All Publications

Max Planck Institute for Molecular Genetics

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Journal Article (238)

Journal Article

Du Bois, I.; Marsico, A.; Bertrams, W.; Schweiger, M. R.; Caffrey, B.; Sittka-Stark, A.; Eberhardt, M.; Vera, J.; Vingron, M.; Schmeck, B. T.: Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2. The Journal of Infectious Diseases 214 (3), pp. 454 - 463 (2016)

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Juan, D.; Perner, J.; Carrillo de Santa Pau, E.; Marsili, S.; Ochoa, D.; Chung, H. R.; Vingron, M.; Rico, D.; Valencia, A.: Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. Cell Reports 14 (5), pp. 1246 - 1257 (2016)

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Ancherbak, S.; Kuruoglu, E. E.; Vingron, M.: Time-Dependent Gene Network Modelling by Sequential Monte Carlo. IEEE ACM Transactions on Computational Biology and Bioinformatics 13 (6), pp. 1183 - 1193 (2016)

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Hu, H.; Haas, S. A.; Chelly, J.; Van Esch, H.; Raynaud, M.; de Brouwer, A. P. M.; Weinert, S.; Froyen, G.; Frints, S. G. M.; Laumonnier, F. et al.; Zemojtel, T.; Love, M. I.; Richard, H.; Emde, A.-K.; Bienek, M.; Jensen, C.; Hambrock, M.; Fischer, U.; Langnick, C.; Feldkamp, M.; Wissink-Lindhout, W.; Lebrun, N.; Castelnau, L.; Rucci, J.; Montjean, R.; Dorseuil, O.; Billuart, P.; Stuhlmann, T.; Shaw, M.; Corbett, M. A.; Gardner, A.; Willis-Owen, S.; Tan, C.; Friend, K. L.; Belet, S.; van Roozendaal, K. E. P.; Jimenez-Pocquet, M.; Moizard, M.-P.; Ronce, N.; Sun, R.; O'Keeffe, S.; Chenna, R.; van Bömmel, A.; Göke, J.; Hackett, A.; Field, M.; Christie, L.; Boyle, J.; Haan, E.; Nelson, J.; Turner, G.; Baynam, G.; Gillessen-Kaesbach, G.; Müller, U.; Steinberger, D.; Budny, B.; Badura-Stronka, M.; Latos-Bieleńska, A.; Ousager, L. B.; Wieacker, P.; Rodríguez Criado, G.; Bondeson, M.-L.; Annerén, G.; Dufke, A.; Cohen, M.; Van Maldergem, L.; Vincent-Delorme, C.; Echenne, B.; Simon-Bouy, B.; Kleefstra, T.; Willemsen, M.; Fryns, J.-P.; Devriendt, K.; Ullmann, R.; Vingron, M.; Wrogemann, K.; Wienker, T. F.; Tzschach, A.; van Bokhoven, H.; Gecz, J.; Jentsch, T. J.; Chen, W.; Ropers, H.-H.; Kalscheuer, V. M.: X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Molecular Psychiatry 21 (1), pp. 133 - 148 (2016)

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Huska, M.; Vingron, M.: Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns. PLoS Computational Biology 12 (12), e1005249 (2016)

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Muino, J. M.; de Bruijn, S.; Pajoro, A.; Geuten, K.; Vingron, M.; Angenent, G. C.; Kaufmann, K.: Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor. Molecular Biology and Evolution 33 (1), pp. 185 - 200 (2016)

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Schöne, S.; Jurk, M.; Helabad, M. B.; Dror, I.; Lebars, I.; Kieffer, B.; Imhof, P.; Rohs, R.; Vingron, M.; Thomas-Chollier, M. et al.; Meijsing, S.: Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity. Nature Communications 7, 13784 (2016)

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Schöne, S.; Jurk, M.; Helabad, M. B.; Dror, I.; Lebars, I.; Kieffer, B.; Imhof, P.; Rohs, R.; Vingron, M.; Thomas-Chollier, M. et al.; Meijsing, S.: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity. Nature Communications 7, 12621 (2016)

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Ganbari, M.; Lasserre, J.; Vingron, M.: Reconstruction of gene networks using prior knowledge. BMC Systems Biology 9, 9:84 (2015)

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Eduati, F.; Mangravite, L. M.; Wang, T.; Tang, H.; Bare, J. C.; Huang, R.; Norman, T.; Kellen, M.; Menden, M. P.; Yang, J. et al.; Zhan, X.; Zhong, R.; Xiao, G.; Xia, M.; Abdo, N.; Kosyk, O.; Collaboration, N.-N.-U. D. T.; van Bömmel, A.; Caffrey, B.; Heinig, M.; Huska, M.; Mammana, A.; Perner, J.; Vingron, M.; Friend, S.; Dearry, A.; Simeonov, A.; Tice, R. R.; Rusyn, I.; Wright, F. A.; Stolovitzky, G.; Xie, Y.; Saez-Rodriguez, J.: Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol 33 (9), pp. 933 - 940 (2015)

