S, Glass R, Herold-Mende C, Meshorer E, Barbus M, Rippe K (2020) Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to loss of DNA repair capacity. Intl J Cancer 146, 1281-1292. doi: 10.1002/ijc.32649 | Abstract | Reprint (6.6 MB) | Article metrics
127. Hoflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Buscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, Konig R, Schroeder C (2020) Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Mol Oncol14, 129-138. doi: 10.1002/1878-0261.12597 | Abstract | Reprint (10.5 MB) | Article metrics
126. Poos AM, Kordass T, Kolte A, Ast V, Oswald M, Rippe K, Konig R (2019) Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 20, 737. doi: 10.1186/s12859-019-3323-2 | Abstract | Reprint (0.9 MB) | Article metrics
125. Tirier SM, Park J, Preusser F, Amrhein L, Gu Z, Steiger S, Mallm JP, Waschow M, Eismann B, Gut M, Gut IG, Rippe K, Schlesner M, Theis F, Fuchs C, Ball CR, Glimm H, Eils R & Conrad C (2019) Pheno-seq - linking 3D phenotypes of clonal tumor spheroids to gene expression. Sci Rep 9, 12367. doi: 10.1038/s41598-019-48771-4 | Abstract | Reprint (5.0 MB) | Article metrics
124. Trojanowski J, Rademacher A, Erdel F & Rippe K (2019) Light-induced transcription activation for time-lapse microscopy experiments in living cells. Methods Mol Biol 2028, 251-270. doi: 10.1007/978-1-4939-9674-2_17 | Abstract | Reprint (0.8 MB)
123. Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2019) GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation. Med Image Anal 56, 68-79. doi: 10.1016/j.media.2019.04.011 | Abstract | Reprint (2.1 MB) | Article metrics
122.Ritter C, Wollmann T, Bernhard P, Gunkel M, Braun DM, Lee JY, Meiners J, Simon R, Sauter G, Erfle H, Rippe K, Bartenschlager R & Rohr K (2019) Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells. Int J Comput Assist Radiol Surg, 14, 1847-1857. doi: 10.1007/s11548-019-02010-3 | Abstract | Reprint (1.8 MB)
121.Feuerbach L, Sieverling L Deeg, KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Peter Lichter P, Fröhling S, Pfister SM, Jones DT, Rippe K & Brors B (2019). TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. BMC Bioinformatics 20, 272. doi: 10.1186/s12859-019-2851-0 | Abstract | Reprint (1.4 MB) | Article metrics
120. Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D & Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: 10.15252/msb.20188339 | Abstract | Reprint (7.1 MB) | Appendix (6.8 MB) | Additional data | Article metrics
119. Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A & Teif VB (2019). DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res, 29, 750-761. doi: 10.1101/gr.239707.118 | Abstract | Reprint (11.8 MB) | Article metrics
118. Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary, ML, Schüler J, Rippe K, Ogawa S & Lübbert M (2019) Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 3, 761-765. doi: 10.1182/bloodadvances.2018023879 | Abstract | Reprint (1.7 MB) | Article metrics
117. Wollmann T, Bernhard P, Gunkel M, Braun DM, Erfle H, Rippe K & Rohr K (2019) Black-box hyperparameter optimization for nuclei segmentation in prostate tissue images. In Bildverarbeitung für die Medizin 2019 (BVM 2019), Handels H, Deserno T, Maier A, Maier-Hein K, Palm C & Tolxdorff T, eds., Springer Vieweg, Wiesbaden, 345-350. doi: 10.1007/978-3-658-25326-4_75 | Reprint (0.7 MB) | Article metrics
116. Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Hoflmayer D, Burandt E, Tsourlakis MC, Sauter G, Buscheck F, Wilczak W, Steurer S, Schlomm T, Huland H, Graefen M, Haese A, Heinzer H, Jacobsen F, Hinsch A, Poos A, Oswald M, Rippe K, Konig R & Schroeder C (2019) Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers. Prostate 79, 302-311. doi: 10.1002/pros.23736 | Abstract | Reprint (1.4 MB) | Article metrics
115. Gao Q, Eck S, Matthias J, Chung I, Engelhardt J, Rippe K & Rohr K (2018) Bayesian joint super-resolution, deconvolution, and denoising of images with Poisson-Gaussian noise. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 938-942. doi: 10.1109/ISBI.2018.8363725 | Abstract | Reprint (0.4 MB)
114. Baltissen D, Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2018) Comparison of segmentation methods for tissue microscopy images of glioblastoma cells. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 396-399. doi: 10.1109/ISBI.2018.8363601 | Abstract | Reprint (0.4 MB)
113. Braun DM, Chung I, Kepper N & Rippe K (2018). TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet 19, 32. doi: 10.1186/s12863-018-0617-8 | Abstract | Reprint (2.4 MB) | Article metrics.
112. Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmuelle J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nuernberg P, Marenduzzo D, Rippe K & Papantonis A (2018). HMGB2 loss upon senescenceentry disrupts genomic organization and induces CTCF clustering across cell types. Mol Cell 70, 730-744. doi: 10.1016/j.molcel.2018.03.030 | Abstract | Reprint (7.7 MB) | Article metrics.
