Publications
Recent publications of the Computational Epigenetics Group:
Journal papers
- Bock, C. (2009) Epigenetic biomarker development, in press at Epigenomics. (preprint available on request)
- Schüffler, P., Mikeska, T., Lengauer, T. and Bock, C. (2009) MethMarker: Optimized assay design for epigenetic biomarker development and high-throughput epigenotyping. submitted. (download software, preprint available on request)
- Bock, C., Von Kuster, G., Halachev, K., Taylor, J., Nekrutenko, A. and Lengauer, T. (2008) Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy, in press at Methods in Molecular Biology. (view manuscript)
- Zhang, Y., Rohde, C., Tierling, S., Jurkowski, T.P., Bock, C., Santacruz, D., Reinhardt, R., Groth, M., Walter, J. and Jeltsch, A. (2009) DNA methylation mapping of chromosome 21 gene promoters at single base pair and single allele resolution, PLoS Genetics 5, e1000438. (view paper or data / website)
- Bock, C., Halachev, K., Büch, J. and Lengauer, T. (2009) User-friendly software for statistical analysis and prediction of (epi-) genomic data. Genome Biology 10: R14. (view paper or use web service)
- Kircher, M., Bock, C. and Paulsen M. (2008) Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region, BMC Genomics, DOI:10.1186/1471-2164-9-346. (view paper)
- Bock, C., Walter, J., Paulsen, M. and Lengauer, T. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping, Nucleic Acids Research 36: e55. (view paper - this paper was on the cover of the June 2008 issue of Nucleic Acids Research
- Moser, D., Ekawardhani, S., Kumsta, R., Palmason, H., Bock, C., Athanassiadou, Z., Lesch, K.-P. and Meyer, J. (2007). Functional promoter variants of the potassium-chloride co-transporter 3 gene (KCC3, SLC12A6) regulate expression via selective DNA methylation, Neuropsychopharmacology, DOI:10.1038/npp.2008.77. (view paper - this paper is not open access, please contact me for a reprint)
- Bock, C. and Lengauer, T. (2008) Computational epigenetics, Bioinformatics, 24, 1-10. (view paper - most frequently accessed Bioinformatics paper in 2008 with >5,000 downloads between January and May)
- Mikeska, T., Bock, C., El-Maarri, O., Hübner, A., Ehrentraut, D., Schramm, J., Felsberg, J., Kahl, P., Büttner, R., Pietsch, T. and Waha, A. (2007) Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis. Journal of Molecular Diagnostics 9, 368-381. (view paper - this paper is not open access, please contact me for a reprint)
- Bock, C., Walter, J., Paulsen, M., and Lengauer, T. (2007). CpG Island Mapping by Epigenome Prediction. PLoS Computational Biology 3, e110. (view paper or data / website or MPG press release)
- Liu, F., Tostesen, E., Sundet, J. K., Jenssen, T. K., Bock, C., Jerstad, G. I., Thilly, W. G., and Hovig, E. (2007). The human genomic melting map. PLoS Computational Biology 3, e93. (view paper or data / website)
- Bock, C., Paulsen, M., Tierling, S., Mikeska, T., Lengauer, T., and Walter, J. (2006). CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats and predicted DNA structure. PLoS Genetics 2, e26. (view paper or MPG press release) - this paper was on the cover of the March 2006 issue of PLoS Genetics
- Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J., and Lengauer, T. (2005). BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21, 4067-4068. (view paper or download software for academic use or buy software for commercial use)
Conference papers, book chapters, opinion articles, etc.
- Bock, C. (2008) IVF: stars may have to consider the risk of stolen parenthood. Nature 454, 938.
- Bock, C. and Lengauer, T. (2007) Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung, Jahrbuch 2007. Max-Planck-Gesellschaft.
- Bock, C. (2006) Bioinformatik: Neue Strategien gegen Krebs, Deutsches Ärzteblatt, 103, Supplement: PRAXiS, 10-11.
- Bock, C., Halachev, K. and Lengauer, T. (2006) Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs. In Haasis, K., Heinzl, A. and Klumpp, D. (eds), Aktuelle Trends in der Softwareforschung. dpunkt.verlag, Heidelberg.
- Bock, C. and Lengauer, T. (2006) Computational epigenetics: bioinformatics prediction for new approaches to cancer treatment, Spotlight 2006 (Featured Research Story of the Max Planck Institute for Informatics). Max Planck Institute for Informatics, Saarbrücken.
Recent theses
- Bock, C. (2008) Computational Epigenetics - Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics, Saarland University. PhD thesis.
- Schüffler, P. (2008) MethMarker: A toolkit for design, optimization and validation of DNA methylation biomarkers for cancer diagnosis and therapy optimization, Saarland University. Master thesis.
- Feuerbach, L. (2007) Towards Comparative Epigenomics: A Pilot Study on DNA Methylation of CpG Islands on Human Chromosome 21, Saarland University. Master thesis.
- Kircher, M. (2007) In silico analysis of microRNA genes on human chromosome 14 and mouse chromosome 12, Saarland University. Master thesis.
- Halachev, K. (2006) EpiGRAPH•regression: A toolkit for (epi-)genomic correlation analysis and prediction of quantitative attributes, Saarland University. Master thesis.