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George, J.; Lim, J. S.; Jang, S. J.; Cun, Y.; Ozretic, L.; Kong, G.; Leenders, F.; Lu, X.; Fernandez-Cuesta, L.; Bosco, G. et al.; Müller, C.; Dahmen, I.; Jahchan, N. S.; Park, K. S.; Yang, D.; Karnezis, A. N.; Vaka, D.; Torres, A.; Wang, M. S.; Korbel, J. O.; Menon, R.; Chun, S. M.; Kim, D.; Wilkerson, M.; Hayes, N.; Engelmann, D.; Putzer, B.; Bos, M.; Michels, S.; Vlasic, I.; Seidel, D.; Pinther, B.; Schaub, P.; Becker, C.; Altmuller, J.; Yokota, J.; Kohno, T.; Iwakawa, R.; Tsuta, K.; Noguchi, M.; Muley, T.; Hoffmann, H.; Schnabel, P. A.; Petersen, I.; Chen, Y.; Soltermann, A.; Tischler, V.; Choi, C. M.; Kim, Y. H.; Massion, P. P.; Zou, Y.; Jovanovic, D.; Kontic, M.; Wright, G. M.; Russell, P. A.; Solomon, B.; Koch, I.; Lindner, M.; Muscarella, L. A.; la Torre, A.; Field, J. K.; Jakopovic, M.; Knezevic, J.; Castanos-Velez, E.; Roz, L.; Pastorino, U.; Brustugun, O. T.; Lund-Iversen, M.; Thunnissen, E.; Köhler, J.; Schuler, M.; Botling, J.; Sandelin, M.; Sanchez-Cespedes, M.; Salvesen, H. B.; Achter, V.; Lang, U.; Bogus, M.; Schneider, P. M.; Zander, T.; Ansen, S.; Hallek, M.; Wolf, J.; Vingron, M.; Yatabe, Y.; Travis, W. D.; Nurnberg, P.; Reinhardt, C.; Perner, S.; Heukamp, L.; Büttner, R.; Haas, S. A.; Brambilla, E.; Peifer, M.; Sage, J.; Thomas, R. K.: Comprehensive genomic profiles of small cell lung cancer. Nature 524 (7563), pp. 47 - 53 (2015)

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Emmerich, D.; Zemojtel, T.; Hecht, J.; Krawitz, P.; Spielmann, M.; Kühnisch, J.; Kobus, K.; Oßwald, M.; Heinrich, V.; Berlien, P. et al.; Müller, U.; Mautner, V.-F.; Wimmer, K.; Robinson, P. N.; Vingron, M.; Tinschert, S.; Mundlos, S.; Kolanczyk, M.: Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient. European journal of human genetics 23 (6), pp. 1870 - 1873 (2015)

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Starick, S. R.; Ibn-Salem, J.; Jurk, M.; Hernandez, C.; Love, M. I.; Chung, H.-R.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Res 25 (6), pp. 825 - 835 (2015)

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Schafer, S.; Adami, E.; Heinig, M.; Rodrigues, K. E.; Kreuchwig, F.; Silhavy, J.; van Heesch, S.; Simaite, D.; Rajewsky, N.; Cuppen, E. et al.; Pravenec, M.; Vingron, M.; Cook, S. A.; Hubner, N.: Translational regulation shapes the molecular landscape of complex disease phenotypes. Nat Commun 6, 6:7200 (2015)

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Fernandez-Cuesta, L.; Sun, R.; Menon, R.; George, J.; Lorenz, S.; Meza-Zepeda, L. A.; Peifer, M.; Plenker, D.; Heuckmann, J. M.; Leenders, F. et al.; Zander, T.; Dahmen, I.; Koker, M.; Schöttle, J.; Ullrich, R. T.; Altmüller, J.; Becker, C.; Nürnberg, P.; Seidel, H.; Böhm, D.; Göke, F.; Ansen, S.; Russell, P. A.; Wright, G. M.; Wainer, Z.; Solomon, B.; Petersen, I.; Clement, J. H.; Sänger, J.; Brustugun, O. T.; Helland, A.; Solberg, S.; Lund-Iversen, M.; Büttner, R.; Wolf, J.; Brambilla, E.; Vingron, M.; Perner, S.; Haas, S. A.; Thomas, R. K.: Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biology: Biology for the Post-Genomic Era 16, 16:7 (2015)

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Heinig, M.; Colome-Tatche, M.; Taudt, A.; Rintisch, C.; Schafer, S.; Pravenec, M.; Hubner, N.; Vingron, M.; Johannes, F.: histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics 16, 16:60 (2015)

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Perner, J.; Lasserre, J.; Kinkley, S.; Vingron, M.; Chung, H.-R.: Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Research (London) 42 (22), pp. 13689 - 13695 (2014)

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Misra, N.; Szczurek, E.; Vingron, M.: Inferring the paths of somatic evolution in cancer. Bioinformatics 30 (17), pp. 2456 - 2463 (2014)

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Meng, G.; Vingron, M.: Condition-specific target prediction from motifs and expression. Bioinformatics 30 (12), pp. 1643 - 1650 (2014)

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Yu, X.; Zheng, G.; Shan, L.; Meng, G.; Vingron, M.; Liu, Q.; Zhu, X.-G.: Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Frontiers in Plant Science 5, p. 5:273 - 5:273 (2014)

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