Overview

The Medical Epigenomics Lab is part of the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. The lab is directed by Christoph Bock, who is a Principal Investigator at CeMM and a Guest Professor in Medical University of Vienna's Department of Laboratory Medicine. He is a member of the European BLUEPRINT project contributing to the work of the International Human Epigenome Consortium to map 1,000 reference epigenomes, and he the project leader of Genom Austria (which is the Austrian member in the International Network of Personal Genome Projects).

The lab's scientific goal is to improve cancer therapy through technology-driven research on the single-cell characterization, computational modeling, and rational reprogramming of the cancer epigenome. An interdisciplinary team of wet-lab and computational researchers combines wet-lab epigenetics research, bioinformatics modeling, and high-throughput sequencing - usually with a translational component and in collaboration with clinical researchers.

Research Topics

• Epigenomics. We perform large-scale epigenome mapping to dissect the dynamics of cancer development and drug resistance. This work is integrated with the BLUEPRINT project and the International Human Epigenome Consortium.
• Technology. Exciting biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell protocols, nanopore sequencing, CRISPR, and epigenome editing.
• Bioinformatics. New algorithms and computational methods allow us to accurately infer epigenetic cell states from large-scale datasets, in order to reconstruct the epigenetic landscape that controls cellular differentiation and reprogramming.
• Diagnostics. Using large-scale DNA methylation mapping, bioinformatic prioritization, and functional characterization, we strive to develop clinically relevant biomarkers for informing personalized cancer therapy.

Key Publications

• Datlinger et al. (2017) Nature Methods  -- First method combining CRISPR genetic screens with single-cell sequencing (preprint posted on bioRxiv 27 Oct 2016), giving rise to a new screening paradigm that combines the throughput of pooled screens with the level of detail provided by arrayed screens with transcriptome read-out
• Farlik/Halbritter/Müller et al. (2016) Cell Stem Cell & Mass/Ballesteros/Farlik/Halbritter/Günther et al. (2016) Science -- Comprehensive mapping of the DNA methylation dynamics in human hematopoietic stem cell differentiation and of the transcriptome dynamics in mouse macrophage specification
• Bock et al. (2016) Nature Biotechnology & Rendeiro/Schmidl et al. (2016) Nature Communications -- Comprehensive benchmarking of DNA methylation assays as diagnostic biomarkers and proof-of-concept for large-scale chromatin accessibility profiling in cancer (focusing on chronic lymphocytic leukemia)
• Schmidl/Rendeiro et al. (2015) Nature Methods & Farlik/Sheffield et al. (2015) Cell Reports & Tomazou/Sheffield et al. (2015) Cell Reports -- Experimental and computational methods for low-input / single-cell epigenome mapping and integrative analysis
• Bock (2012) Nature Reviews Genetics -- Critical review of the state-of-the-art in the genome-wide analysis and interpretation of DNA methylation
• Bock and Lengauer (2012) Nature Reviews Cancer -- Roadmap to personalized cancer therapy using rationally designed drug combinations (inspired by successes in personalized HIV therapy)
• Assenov/Müller/Lutsik et al. (2014) Nature Methods, Halachev et al. (2012) Genome Biology, Lutsik et al. (2011) Nucleic Acids Research, Schüffler et al. (2009) Genome Biology, Bock et al. (2009) Genome Biology, Bock et al. (2005) Bioinformatics -- Development of widely used software tools for user-friendly analysis of DNA methylation data.
• Bock et al. (2012) Molecular Cell -- Comprehensive experimental and computational reconstruction of the epigenome dynamics in adult stem cell differentiation
• Bock et al. (2011) Cell -- Development of a computational scorecard for predictive diagnostics of stem cell quality in regenerative medicine.
• Bock et al. (2010) Nature Biotechnology -- Computational and experimental benchmarking study of different methods for genome-wide analysis of DNA methylation.
• Bock and Lengauer (2008) Bioinformatics -- An early attempt at reviewing and systematizing the new field of computational epigenetics.