1. 2018
  2. Monteiro Morgado, L. (2018). Computational Methods for High-Throughput Small RNA Analysis in Plants [Groningen]: University of Groningen
  3. Behrouzi, P. (2018). Extensions of graphical models with applications in genetics and genomics [Groningen]: University of Groningen
  4. 2017
  5. Lauss, K., Wardenaar, R., Oka, R., van Hulten, M. H. A., Guryev, V., Keurentjes, J. J. B., ... Johannes, F. (2017). Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiology, 175(4), 1627-1645. DOI: 10.1104/pp.17.01054
  6. Morgado, L., Preite, V., Oplaat, C., Anava, S., de Carvalho, J. F., Rechavi, O., ... Verhoeven, K. J. F. (2017). Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Molecular Biology and Evolution, 34(8), 2035-2040. DOI: 10.1093/molbev/msx150
  7. Vidalis, A., Živković, D., Wardenaar, R., Roquis, D., Tellier, A., & Johannes, F. (2017). Erratum to: Methylome Evolution in plants. Genome Biology, 18(1), 1-3. [41]. DOI: 10.1186/s13059-017-1176-4
  8. 2016
  9. Vidalis, A., Živković, D., Wardenaar, R., Roquis, D., Tellier, A., & Johannes, F. (2016). Methylome evolution in plants. Genome Biology, 17(1), 1-14. [264]. DOI: 10.1186/s13059-016-1127-5
  10. Hehir-Kwa, J. Y., Marschall, T., Kloosterman, W. P., Francioli, L. C., Baaijens, J. A., Dijkstra, L. J., ... Genome Netherlands Consortium (2016). A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7, [12989]. DOI: 10.1038/ncomms12989
  11. Wardenaar, R. (2016). DNA methylation inheritance in Arabidopsis: The next generation [Groningen]: Rijksuniversiteit Groningen
  12. 2015
  13. Prins, P., de Ligt, J., Tarasov, A., Jansen, R. C., Cuppen, E., & Bourne, P. E. (2015). Toward effective software solutions for big biology. Nature Biotechnology, 33(7), 686-687. [nbt.3240]. DOI: 10.1038/nbt.3240
  14. Westra, H-J., Arends, D., Esko, T., Peters, M. J., Schurmann, C., Schramm, K., ... Franke, L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PLOS Genetics, 11(5), [1005223]. DOI: 10.1371/journal.pgen.1005223
  15. Kooke, R., Johannes, F., Wardenaar, R., Becker, F., Etcheverry, M., Colot, V., ... Keurentjes, J. J. B. (2015). Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana. Plant Cell. DOI: 10.1105/tpc.114.133025
  16. 2014
  17. Pino Del Carpio, D., Basnet, R. K., Arends, D., Lin, K., De Vos, R. C. H., Muth, D., ... Bonnema, G. (2014). Regulatory network of secondary metabolism in Brassica rapa: insight into the glucosinolate pathway. PLoS ONE, 9(9), [e107123]. DOI: 10.1371/journal.pone.0107123
  18. Rintisch, C., Heinig, M., Bauerfeind, A., Schafer, S., Mieth, C., Patone, G., ... Hubner, N. (2014). Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research, 24(6), 942-953. DOI: 10.1101/gr.169029.113
  19. Cortijo, S., Wardenaar, R., Colome-Tatche, M., Gilly, A., Etcheverry, M., Labadie, K., ... Johannes, F. (2014). Mapping the Epigenetic Basis of Complex Traits. Science, 343(6175), 1145-1148. DOI: 10.1126/science.1248127
  20. Medema, M., Paalvast, Y., Nguyen, D. D., Melnik, A., Dorrestein, P. C., Takano, E., & Breitling, R. (2014). Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products. PLoS Computational Biology, [e1003822]. DOI: 10.1371/journal.pcbi.1003822
  21. 2013
  22. Kerkhoven, E. J., Achcar, F., Alibu, V. P., Burchmore, R. J., Gilbert, I. H., Trybilo, M., ... Barrett, M. P. (2013). Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Computational Biology, 9(12), [1003371]. DOI: 10.1371/journal.pcbi.1003371