111. Wollmann T, Ivanova J, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2018). Multi-channel deep transfer learning for nuclei segmentation in glioblastoma cell tissue images. In Bildverarbeitung für die Medizin 2018 (BVM 2018), Springer Berlin Heidelberg, 316-321. doi: 10.1007/978-3-662-56537-7_83 | Abstract | Reprint (0.6 MB)
110. Chudasama P, Mughal S, Sanders M, Hübschmann D, Chung I, Deeg KI, Wong SH, Rabe S, Hlevnjak M, Zapatka M, Ernst A, Kleinheinz K, Schlesner M, Sieverling L, Klink B, Schröck E, Hoogenboezem R, Kasper B, Heilig C, Egerer G, Wolf S, von Kalle C, Eils R, Stenzinger A, Weichert W, Glimm H, Gröschel S, Kopp H-G, Omlor G, Lehner B, Bauer S, Schimmack S, Ulrich A, Mechtersheimer G, Rippe K, Brors B, Hutter B, Renner M, Hohenberger P, Scholl C & Fröhling S (2018). Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nat Commun 9, 144. doi: 10.1038/s41467-017-02602-0 | Abstract | Reprint (3.1 MB) | Article metrics
109. Rademacher A, Erdel F, Trojanowski J, Schumacher S & Rippe K (2017). Real-time observation of light-controlled transcription in living cells. J Cell Sci 130, 4213-4224. doi: 10.1242/jcs.205534 | Abstract | Reprint (12.9 MB) | JCS First person | Article metrics
108. Erdel F (2017). How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications. Bioessays 39, 1700053. doi: 10.1002/bies.201700053 | Abstract | Article metrics.
107. Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, RippeK & Längst G (2017). CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 45, 10534-10554. doi: 10.1093/nar/gkx711 | Abstract | Reprint (7.3 MB) | Article metrics.
106. Delacher M, Imbusch CD, Weichenhan D, Breiling A, Hotz-Wagenblatt A, Trager U, Hofer AC, Kagebein D, Wang Q, Frauhammer F, Mallm JP, Bauer K, Herrmann C, Lang PA, Brors B, Plass C & Feuerer M (2017). Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. Nat Immunol 18, 1160-1172. doi: 10.1038/ni.3799 | Abstract | Article metrics.
105. Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T & Plass C (2017). DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 49, 1052-106. doi: 10.1038/ng.3889 | Abstract | Reprint (8.7 MB) | Article metrics.
104. Chaturvedi A, Herbst L, Pusch S, Klett L, Goparaju R, Stichel D, Kaulfuss S, Panknin O, Zimmermann K, Toschi L, Neuhaus R, Haegebarth, A, Rehwinkel H, Hess-Stumpp H, Bauser M, Bochtler T, Struys EA, Sharma A, Bakkali A, Geffers R, Araujo-Cruz MM, Thol F, Gabdoulline R, Ganser A, Ho AD, von Deimling A, Rippe K, Heuser M & Kraemer A (2017). Pan-mutant IDH1 inhibitor BAY1436032 is highly effective against human IDH1 mutant acute myeloid leukemia in vivo. Leukemia 31, 2020-2028. doi: 10.1038/leu.2017.46 | Abstract | Reprint (2.2 MB) | Article metrics.
103. Teif VB, Mallm JP, Sharma T, Welch DBM, Rippe K, Eils R, Langowski J, Olins AL & Olins DE (2017). Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus 8, 188-204. doi: 10.1080/19491034.2017.1295201 | Abstract | Reprint (1.8 MB) | Article metrics.
102. Pankert T, Jegou T, Caudron-Herger M & Rippe K (2017). Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 123, 98-101. doi: 10.1016/j.ymeth.2017.01.010 | Abstract | Reprint (4.2 MB) | Article metrics.
101. Vainshtein Y, Rippe K & Teif VB (2017). NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 18, 158. doi: 10.1186/s12864-017-3580-2 | Abstract | Reprint (9.7 MB) | Article metrics.
100. Molitor J, Mallm JP, Rippe K & Erdel F (2017). Retrieving chromatin patterns from deep sequencing data with correlation functions. Biophys J 112, 473-490. doi: 10.1016/j.bpj.2017.01.001 | Abstract | Reprint (10.3 MB) | Article metrics.
99. Gunkel M, Chung I, Wörz S, Deeg KI, Simon R, Sauter G, Jones DT, Korshunov A, Rohr K, Erfle H & Rippe K (2017). Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Methods 114, 60-73. doi: 10.1016/j.ymeth.2016.09.014 | Abstract | Reprint (7.3 MB) | Article metrics.
98. Wachsmuth M, Knoch TA & Rippe K (2016). Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 9, 57. doi: 10.1186/s13072-016-0093-1 | Abstract | Reprint (5.1 MB) | Article metrics.
97. Deeg KI, Chung I, Bauer C & Rippe K (2016). Cancer cells with alternative lengthening of telomeres do not display a general hypersensitivity to ATR inhibition. Front Oncol 6, 186. doi: 10.3389/fonc.2016.00186 | Abstract | Reprint (1.4 MB) | Article metrics.
