Publications

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 (11)

Journal Article

Adachi, K.; Kopp, W.; Wu, G.; Heising, S.; Greber, B.; Stehling, M.; Araúzo-Bravo, M. J.; Boerno, S. T.; Timmermann, B.; Vingron, M. et al.; Schöler, H. R.: Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency - Correction. Cell Stem Cell 23 (6), pp. 900 - 904 (2018)

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Journal Article

Yang, X.; Vingron, M.: Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions. BMC Biology 16 (1), 138 (2018)

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Journal Article

Schöne, S.; Bothe, A. M.; Einfeldt, E.; Borschiwer, M.; Benner, P. F.; Vingron, M.; Thomas-Chollier, M.; Meijsing, S. H.: Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genetics 14 (11), e1007793 (2018)

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Journal Article

Kragesteen , B. K.; Spielmann, M.; Paliou, C.; Heinrich, V.; Schöpflin, R.; Esposito, A.; Annunziatella, C.; Bianco , S.; Chiariello, A. M.; Jerković , I. et al.; Harabula, I.; Guckelberger, P.; Pechstein, M.; Wittler, L.; Chan, W.-L.; Franke, M.; Lupiáñez , D. G.; Kraft, K.; Timmermann, B.; Vingron, M.; Visel, A.; Nicodemi, M.; Mundlos, S.; Andrey, G.: Dynamic 3D chromatin architecture determines enhancer specificity and morphogenetic identity in limb development. Nature Genetics 50 (10), pp. 1463 - 1473 (2018)

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supplementary-material

Journal Article

Grassi, L.; Pourfarzad, F.; Ullrich, S.; Merkel, A.; Were, F.; Carrillo-de-Santa-Pau, E.; Yi, G.; Hiemstra, I. H.; Tool, A. T. J.; Mul, E. et al.; Perner, J.; Janssen-Megens, E.; Berentsen, K.; Kerstens, H.; Habibi, E.; Gut, M.; Yaspo, M. L.; Linser, M.; Lowy, E.; Datta, A.; Clarke, L.; Flicek, P.; Vingron, M.; Roos, D.; van den Berg, T. K.; Heath, S.; Rico, D.; Frontini, M.; Kostadima, M.; Gut, I.; Valencia, A.; Ouwehand, W. H.; Stunnenberg, H. G.; Martens, J. H. A.; Kuijpers, T. W.: Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils. Cell Reports 24 (10), pp. 2784 - 2794 (2018)

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van Bömmel, A.; Love, M. I.; Chung, H.-R.; Vingron, M.: coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Computational Biology 14 (8), e1006372 (2018)

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Journal Article

Adachi, K.; Kopp, W.; Wu, G.; Heising, S.; Greber, B.; Stehling , M.; Araúzo-Bravo, M. J.; Boerno, S. T.; Timmermann, B.; Vingron, M. et al.; Schöler, H. R.: Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency. Cell Stem Cell 23 (2), pp. 266 - 275 (2018)

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Grasse, S.; Lienhard, M.; Frese, S.; Kerick, M.; Steinbach, A.; Grimm, C.; Hussong, M.; Rolff, J.; Becker, M.; Dreher, F. et al.; Schirmer, U.; Boerno, S. T.; Ramisch, A.; Leschber, G.; Timmermann, B.; Grohé, C.; Lüders, H.; Vingron, M.; Fichtner, I.; Klein, S.; Odenthal, M.; Büttner, R.; Lehrach, H.; Sültmann, H.; Herwig, R.; Schweiger, R. M.: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Medicine 10 (1), 10:55 (2018)

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Bianco, S.; Lupiáñez, D. G.; Chiariello, A. M.; Annunziatella, C.; Kraft, K.; Schöpflin, R.; Wittler, L.; Andrey, G.; Vingron, M.; Pombo, A. et al.; Mundlos, S.; Nicodemi, M.: Polymer physics predicts the effects of structural variants on chromatin architecture. Nature Genetics 50 (5), pp. 662 - 667 (2018)

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Thormann, V.; Rothkegel, M. C.; Schöpflin, R.; Glaser, L. V.; Djuric, P.; Li, N.; Chung, H.-R.; Schwahn, K.; Vingron, M.; Meijsing, S.: Genomic dissection of enhancers uncovers principles of combinatorial regulation and dynamic wiring of enhancer-promoter contacts. Nucleic Acids Research (London) 46 (6), pp. 2868 - 2882 (2018)

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George, J.; Walter, V.; Peifer, M.; Alexandrov, L. B.; Seidel, D.; Leenders, F.; Maas, L.; Müller, C.; Dahmen, I.; Delhomme, T. M. et al.; Ardin, M.; Leblay, N.; Byrnes, G.; Sun, R.; De Reynies, A.; McLeer-Florin, A.; Bosco, G.; Malchers, F.; Menon, R.; Altmüller, J.; Becker, C.; Nürnberg, P.; Achter, V.; Lang, U.; Schneider, P. M.; Bogus, M.; Soloway, M. G.; Wilkerson, M. D.; Cun, Y.; McKay, J. D.; Moro-Sibilot, D.; Brambilla, C. G.; Lantuejoul, S.; Lemaitre, N.; Soltermann, A.; Weder, W.; Tischler, V.; Brustugun, O. T.; Lund-Iversen, M.; Helland, A.; Solberg, S.; Ansen, S.; Wright, G.; Solomon, B.; Roz, L.; Pastorino, U.; Petersen, I.; Clement, J. H.; Sanger, J.; Wolf, J.; Vingron, M.; Zander, T.; Perner, S.; Travis, W. D.; Haas, S. A.; Olivier, M.; Foll, M.; Buttner, R.; Hayes, D. N.; Brambilla, E.; Fernandez-Cuesta, L.; Thomas, R. K.: Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors. Nature Communications 9 (1), 1048 (2018)

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Thesis - PhD (2)

Thesis - PhD

Steiger, E.: Efficient Sparse-Group Bayesian Feature Selection for Gene Network Reconstruction. Dissertation, Freie Universität, Berlin (2018)

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Thesis - PhD

Huska, M. R.: Using machine learning to predict and better understand DNA methylation and genomic enhancers. Dissertation, viii, 143 pp., Freie Universität, Berlin (2018)

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