  23. Berg, M., Vanaerschot, M., Jankevics, A., Cuypers, B., Maes, I., Mukherjee, S., ... Dujardin, J-C. (2013). Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure. Molecular Microbiology, 90(2), 428-442. DOI: 10.1111/mmi.12374
  24. Westra, H-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., ... Hoen, P. A. C. . (2013). Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics, 45(10), 1238-1243. DOI: 10.1038/ng.2756
  25. Don Duy Nguyen, . N. V., Wu, C-H., Moree, W. J., Lamsa, A., Medema, M. H., Zhao, X., ... Dorrestein, P. C. (2013). MS/MS networking guided analysis of molecule and gene cluster families. Proceedings of the National Academy of Sciences of the United States of America, 110(28), E2611-E2620. DOI: 10.1073/pnas.1303471110
  26. Blin, K., Medema, M. H., Kazempour, D., Fischbach, M. A., Breitling, R., Takano, E., & Weber, T. (2013). antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Research, 41(W1), W204-W212. DOI: 10.1093/nar/gkt449
  27. Joosen, R. V. L., Arends, D., Li, Y., Willems, L. A. J., Keurentjes, J. J. B., Ligterink, W., ... Hilhorst, H. W. M. (2013). Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics. Plant Physiology, 162(2), 553-566. DOI: 10.1104/pp.113.216176
  28. Medema, M. H., Takano, E., Breitling, R., & Nowick, K. (Ed.) (2013). Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast. Molecular Biology and Evolution, 30(5), 1218-1223. DOI: 10.1093/molbev/mst025
  29. Bui Quang Minh, . N. V., Nguyen, T., & von Haeseler, A. (2013). Ultrafast Approximation for Phylogenetic Bootstrap. Molecular Biology and Evolution, 30(5), 1188-1195. DOI: 10.1093/molbev/mst024
  30. Tretyakov, K., Laur, S., Smant, G., Vilo, J., & Prins, P. (2013). Fast probabilistic file fingerprinting for big data. BMC Genomics, 14(Suppl 2), [8]. DOI: 10.1186/1471-2164-14-S2-S8
  31. Tobias, N. J., Doig, K. D., Medema, M. H., Chen, H., Haring, V., Moore, R., ... Stinear, T. P. (2013). Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii. Journal of Bacteriology, 195(3), 556-564. DOI: 10.1128/JB.02132-12
  32. Chokkathukalam, A., Jankevics, A., Creek, D. J., Achcar, F., Barrett, M. P., Breitling, R., & Ideker, T. (Ed.) (2013). mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29(2), 281-283. DOI: 10.1093/bioinformatics/bts674
  33. Frasch, H-J., Medema, M. H., Takano, E., Breitling, R., Gago, F. (Ed.), & Parayil, A. (Ed.) (2013). Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice. Current Opinion in Biotechnology, 24(6), 1144-1150. DOI: 10.1016/j.copbio.2013.03.006
  34. Dunn, W. B., Erban, A., Weber, R. J. M., Creek, D. J., Brown, M., Breitling, R., ... Viant, M. R. (2013). Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics, 9(1), S44-S66. DOI: 10.1007/s11306-012-0434-4
  35. 2012
  36. Fischer, M., Klaere, S., Minh Anh Thi Nguyen, . N. V., & von Haeseler, A. (2012). On the group theoretical background of assigning stepwise mutations onto phylogenies. Algorithms for molecular biology, 7, [36]. DOI: 10.1186/1748-7188-7-36
  37. Zakrzewski, P., Medema, M. H., Gevorgyan, A., Kierzek, A. M., Breitling, R., Takano, E., & Fong, S. S. (Ed.) (2012). MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models. PLoS ONE, 7(12), e51511-1-e51511-9. [51511]. DOI: 10.1371/journal.pone.0051511
  38. Chaneton, B., Hillmann, P., Zheng, L., Martin, A. C. L., Maddocks, O. D. K., Chokkathukalam, A., ... Gottlieb, E. (2012). Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature, 491(7424), 458-+. DOI: 10.1038/nature11540
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