96. Caudron-Herger M, Pankert T & Rippe K (2016). Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts. Nucleus 7, 308-318. doi: 10.1080/19491034.2016.1190890 | Abstract | Reprint (0.7 MB) | Article metrics
95. Eck S, Wörz S, Müller-Ott K, Hahn M, Biesdorf A, Schotta G, Rippe K & Rohr K (2016). A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci. Medical Image Analysis 32,18-31. doi: 10.1016/j.media.2016.03.001 | Abstract | Reprint (4.9 MB) | Article metrics.
94. Bauer T, Trump S, Ishaque N, Thürmann L, Gu L, Bauer M, Bieg M, Gu Z, Weichenhan D, Mallm JP, Röder S, Herberth G, Takada E, Mücke O, Winter M, Junge KM, Grützmann K, Rolle-Kampczyk U, Qi W, Lawerenz C, Borte M, Polte T, Schlesner M, Schanne M, Wiemann S, Geörg C, Stunnenberg HG, Plass C, Rippe K, Mizuguchi J, Herrmann C, Eils R & Lehmann I (2016). Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children. Mol Syst Biol 12, 861. doi: 10.15252/msb.20156520 | Abstract | Reprint (6.0 MB) | Cover | Article metrics.
93. Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook, PR & Papantonis A (2016). Isolation of the protein and RNA content of active sites of transcription in mammalian cells. Nat Protoc 11, 553-565. doi: 10.1038/nprot.2016.032 | Abstract | Reprint (1.4 MB) | Article metrics.
92. Ernst A, Jones D, Maass KK, Rode A, Deeg KI, Jebaraj BM, Korshunov A, Hovestadt V, Tainsky MA, Pajtler KW, Bender S, Brabetz S, Gröbner S, Kool M, Devens F, Edelmann J, Zhang C, Castelo-Branco P, Tabori U, Malkin D, Rippe K, Stilgenbauer S, Pfister SM, Zapatka M, Lichter P (2016). Telomere dysfunction and chromothripsis. Int J Cancer 138, 2905-2914. doi: 10.1002/ijc.30033 | Abstract | Reprint (0.6 MB) | Article metrics
91. Junge KM, Bauer T, Geissler S, Hirche F, Thürmann L, Bauer M, Trump S, Bieg M, Weichenhan D, Malm JP, Ishaque N, Mücke O, Röder S, Herberth G, Diez U, Borte M, Rippe K, Plass C, Hermann C, Stangl G, Eils R & Lehmann I (2016). Increased vitamin D levels at birth and in early infancy increase offspring allergy risk — evidence for involvement of epigenetic mechanisms, J Allergy Clin Immunol 137, 610-613. doi: 10.1016/j.jaci.2015.06.040 | Abstract | Reprint (20.9 MB) | Article metrics
90. Caudron-Herger M, Pankert T, Seiler J, Nemeth A, Voit R, Grummt I & Rippe K (2015). Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 34, 2758-2771. doi: 10.15252/embj.201591458 | Abstract | Reprint (4.6 MB) | Comment | Cover | Article metrics
89. Mattout A, Aaronso Y, Sailaja BS, Raghu Ram EV, Harikumar A, Mallm JP, Sim KH, Nissim-Rafinia M, Supper E, Singh PB, Sze SK, Gasser SM, Rippe & Meshorer E (2015). Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol 16, 213. doi: 10.1186/s13059-015-0760-8 | Abstract | Reprint (5.5 MB) | Supplementary Table S4 | Supplementary Movie S7 | Article metrics
88. Mallm JP & Rippe K (2015). Aurora kinase B regulates telomerase activity via a centromeric RNA in stem cells. Cell Rep 11, 1667-1678. doi: 10.1016/j.celrep.2015.05.015 | Abstract | Reprint (5.9 MB) | Article metrics
87. Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, Erfle H & Rippe K (2015). PML induces compaction, partial TRF2 depletion and DNA damage signaling at telomeres and promotes alternative lengthening of telomeres. J Cell Sci 128, 1887-1900. doi: 10.1242/jcs.148296 | Abstract | Reprint (4.3 MB) | Article metrics
86. Caudron-Herger M, Cook PR, Rippe K & Papantonis A (2015). Dissecting the nascent human transcriptome by analyzing the RNA content of transcription factories. Nucleic Acids Res 43, e95. doi: 10.1093/nar/gkv390 | Abstract | Reprint (5.3 MB) | Article metrics
85. Yearim A, Gelfman S, Shayevitch R, Melcer S, Glaich O, Mallm JP, Nissim-Rafinia M, Cohen AH, Rippe K, Meshorer E & Ast G (2015). HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell Rep 10, 1122-1134. doi: 10.1016/j.celrep.2015.01.038 | Abstract | Reprint (6.1 MB) | Article metrics
84. Teif VB, Kepper N, Yserentant K, Wedemann G & Rippe K (2015). Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. J Phys Condens Matter 27, 064110. doi: 10.1088/0953-8984/27/6/064110 | Abstract | Reprint (1.5 MB)
83. Erdel F, Baum M & Rippe K (2015). The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility. J Phys Condens Matter 27, 064115. doi: 10.1088/0953-8984/27/6/064115 | Abstract | Reprint (1.1 MB)
82. Bhattacharya N, Reichenzeller M, Caudron-Herger M, Haebe S, Brady N, Diener S, Nothing M, Döhner H, Stilgenbauer S, Rippe K & Mertens D (2015). Loss of cooperativity of secreted CD40L and increased dose-response to IL4 on CLL cell viability correlates with enhanced activation of NF-kB and STAT6. Int J Cancer 136, 65-73. doi: 10.1002/ijc.28974 | Abstract | Reprint (3.0 MB) | Article metrics
81. Müller, O., Kepper, N., Schöpflin, R., Ettig, R., Rippe, K. & Wedemann, G. (2014). Changing chromatin fiber conformation by nucleosome repositioning. Biophys. J. 107, 2141-2150. doi: 10.1016/j.bpj.2014.09.026 | Abstract | Reprint (2.5 MB).
