Publications

Publications Department Computational Molecular Biology

Journal Article (398)

  1. 1.
    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 naïve pluripotency. Cell Stem Cell 23 (2), pp. 266 - 275 (2018)
  2. 2.
    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 (2018)
  3. 3.
    Frints, S. G. M.; Ozanturk, A.; Rodríguez Criado, G.; Grasshoff, U.; de Hoon, B.; Field, M.; Manouvrier-Hanu, S.; Hickey, S. E.; Kammoun, M.; Gripp, K. W. et al.; Bauer, C.; Schroeder, C.; Toutain, A.; Mihalic Mosher, T.; Kelly, B. J.; White, P.; Dufke, A.; Rentmeester, E.; Moon, S.; Koboldt, D. C.; van Roozendaal, K. E. P.; Hu, H.; Haas, S. A.; Ropers, H.-H.; Murray, L.; Haan, E.; Shaw, M.; Carroll, R.; Friend, K.; Liebelt, J.; Hobson, L.; De Rademaeker, M.; Geraedts, J.; Fryns, J.-P.; Vermeesch, J.; Raynaud, M.; Riess, O.; Gribnau, J.; Katsanis, N.; Devriendt, K.; Bauer, P.; Gecz, J.; Golzio, C.; Gontan, C.; Kalscheuer, V. M.: Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Molecular Psychiatry (2018)
  4. 4.
    Hu, H.; Kahrizi, K.; Musante, L.; Fattahi, Z.; Herwig, R.; Hosseini, M.; Oppitz, C.; Abedini, S. S.; Suckow, V.; Farzaneh, L. et al.; Beheshtian, M.; Lipkowitz, B.; Akhtarkhavari, T.; Mehvari, S.; Otto, S.; Mohseni, M.; Arzhangi, S.; Jamali, P.; Mojahedi, F.; Taghdiri, M.; Papari, E.; Soltani Banavandi, M. J.; Akbari, S.; Tonekaboni, S. H.; Dehghani, H.; Ebrahimpou, M. R.; Bader, I.; Davarnia, B.; Cohen, M.; Khodaei, H.; Albrecht, B.; Azimi, S.; Zirn, B.; Bastami, M.; Wieczorek, D.; Bahrami, G.; Keleman, K.; Vahid, L. N.; Timmermann, B.; Pourfatemi, F.; Jankhah, A.; Chen, W.; Nikuei, P.; Kalscheuer, V. M.; Oladnabi, M.; Wienker, T. F.; Ropers, H.-H.; Najmabadi, H.: Genetics of intellectual disability in consanguineous families. Molecular Psychiatry (2018)
  5. 5.
    Kuepfer, L.; Clayton, O.; Thiel, C.; Cordes, H.; Nudischer, R.; Blank, L. M.; Baier, V.; Heymans, S.; Caiment, F.; Roth, A. et al.; Fluri, D. A.; Kelm, J. M.; Castell, J.; Selevsek, N.; Schlapbach, R.; Keun, H.; Hynes, J.; Sarkans, U.; Gmuender, H.; Herwig, R.; Niederer, S.; Schuchhardt, J.; Segall, M.; Kleinjans, J.: A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity. Archives of Toxicology 92 (1), pp. 553 - 555 (2018)
  6. 6.
    Kopp, W.; Vingron, M.: An improved compound Poisson model for the number of motif hits in DNA sequences. Bioinformatics 33 (24), pp. 3929 - 3937 (2017)
  7. 7.
    Hoehe, M. R.; Herwig, R.; Mao, Q.; Peters, B. A.; Drmanac, R.; Church, G. M.; Huebsch, T.: Significant abundance of cis configurations of mutations in diploid human genomes. bioRxiv (2017)
  8. 8.
    Heller, D.; Krestel, R.; Ohler, U.; Vingron, M.; Marsico, A.: ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. Nucleic Acids Research (London) 45 (19), pp. 11004 - 11018 (2017)
  9. 9.
    Niturad, C. E.; Lev, D.; Kalscheuer, V. M.; Charzewska, A.; Schubert, J.; Lerman-Sagie, T.; Kroes, H. Y.; Oegema, R.; Traverso, M.; Specchio, N. et al.; Lassota, M.; Chelly, J.; Bennett-Back, O.; Carmi, N.; Koffler-Brill, T.; Iacomino, M.; Trivisano, M.; Capovilla, G.; Striano, P.; Nawara, M.; Rzonca, S.; Fischer, U.; Bienek, M.; Jensen, C.; Hu, H.; Thiele, H.; Altmüller, J.; Krause, R.; May, P.; Becker, F.; Euro, E. C.; Balling, R.; Biskup, S.; Haas, S. A.; Nürnberg, P.; van Gassen, K. L. I.; Lerche, H.; Zara, F.; Maljevic, S.; Leshinsky-Silver, E.: Rare GABRA3 variants are associated with epileptic seizures, encephalopathy and dysmorphic features. Brain 140 (11), pp. 2879 - 2894 (2017)
