Recent advances in microarray and sequencing technologies made the genome-wide profiling of DNA methylation and histone modifications feasible and scalable to cohorts containing hundreds or even thousands of samples. Large international consortia, such as the Encylopedia of DNA Elements, The Cancer Genome Atlas Project, the International Cancer Genome Consortium and the International Human Epigenome Consortium have systematically generated comprehensive epigenome-wide datasets on tissue samples and cell lines in human. These vast cohorts open unprecedented opportunities to study the genetic regulation, intracellular heterogeneity and disease progression at the molecular level, but they also bring up enormous challenges in data processing and analysis.

Major Research Directions

Our major goal is to improve the knowledge about the role of epigenetic processes by designing and using novel, integrative analysis techniques and advanced visualization approaches to map the complex interplay between genome, epigenome and transcriptome in the initiation and progression of cardiovascular diseases and cancer.
We also design custom strategies for biomarker prioritization and validation for various purposes, including therapy suggestions in early onset prostate cancer, classification of rare tumors and non-invasive diagnosis of cardiovascular diseases. We also study the predictive potential of DNA methylation and the applicability of methylation-based prediction models in clinical settings.
To improve the reproducibility and comparability of the currently used genome-wide technologies in detecting local and global changes in DNA methylation and histone marks, we investigate the strengths and limitations of these methods and their processing pipelines.

Selected Recent Publications

  • Jäkel C, Bergmann F, Toth R, Assenov Y, van der Duin D, Strobel O, Hank T, Klöppel G, Dorrell C, Grompe M, Moss J, Dor Y, Schirmacher P, Plass C, Popanda O, Schmezer P. Genome-wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stability. Nature Communications 8(1):1323, 2017
  • Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C. DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nature Genetics 49(7):1052-1060, 2017
  • Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biology 18(1): 55, 2017
  • Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, ... Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology, 34(7):726-737, 2016
  • Schramm A, Köster J, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Schröder C, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, Altmüller J, Nürnberg P, Astrahantseff K, Gloeckner C, De Preter K, Plass C, Lee S, Lode HN, Henrich KO, Gartlgruber M, Speleman F, Schmezer P, Westermann F, Rahmann S, Fischer M, Eggert A, Schulte JH. Mutational dynamics between primary and relapse neuroblastomas. Nature Genetics, doi:10.1038/ng.3349, 2015
  • Liesenfeld DB, Habermann N, Toth R, Owen RW, Frei E, Böhm J, Schrotz-King P, Klika KD, Ulrich CM: Changes in urinary metabolic profiles of colorectal cancer patients enrolled in a prospective cohort study (ColoCare). Metabolomics, 11(4):998-1012, 2015
  • Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods, 11(11):1138-1140, 2014
  • Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes CC, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sallari R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Reports, 8(3):798-806, 2014
  • Rakosy Z, Ecsedi S, Toth R, Vizkeleti L, Herandez-Vargas H, Lazar V, Emri G, Szatmari I, Herceg Z, Adany R, Balazs M. Integrative Genomics Identifies Gene Signature Associated with Melanoma Ulceration PLoS ONE, 8(1):e54958, 2013.
  • Doncheva NT, Assenov Y, Domingues FS, Albrecht M. Topological analysis and interactive visualization of biological networks and protein structures. Nature Protocols, 7(4):670-685, 2012
  • Toth R, Pocsai Z, Fiatal S, Szeles G, Kardos L, Petrovski B, McKee M, Adany R. ADH1B*2 allele is protective against alcoholism but not chronic liver disease in the Hungarian population Addiction, 105(5):891-896, 2010.

The full list of publications is available in a dedicated web page.

The publication lists of individual members can be seen on their Google Profiles:

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