80. Müller-Ott K, Erdel F, Matveeva A, Hahn M, Mallm, JP, Rademacher A, Marth C, Zhang Q, Kaltofen S, Schotta G, Höfer T & Rippe K (2014). Specificity, propagation and memory of pericentric heterochromatin. Mol. Syst. Biol. 10, 746. doi: 10.15252/msb.20145377 | Abstract | Reprint (7.4 MB) | Article metrics
79. Baum M, Wachsmuth M, Erdel F & Rippe K (2014). Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat. Commun. 5, 4494. doi: 10.1038/ncomms5494 | Abstract | Reprint (6.4 MB) | Article metrics
78. Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T & Rippe K (2014). Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res. 24, 1285-1295. doi: 10.1101/gr.164418.113 | Abstract | Reprint (3.3 MB) | Article metrics
77. Jäger, N., Schlesner, M., Jones, D. T. W., Raffel, S., Mallm, J.-P., Junge, K. M., Weichenhan, D., Bauer, T., Ishaque, N., Kool, M., Northcott, P. A., Korshunov, A., Drews, R. M., Koster, J., Versteeg, R., Richter, J., Hummel, M., Mack, S. C., Taylor, M. D., Witt, H., Swartman, B., Schulte-Bockholt, D., Sultan, M., Yaspo, M.-L., Lehrach, H., Hutter, B., Brors, B., Wolf, S., Plass, C., Siebert, R., Trumpp, A., Rippe, K., Lehmann, I., Lichter, P., Pfister, S. M., Eils, R. (2013). Hypermutation of the inactive X chromosome is a frequent event in cancer. Cell 155, 567-581. doi: 10.1016/j.cell.2013.09.042 | Abstract | Reprint (2.9 MB).
76. Erdel, F., Müller-Ott, K. & Rippe, K. (2013). Establishing epigenetic domains via chromatin-bound histone modifiers. Ann. N. Y. Acad. Sci. 1305, 29-43. doi: 10.1111/nyas.12262 | Abstract | Reprint (0.8 MB).
75. Eck, S., Rohr, K., Biesdorf, A., Müller-Ott, K., Rippe, K. & Wörz, S. (2013). A 3D intensity model based on spherical harmonics for automatic 3D segmentation of heterochromatin foci. Proc. IEEE Internat. Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2013), 1484-1487. doi: 10.1109/ISBI.2013.6556815 | Abstract | Reprint (1.3 MB).
74. Toiber, D., Erdel, F., Silberman, D. M., Zhong, L., Mulligan, P., Bouazoune, K., Sebastian, C., Cosentino, C., Martinez-Pastor, B., Giacosa, S., D'Urso, A., Naar, A., Kingston, R., Rippe, K. & Mostoslavsky, R. (2013). SIRT6 recruits SNF2H to sites of DNA breaks, preventing genomic instability through chromatin remodeling. Mol. Cell 51, 454-468. doi: 10.1016/j.molcel.2013.06.018 | Abstract | Reprint (6.2 MB).
73. Schöpflin, R., Teif, V. B., Müller, O., Weinberg, C., Rippe, K. & Wedemann, G. (2013). Modeling nucleosome position distributions from experimental nucleosome positioning maps. Bioinformatics 29, 2380-2386. doi: 10.1093/bioinformatics/btt404 | Abstract | Reprint (1.1 MB).
72. Eck, S., Wörz, S., Biesdorf, A., Müller-Ott, K., Rippe, K. & Rohr, K.(2013). Segmentation of heterochromatin foci using a 3D spherical harmonics intensity model (2013). In Bildverarbeitung für die Medizin 2013, Meinzer, H.-P., Deserno, T. M., Handels, H., Tolxdorff, T., eds., 308-313. Springer Berlin Heidelberg. doi: 10.1007/978-3-642-36480-8_54 | Abstract | Reprint (0.3 MB).
71. Hahn, M., Dambacher, S., Dulev, S., Kusnezova, A., Eck, S., Worz, S. , Sadic, D., Schulte, M., Mallm, J.-P., Schermelleh, L., Debs, P., Leonhardt, H., Rohr, K., Rippe, K., Storchova, Z. & Schotta, G. (2013). Chromatin compaction by Suv4-20h2 is essential for cohesion loading in heterochromatin. Genes & Dev. 27, 859-872. doi: 10.1101/gad.210377.112 | Abstract | Reprint (15.9 MB).