  10. 10.
    Bhat, J.; Helmuth, J.; Chitadze, G.; Kouakanou, L.; Peters, C.; Vingron, M.; Ammerpohl, O.; Kabelitz, D.: Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T-Cell Differentiation and Functional Plasticity. Scand J Immunol 86 (4), pp. 184 - 195 (2017)
  11. 11.
    Will , A. J.; Cova, G.; Osterwalder, M.; Chan, W. L.; Wittler, L.; Brieske, N.; Heinrich, V.; de Villartay, J. P.; Vingron, M.; Klopocki, E. et al.; Visel, A.; Lupianez, D. G.; Mundlos, S.: Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog). Nature Genetics 49 (10), pp. 1539 - 1545 (2017)
  12. 12.
    Thibaut, F.; Hoehe, M. R.: Addictive behaviors: where do we stand, and where are we going? Dialogues in Clinical Neuroscience (2017)
  13. 13.
    Yang, J.; Moeinzadeh, M. H.; Kuhl, H.; Helmuth, J.; Xiao, P.; Haas, S.; Liu, G.; Zheng, J.; Sun, Z.; Fan, W. et al.; Deng, G.; Wang, H.; Hu, F.; Zhao, S.; Fernie, A. R.; Börno, S. T.; Timmermann, B.; Zhang, P.; Vingron, M.: Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants (2017)
  14. 14.
    Klaßen, C.; Karabinskaya, A.; Dejager, L.; Vettorazzi, S.; Van Moorleghem, J.; Lühder, F.; Meijsing, S. H.; Tuckermann, J. P.; Bohnenberger, H.; Libert, C. et al.; Reichardt, H. M.: Airway Epithelial Cells Are Crucial Targets of Glucocorticoids in a Mouse Model of Allergic Asthma. Journal of Immunology 199 (1), pp. 48 - 61 (2017)
  15. 15.
    Kuruoglu, E. E.; Arndt, P. F.: The information capacity of the genetic code: Is the natural code optimal? Journal of Theoretical Biology 419, pp. 227 - 237 (2017)
  16. 16.
    Lienhard, M.; Grasse, S.; Rolff, J.; Frese, S.; Schirmer, U.; Becker, M.; Börno, S. T.; Timmermann, B.; Chavez, L.; Sültmann, H. et al.; Leschber, G.; Fichtner, I.; Schweiger, M. R.; Herwig, R.: QSEA – modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Research (London) (2017)
  17. 17.
    Skopkova, M.; Hennig, F.; Shin, B. S.; Turner, C. E.; Stanikova, D.; Brennerova, K.; Stanik, J.; Fischer, U.; Henden, L.; Müller, U. et al.; Steinberger, D.; Leshinsky-Silver, E.; Bottani, A.; Kurdiova, T.; Ukropec, J.; Nyitrayova, O.; Kolnikova, M.; Klimes, I.; Borck, G.; Bahlo, M.; Haas, S. A.; Kim, J. R.; Lotspeich-Cole, L. E.; Gasperikova, D.; Dever, T. E.; Kalscheuer, V. M.: EIF2S3 Mutations Associated with Severe X-Linked Intellectual Disability Syndrome MEHMO. Human Mutation 38 (4), pp. 409 - 425 (2017)
  18. 18.
    Love, M. I.; Huska, M.; Jurk, M.; Schöpflin, R.; Starick, S. R.; Schwahn, K.; Cooper, S. B.; Yamamoto, K. R.; Thomas-Chollier, M.; Vingron, M. et al.; Meijsing, S. H.: Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Research (London) 45 (4), pp. 1805 - 1819 (2017)
  19. 19.
    Andrey, G.; Schöpflin, R.; Jerković, I.; Heinrich, V.; Ibrahim, D.; Paliou, C.; Hochradel, M.; Timmermann, B.; Haas, S.; Vingron, M. et al.; Mundlos, S.: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Research 27 (2), pp. 223 - 233 (2017)
  20. 20.
    Jerković, I.; Ibrahim, D.; Andrey, G.; Haas, S.; Hansen, P.; Janetzki, C.; Gonzalez Navarrete, I.; Robinson, P. N.; Hecht, J.; Mundlos, S.: Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. PLoS Genetics (2017)
 
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