Publications - Computational Epigenetics
Selected publications
- Halachev K, Bast H, Albrecht F, Lengauer T, Bock C (2012). EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology 13, R96.
- Bock C (2012). Analysing and interpreting DNA methylation data. Nature Reviews Genetics 13, 705-719.
- Bock C, Lengauer T (2012). Managing drug resistance in cancer: Lessons from HIV therapy. Nature Re-views Cancer, 12, 494-501.
- Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C (2011). BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing, Nucleic Acids Res 39 Suppl 2, W551-556.
- Fernandez AF, Assenov Y, Martin-Subero J, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Grana O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M (2011) A DNA methylation fingerprint of 1628 human samples. Genome Res, 10.1101/gr.119867.110.
- Feuerbach L, Lyngsø RB, Lengauer T, Hein J (2011). Reconstructing the ancestral germ line methylation state of young repeats. Mol Biol Evol. 2011 Jun;28(6):1777-84.
- Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T (2010) Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods Mol Biol, 628, 275-296
- Bock C (2009) Epigenetic biomarker development. Epigenomics 1: 99-110.
- Schüffler P, Mikeska T, Waha A, Lengauer T, Bock C (2009). MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol 10: R105.
- Bock C, Halachev K, Büch J, Lengauer T (2009). EpiGRAPH: User-friendly software for statistical analysis and prediction of (epi-) genomic data. Genome Biol 10: R14.
- Bock C, Walter J, Paulsen M, Lengauer T (2008). Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res 36: e55.
- Kircher M, Bock C, Paulsen M (2008) Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics 9: 346.
- Bock C, Lengauer T (2008). Computational epigenetics, Bioinformatics, 24, 1-10.
- Bock C, Walter J, Paulsen M, Lengauer T (2007) CpG island mapping by epigenome prediction. PLoS Comput Biol 3: e110.
- Mikeska T, Bock C, El-Maarri O, Hübner A, Ehrentraut D, Schramm J, Felsberg J, Kahl P, Büttner R, Pietsch T, Waha A (2007) Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. J Mol Diagn 9: 368-381.
- Bock C, Paulsen M, Tierling S, Mikeska T, Lengauer T, Walter J (2006). CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet 2: e26.
- Bock C, Hesser J (2006). Analysis and prediction of helix shift errors in homology modeling. In Silico Biol 6: 131-145.
- Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T (2005). BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21: 4067-4068.
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.
- Glaab, E. (2006) On the predictability of CpG methylation in human tissue at single basepair resolution, Saarland University. Bachelor thesis.