70. Garding, A., Bhattacharya, N., Claus, R., Ruppel, M., Tschuch, C., Filarsky, K., Idler, I., Zucknick, M., Caudron-Herger, M., Oakes, C., Fleig, V., Keklikoglou, I., Allegra, D., Serra, L., Thakurela, S., Tiwari, V., Weichenhan, D., Benner, A., Radlwimmer, B., Zentgraf, H., Wiemann, S., Rippe, K., Plass, C., Döhner, H., Lichter, P. Stilgenbauer, S., Mertens, D. (2013). Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the in cis downregulation of a gene cluster that targets NF-kB. PLoS Genetics 9, e1003373. doi: 10.1371/journal.pgen.1003373 | Abstract | Reprint (10.8 MB).
69. Teif, V. B., Erdel, F., Beshnova, D. A., Vainshtein, Y., Mallm, J. P. & Rippe, K. (2013). Taking into account nucleosomes for predicting gene expression. Methods 62, 26-38. doi: dx.doi.org/10.1016/j.ymeth.2013.03.011| Abstract | Reprint (1.0 MB)
68. Erdel F & Rippe K (2012). Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis. Proc. Natl. Acad. Sci. USA 109, E3221-E3230. doi: 10.1073/pnas.1209579109 | Abstract | Reprint (3.4 MB) | Article metrics
67. Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T & Rippe K (2012). Genome-wide nucleosome positioning during embryonic stem cell development. Nat. Struct. Mol. Biol. 19, 1185-1191. doi: 10.1038/nsmb.2419 | Abstract | Reprint (7.4 MB)| Article metrics
66. Eißmann, M., Gutschner, T., Hämmerle, M., Günther, S., Caudron-Herger, M., Groß, M., Schirmacher, P., Rippe, K., Braun, T., Zornig, M. & Diederichs, S. (2012). Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biology 9, 1076-1087. doi: 10.4161/rna.21089 | Abstract | Reprint (5.9 MB)
65. Eck, S., Rohr, K., Müller-Ott, K., Rippe, K. & Wörz, S. (2012). Combined model-based and region-adaptive 3D segmentation and 3D co-localization analysis of heterochromatin foci. In Bildverarbeitung für die Medizin 2012. Tolxdorff, T., Deserno, T. M., Handels, H. & Meinzer, H.-P., eds., pp. 9-14. Springer Berlin Heidelberg. doi: 10.1007/978-3-642-28502-8_4 | Abstract | Reprint
64. Osterwald, S., Wörz, S., Reymann, J., Sieckmann, F., Rohr, K., Erfle, H. & Rippe, K. (2012). A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathway. Biotechnol. J. 7, 103-116. doi: 10.1002/biot.201000474 | Abstract | Reprint (1.8 MB)
63. Teif, V. B. & Rippe, K. (2012). Calculating transcription factor binding to nucleosomal DNA for large genomic regions. Briefings Bioinf. 13, 187-201. doi: 10.1093/bib/bbr037 | Abstract | Reprint (0.4 MB)
62. Chung I, Leonhardt H & Rippe K (2011). De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation. J. Cell Sci. 124, 3603-3618. doi: 10.1242/jcs.084681 | Abstract | Reprint (9.4 MB) | Comment | Article metrics
61. Ettig R, Kepper N, Stehr R, Wedemann G & Rippe K (2011). Dissecting DNA-histone interactions by molecular dynamics simulations of unwrapping DNA from the nucleosome. Biophys J 101, 1999-2008. doi: 10.1016/j.bpj.2011.07.057 | Abstract | Reprint (5.8 MB) | Article metrics
60. Caudron-Herger, M., Müller-Ott, K., Mallm, J.-P., Marth, C., Schmidt, U., Fejes-Tóth, K. & Rippe, K. (2011). Coding RNAs with a non-coding function: maintenance of open chromatin structure, Nucleus 2, 410-424. doi: 10.4161/nucl.2.5.17736 | Abstract | Reprint (4.4 MB) | Comment
59. Teif, V. & Rippe, K. (2011). Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers, Phys. Biol. 8, 044001. doi: 10.1088/1478-3975/8/4/044001 | Abstract | Reprint (0.4 MB)
58. Erdel, F. & Rippe, K. (2011). Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism, Nucleus 2, 105-112. doi: 10.4161/nucl.2.2.15209 | Abstract | Reprint
57. Kepper, N., Ettig, R., Stehr, R., Wedemann, G. & Rippe, K. (2011). Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations, Biopolymers 95, 435-447. doi: 10.1002/bip.21598 | Abstract | Reprint (4.3 MB)
