Bioinformatics

Organisational unit: Research Group

  1. 2017
  2. 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
  3. 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. DOI: 10.1186/s13059-017-1176-4
  4. Zych, K., Snoek, L. B., Elvin, M., Rodriguez, M., van der Velde, K. J., Arends, D., ... Li, Y. (2017). reGenotyper: Detecting mislabeled samples in genetic data. PLoS ONE, 12(2). DOI: 10.1371/journal.pone.0171324
  5. 2016
  6. 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
  7. 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
  8. Wardenaar, R. (2016). DNA methylation inheritance in Arabidopsis: The next generation [Groningen]: Rijksuniversiteit Groningen
  9. 2015
  10. 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
  11. 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
  12. 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
  13. 2014
  14. 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
  15. 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
  16. 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
  17. 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
  18. 2013
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Tretyakov, K., Laur, S., Smant, G., Vilo, J., & Prins, P. (2013). Fast probabilistic file fingerprinting for big data. BMC Genomics, 14, [8]. DOI: 10.1186/1471-2164-14-S2-S8
  28. 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
  29. 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
  30. 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
  31. 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
  32. 2012
  33. 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
  34. 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
  35. 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
  36. Lendvai, Á., Johannes, F., Grimm, C., Eijsink, J. J. H., Wardenaar, R., Volders, H. H., ... van der Zee, A. G. J. (2012). Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics, 7(11), 1268-1278. DOI: 10.4161/epi.22301
  37. Creek, D. J., Chokkathukalam, A., Jankevics, A., Burgess, K. E. V., Breitling, R., & Barrett, M. P. (2012). Stable Isotope-Assisted Metabolomics for Network-Wide Metabolic Pathway Elucidation. Analytical Chemistry, 84(20), 8442-8447. DOI: 10.1021/ac3018795
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