Publications

Publications Department Computational Molecular Biology

Journal Article (371)

  1. 1.
    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)
  2. 2.
    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)
  3. 3.
    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)
  4. 4.
    Hackmann, K.; Rump, A.; Haas, S.; Lemke, J. R.; Fryns, J.-P.; Tzschach, A.; Wieczorek, D.; Albrecht, B.; Kuechler, A.; Rippberger, T. et al.; Kobelt, A.; Oexle, K.; Tinschert, S.; Schrock, E.; Kalscheuer, V. M.; Di Donato, N.: Tentative clinical diagnosis of Lujan-Fryns syndrome--A conglomeration of different genetic entities? American Journal of Medical Genetics Part A 170A (1), pp. 94 - 102 (2016)
  5. 5.
    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)
  6. 6.
    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 (2016)
  7. 7.
    Batalha, V.; Ferreira, D. G.; Coelho, J. E.; Valadas, J. S.; Gomes, R.; Temido-Ferreira, M.; Shmidt, T.; Baqi, Y.; Buée, L.; Müller, C. E. et al.; Hamdane, M.; Outeiro, T. F.; Bader, M.; Meijsing, S.; Sadri-Vakili, G.; Blum, D.; Lopes, L. V.: The caffeine-binding adenosine A2A receptor induces age-like HPA-axis dysfunction by targeting glucocorticoid receptor function. Scientific Reports (2016)
  8. 8.
    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)
  9. 9.
    Franke, M.; Ibrahim, D.; Andrey, G.; Schwarzer, W.; Heinrich, V.; Schöpflin, R.; Kraft, K.; Kempfer, R.; Jerković, I.; Chan, W.-L. et al.; Spielmann, M.; Timmermann, B.; Wittler, L.; Kurth, I.; Cambiaso, P.; Zuffardi, O.; Houge, G.; Lambie, L.; Brancati, F.; Pombo, A.; Vingron, M.; Spitz, F.; Mundlos, S.: Formation of novel chromatin domains determines pathogenicity of genomic duplications. Nature 538 (7624), pp. 265 - 269 (2016)
  10. 10.
    Hackmann, K.; Rump, A.; Haas, S. A.; Lemke, J. R.; Fryns, J. P.; Tzschach, A.; Wieczorek, D.; Albrecht, B.; Kuechler, A.; Ripperger, T. et al.; Kobelt, A.; Oexle, K.; Tinschert, S.; Schrock, E.; Kalscheuer, V. M.; Di Donato, N.: Tentative clinical diagnosis of Lujan-Fryns syndrome-A conglomeration of different genetic entities? American Journal of Medical Genetics Part A 170 (1), pp. 94 - 102 (2016)
  11. 11.
    Hardt, C.; Beber, M. E.; Rasche, A.; Kamburov, A.; Hebels, D. G.; Kleinjans, J. C.; Herwig, R.: ToxDB: pathway-level interpretation of drug-treatment data. Database (Oxford) (2016)
  12. 12.
    Heinrich, V.; Kamphans, T.; Mundlos, S.; Robinson, P. N.; Krawitz, P. M.: A likelihood ratio based method to predict exact pedigrees for complex families from next-generation sequencing data. Bioinformatics (2016)
  13. 13.
    Herwig, R.; Gmuender, H.; Corvi, R.; Bloch, K. M.; Brandenburg, A.; Castell, J.; Ceelen, L.; Chesne, C.; Doktorova, T. Y.; Jennen, D. et al.; Jennings, P.; Limonciel, A.; Lock, E. A.; McMorrow, T.; Phrakonkham, P.; Radford, R.; Slattery, C.; Stierum, R.; Vilardell, M.; Wittenberger, T.; Yildirimman, R.; Ryan, M.; Rogiers, V.; Kleinjans, J.: Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective. Archives of Toxikology 90 (9), pp. 2215 - 2229 (2016)
  14. 14.
    Herwig, R.; Hardt, C.; Lienhard, M.; Kamburov, A.: Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nature Protocols 11 (10), pp. 1889 - 1907 (2016)
  15. 15.
    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)
  16. 16.
    Huska, M.; Vingron, M.: Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns. PLoS Computational Biology 12 (12), e1005249 (2016)
  17. 17.
    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)
  18. 18.
    Massip, F.; Sheinman, M.; Schbath, S.; Arndt, P.: Comparing the Statistical Fate of Paralogous and Orthologous Sequences. Genetics 204 (2), pp. 475 - 482 (2016)
  19. 19.
    Moorjani, P.; Amorim, C. E.; Arndt, P. F.; Przeworski, M.: Variation in the molecular clock of primates. Proceedings of the National Academy of Sciences of the United States of America 113 (38), pp. 10607 - 10612 (2016)
  20. 20.
    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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