56. Vogler, C., Huber, C., Waldmann, T., Ettig, R., Braun, L., Chassignet, I., Lopez-Contreras, A. J., Fernandez-Capetillo, O., Dundr, M., Rippe, K., Längst, G. & Schneider, R. (2010). Histone H2A C-terminus regulates chromatin dynamics, remodeling and histone H1 binding. PLoS Genet. 6, e1001234. Abstract | Reprint (2.7 MB)
55. Erdel F, Schubert T, Marth C, Längst G & Rippe K (2010). Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc. Natl. Acad. Sci. USA 107, 19873-19878. doi: 10.1073/pnas.1003438107 | Abstract | Reprint (1.4 MB) | Commtent 1 | Comment 2 | Article metrics
54. Teif, V. B., Ettig, R. & Rippe, K. (2010). A lattice model for transcription factor access to nucleosomal DNA. Biophys. J. 99, 2597-2607. Abstract | Reprint (0.6 MB)
53. Derrer, B., Windeisen, V., Rodriguez, G. G., Seidler, J., Gengenbacher, M., Lehmann, W. D., Rippe, K., Sinning, I., Tews, I. & Kappes, B. (2010). Defining the structural requirements of ribose 5-phosphate-binding and intersubunit cross-talk of the malarial pyridoxal 5-phosphate synthase. FEBS Lett. 584, 4169-4174. Abstract | Reprint (0.7 MB)
52. Wirtz, M., Birke, H., Heeg, C., Throm, C., Hosp, F., Müller, C., König, S., Feldman-Salit, A., Rippe, K., Petersen, G., Wade, R. C., Rybin, V., Scheffzek, K. & Hell, R. (2010). Structure and function of hetero-oligomeric cysteine synthase complex in plants. J. Biol. Chem. 285, 32810-32817. Abstract | Reprint (2.5 MB)
51. Stehr, R., Schöpflin, R., Ettig, R., Kepper, N., Rippe, K. & Wedemann, G. (2010) Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams. Biophys. J. 98, 1028-1037. Abstract | Reprint (2.3 MB pdf file)
50. Lang, M., Jegou, T., Chung, I., Richter, K., Udvarhelyi, A., Münch, S., Cremer, C., Hemmerich, P., Engelhardt, J., Hell, S. W. & Rippe, K. (2010). Three-dimensional organization of PML nuclear bodies. J. Cell Sci. 123, 392-400. Abstract | Reprint (4.3 MB pdf file) | Comment
49. Bozkurt, G., Stjepanovic, G., Vilardi, F., Amlacher, S., Wild, K., Bange, G., Favaloro, V., Rippe, K., Hurt, E., Dobberstein, B. & Sinning, I. (2009). Structural insights into tail-anchored protein binding and membrane insertion by Get3. Proc. Natl. Acad. Sci. USA 106, 21131-21136. Abstract | Reprint (4.1 MB pdf file)
48. Müller KP, Erdel F, Caudron M, Marth C, Fodor BD, Richter M, Scaranaro M, Beoudoin J, Wachsmuth M & Rippe K (2009). A multi-scale analysis of dynamics and interactions of heterochromatin protein 1 in the nucleus by fluorescence fluctuation microscopy. Biophys J 97, 2876-2885. Abstract | Reprint (3.3 MB pdf file) | Article metrics
47. Teif, V. B. & Rippe, K. (2009). Predicting nucleosome positions on the DNA: combining chromatin remodeling activity with intrinsic binding affinities. Nucleic Acids Res. 37, 5641-5655. Abstract | Reprint (0.8 MB pdf file)
46. Heuvelmann, G., Erdel, F., Wachsmuth, M. & Rippe, K. (2009). Analysis of protein mobilities and interactions in living cells by multi-focal fluorescence fluctuation microscopy. Eur. Biophys. J. 38, 813-828. Abstract | Reprint (0.8 MB pdf file)
45. Gunkel, M., Erdel, F., Rippe, K., Lemmer, P., Kaufmann, R., Hörmann, C., Amberger, R. & Cremer, C. (2009). Dual color localization microscopy of cellular nanostructures. Biotechnol. J. 4, 927-938. Abstract | Reprint (2.0 MB pdf file)
44. Neuwirth, M, Strohmeier, M, Windeisen, V, Wallner, S, Deller, S, Rippe, K, Sinning, I, Macheroux, P. & Tews, I (2009) X-ray crystal structure of Saccharomyces cerevisiae SNZ1 provides insights into the oligomeric nature of PLP synthases. FEBS Lett. 583, 2179-2186. Abstract | Reprint (1.6 MB pdf file).
