Publications

Selected publications

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. [highlighted by the editor as a featured top-5% article]
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, Kiskinis E#, Verstappen G#, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K*, Meissner A* (2011). Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell 144, 439-452. [press releases by the Broad Institute and Harvard University; summary/comment articles in Nature Reviews Genetics, Nature Biotechnology, Nature Methods, Molecular Therapy and F1000]
Bock C*, Tomazou EM#, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A* (2010). Quantitative comparison of genome-wide DNA methylation mapping technologies, Nat Biotechnol 28, 1106-1114. [highlighted in a News & Views article in the same issue]
Gu H, Bock C#, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A* (2010). Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods, 7, 133-136. [highlighted on cover; summary/comment article in F1000]
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. [invited review]
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. [marked as “highly accessed” on the journal’s website]
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. [cover image of the February 2009 issue]
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 [cover image of the June 2008 issue]
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. [invited review. Most frequently accessed Bioinformatics paper in 2008]
Bock C*, Walter J, Paulsen M, Lengauer T (2007) CpG island mapping by epigenome prediction. PLoS Comput Biol 3: e110. [press release by the Max Planck Society]
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. [cover image of the March 2006 issue; press release by the Max Planck Society]
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. [thousands of software downloads since 2005; currently dozens of downloads per week]

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.