43. Schmidt, U., Im, K.-B., Benzing, C., Janjetovic, S., Rippe, K., Lichter, P. & Wachsmuth, M. (2009). Assembly and mobility of exon-exon junction complexes with mRNA in the nucleus. RNA 15, 862-876. Abstract | Reprint (1.6 MB pdf file)
42. Jegou, T., Chung, I., Heuvelmann, G., Wachsmuth, M., Görisch, S. M., Greulich-Bode, K., Boukamp, P., Lichter, P. & Rippe, K. (2009). Dynamics of telomeres and promyelocytic leukemia nuclear bodies in a telomerase negative human cell line. Mol Biol Cell 20, 2070-2082. Abstract | Reprint (3.3 MB pdf file)
41. Stehr, R., Kepper, N., Rippe, K. & Wedemann, G. (2008). The effect of the internucleosomal interaction potential on the folding of the chromatin fiber. Biophys. J. 95, 3677-3691. Abstract | Reprint (1.8 MB pdf file)
40. Koenig, P., Oreb, M., Rippe, K., Muhle-Goll, C., Sinning, I., Schleiff, E. & Tews, I. (2008). On the significance of TOC-GTPase homodimers. J. Biol. Chem. 283, 23104-23112. Abstract | Reprint (0.8 MB pdf file)
39. Reymann, J., Baddeley, D., Gunkel, M., Lemmer, P., Stadter, W., Jegou, T., Rippe, K., Cremer, C. & Birk, U. (2008). High precision structural analysis of subnuclear complexes in fixed and living specimens via Spatially Modulated Illumination (SMI) microscopy. Chrom. Res. 16, 367-382. Abstract | Reprint (0.75 MB pdf file)
38. Koenig, P., Oreb, M., Höfle, A., Kaltofen, S., Rippe, K., Sinning, I., Schleiff, E. & Tews, I. (2008). The GTPase cycle of the chloroplast import receptors Toc33/Toc34 - implications from monomeric and dimeric structures. Structure 16, 585-596. Abstract | Reprint (3.5 MB pdf file)
37. Kepper, N., Foethke, D., Stehr, R., Wedemann, G. & Rippe, K. (2008). Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation, Biophys. J. 95, 3692–3705. Abstract | Reprint (3.2 MB pdf file)
36. Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E., & Längst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc. Natl. Acad. Sci. USA 104, 15635-15640. Abstract | Reprint (1.4 MB pdf file) | Comment
35. Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. & Tews, I. (2006). Structure of a bacterial pyridoxal 5’-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103, 19284-19289. Abstract | Reprint (2.5 MB pdf file)
34. Mazurkiewicz, J., Kepert, J. F. & Rippe, K. (2006) On the mechanism of nucleosome assembly by histone chaperone NAP1. J. Biol. Chem. 281, 16462-16472. Abstract | Reprint (2.4 MB pdf file)
33. Görisch, S. M., Wachsmuth, M., Fejes Tóth, K., Lichter, P. & Rippe, K. (2005). Histone acetylation increases chromatin accessibility. J. Cell Sci. 118, 5825-5834. Abstract | Reprint (0.7 MB pdf file) | Comment
32. Kepert, J. F., Mazurkiewicz, J., Heuvelman, G., Fejes Tóth, K. & Rippe, K. (2005). NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformation. J. Biol. Chem. 280, 34063-34072. Abstract | Reprint (1.1 MB pdf file)
31. Strohner, R., Wachsmuth, M., Dachauer, K., Mazurkiewicz, J., Rippe, K. & Längst, G. (2005). A ‘loop recapture’ mechanism for ACF-dependent nucleosome remodelling. Nat. Struct. Mol. Biol. 12, 683-690. Abstract | Reprint (3.7 MB pdf file) | Comment
30. Fejes Tóth, K., Mazurkiewicz, J. & Rippe, K. (2005). Association states of the nucleosome assembly protein 1 and its complexes with histones. J. Biol. Chem. 280, 15690-15699. Abstract | Reprint (0.6 MB pdf file)
29. Görisch, S. M., Wachsmuth, M., Ittrich, C., Bacher, C. P., Rippe, K. & Lichter, P. (2004). Nuclear body movement is determined by chromatin accessibility and dynamics. Proc. Nat. Acad. Sci. USA 101, 13221-13226. Abstract | Reprint (2.1 MB pdf file)
28. Fejes Tóth, K., Knoch, T. A., Wachsmuth, M., Stöhr, M., Frank-Stöhr, M., Bacher, C. P., Müller, G. & Rippe, K. (2004). Trichostatin A induced histone acetylation causes decondensation of interphase chromatin. J. Cell Sci. 117, 4277-4287. Abstract | Reprint (0.4 MB pdf file)
27. Kepert, J. F., Fejes Tóth, K., Caudron, M., Mücke, N., Langowski, J. & Rippe, K. (2003). Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy. Biophys. J., 85,4012-4022. Abstract | Reprint (0.3 MB pdf file)
26. Perraud, A. L., Shen, B., Dunn, C. A., Rippe, K., Smith, M. K., Bessman, M. J., Stoddard, B. L. & Scharenberg, A. M. (2003). NUDT9, a Member of the Nudix Hydrolase Family, Is an Evolutionarily Conserved Mitochondrial ADP-ribose Pyrophosphatase. J. Biol. Chem. 278,1794-1801. Abstract | Reprint (0.6 MB pdf file)
25. Vogel, S. K., Schulz, A. & Rippe, K. (2002). Binding affinity of Escherichia coli RNA polymerase·sigma54 holoenzyme for the glnAp2, nifH and nifL promoters. Nucleic Acids Res. 30, 4094-4101. Abstract | Reprint (0.2 MB pdf file)
24. Weidemann, T., Wachsmuth, M., Tewes, M., Rippe, K. & Langowski, J. (2002). Analysis of ligand binding by two-colour fluorescence cross-correlation spectroscopy. Single Mol. 3, 49-61. Abstract | Reprint (0.3 MB pdf file)
23. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. (2002). Capturing chromatin conformation. Science 295, 1306-1311. Abstract | Reprint (0.6 MB pdf file)
22. Bock, A., Bantscheff, M., Perraud, A. L., Rippe, K., Weiss, V., Glocker, M. O. & Gross, R. (2001). Rational design and molecular characterization of a chimaeric response regulator protein. J. Mol. Biol. 310, 283-290. Abstract | Reprint (0.2 MB pdf file)
21. Perraud, A.-L., Rippe, K., Bantscheff, M., Glocker, M., Lucassen, M., Jung, K., Sebald, W., Weiss, V. & Gross, R. (2000) Dimerization of signalling domains of the EvgAS and BvgAS phosphorelay systems. Biochim. Biophys. Acta 1478, 341-354. Abstract | Reprint (0.5 MB pdf file)
20. Schulz, A., Langowski, J. & Rippe, K. (2000). The effect of the DNA conformation on the transcription activation rate of E. coli RNA Polymerase·sigma 54 holoenzyme by NtrC. J. Mol. Biol 300, 709-725. Abstract | Reprint (0.4 MB pdf file)
19. Rippe, K. (2000). Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy. Biochemistry 39, 2131-2139. Abstract | Reprint (0.1 MB pdf file)
18. Schulz, A., Mücke, N., Langowski, J. & Rippe, K. (1998). Scanning force microscopy of E. coli RNA polymerase-sigma 54 holoenzyme complexes with DNA in buffer and in air. J. Mol. Biol. 283, 821-836. Abstract | Reprint (0.7 MB pdf file)
17. Rippe, K., Mücke, N. & Schulz, A. (1998). Association states of E. coli NtrC protein determined by analytical ultracentrifugation. J. Mol. Biol. 278, 915-933. Abstract | Reprint (1.3 MB pdf file)
16. Sevenich, F. W., Langowski, J., Weiss, V. & Rippe, K. (1998). DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy. Nucleic Acids Res. 26, 1373-1381. Abstract | Reprint (0.2 MB pdf file)
15. Merlitz, H., Rippe, K., Klenin, K. & Langowski, J. (1998). Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation. Biophys. J. 74, 773-779. Abstract | Reprint (0.1 MB pdf file)
14. Spiess, C., Happersberger, H. P., Glocker, M. O., Spiess, E., Rippe, K. & Ehrmann, M. (1997). Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli. J. Biol. Chem. 272, 22125-22133. Abstract | Reprint (0.5 MB pdf file)
13. Rippe, K., Guthold, M., von Hippel, P. H. & Bustamante, C. (1997). Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase-sigma 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270, 125-138. Abstract | Reprint (4.6 MB pdf file)
12. Rippe, K., Mücke, N. & Langowski, J. (1997). Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution. Nucleic Acids Res. 25, 1736-1744. Abstract | Reprint (0.4 MB pdf file)
11. Evertsz, E. M., Rippe, K. & Jovin, T. M. (1994). Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs. Nucleic Acids Res. 22, 3293-3303. Abstract | Reprint (2.1 MB pdf file)
10. Fritzsche, H., Akhebat, A., Taillandier, E., Rippe, K. & Jovin, T. M. (1993). Structure and drug interactions of parallel-stranded DNA studied by infrared spectroscopy and fluorescence. Nucleic Acids Res. 21, 5085-5091. Abstract | Reprint (1.4 MB pdf file)
9. Rippe, K., Fritsch, V., Westhof, E. & Jovin, T. M. (1992). Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11, 3777-3786. Abstract | Reprint (2.2 MB pdf file)
8. Rentzeperis, D., Rippe, K., Jovin, T. M. & Marky, L. A. (1992). Calorimetric characterisation of parallel-stranded DNA: Stability, conformational flexibility, and ion binding. J. Am. Chem. Soc. 114, 5926-5928. Abstract | Reprint (0.4 MB pdf file)
7. Klysik, J., Rippe, K. & Jovin, T. M. (1991). Parallel-stranded DNA under topological stress: rearrangement of (dA)15-(dT)15 to a d(A-A-T)n triplex. Nucleic Acids Res. 19, 7145-7154. Abstract | Reprint (2.6 MB pdf file)
6. Otto, C., Thomas, G. A., Rippe, K., Jovin, T. M. & Peticolas, W. L. (1991). The hydrogen bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. Biochemistry 30, 3062-3069. Abstract | Reprint (1.0 MB pdf file)
5. Klysik, J., Rippe, K. & Jovin, T. M. (1990). Reactivity of parallel-stranded DNA to chemical modification reagents. Biochemistry 29, 9831-9839. Abstract | Reprint (4.3 MB pdf file)
4. Rippe, K., Ramsing, N. B., Klement, R. & Jovin, T. M. (1990). A parallel stranded linear DNA duplex Incorporating dG-dC Base Pairs. J. Biomol. Struct. Dynam. 7, 1199-1209. Abstract | Reprint (4.9 MB pdf file)
3. Rippe, K. & Jovin, T. M. (1989). Substrate properties of 25-nt parallel-stranded linear DNA duplexes. Biochemistry 28, 9542-9549. Abstract | Reprint (3.1 MB pdf file)
2. Ramsing, N. B., Rippe, K. & Jovin, T. M. (1989). Helix-Coil Transition of Parallel-Stranded DNA. Thermodynamics of Hairpin and Linear Duplex Oligonucleotides. Biochemistry 28, 9528-9535. Abstract | Reprint (0.9 MB pdf file)
1. Rippe, K., Ramsing, N. B. & Jovin, T. M. (1989). Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes. Biochemistry 28, 9536-9541. Abstract | Reprint (1.8 MB pdf file)