Computational Oncoepigenomics
 
Group Members
Lukas Chavez, PhD (Group Leader)
Konstantin Okonechnikov (PostDoc)
Serap Erkek, PhD (PostDoc)
Susanne Gröbner (PhD Student)
Sander Lambo (PhD Student)
Anshupa Sahu (Master Student)
 
Research interests
The Computational Oncoepigenomics group aims to comprehensively understand the genetic and epigenetic diversity of childhood brain tumors by developing and applying bioinformatics methods for the analysis of large-scale biological data. Our focus is mainly on pediatric brain tumors such as medulloblastoma, glioblastoma, ependymoma, and pilocytic astrocytoma. We analyze tumors by genome-wide DNA sequencing, bisulfite sequencing, RNA sequencing, and by histone modification and transcription factor ChIP sequencing. All of these analyses generate a tremendous amount of data that serves as a unique resource for sophisticated modeling, visualization, and interpretation by computer-assisted methods.

Specific research interests:
• Comparative enhancer mapping between different types of pediatric brain tumors,
• Characterization of histone modification states across medulloblastoma types,
• Analysis of genomic structural variants and their effects on enhancer activity and gene expression,
• Integration of different levels of genomic and epigenomic data,
• Identification of drug targets and drug matching for recurrent malignant childhood brain tumors based on high dimensional biological data to improve treatment decisions.
 
Our group has solid experiences in developing bioinformatics tools for high-throughput sequencing data analysis and we routinely apply our and other bioinformatics tools in the context of large-scale DNA modification and enhancer mapping studies in health and disease.
 
For more information contact:
Dr. Lukas Chavez
Group Leader - Computational Oncoepigenomics
Division of Pediatric Neurooncology (B062)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 280
D-69120 Heidelberg
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Selected publications (reverse chronological order)

Lienhard M, Chavez L. Quantitative comparison of large scale DNA enrichment sequencing data. In Statistical Genomics. Springer 2016


• Äijö T, Huang Y, Mannerström H, Chavez L et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biology 2016


• Engel I*, Seumois G*, Chavez L* et al. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs. Nature Immunology 2016


• Johann PD*, Erkek S*, (…) Chavez L, Bens S, Gröschel S, et al. Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes. Cancer Cell 2016


• Lin CY*, Erkek S*, Tong Y, (…) Chavez L, Gröschel S et al. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature 2016


• An J, (…) Li W, Goodell MA, Chavez L*, Ko M*, Rao A*. Acute loss of TET function results in aggressive myeloid cancer in mice. Nature Communications 2015


• Kang J, Lienhard M, Pastor WA, (...) Chavez L*, Rao A*. Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis. PNAS 2015


• Etchegaray JP, Chavez L et al. Sirt6 Regulates Embryonic Stem Cell Differentiation Via Tet-dependent 5-Hydroxymethylcytosine. Nature Cell Biology 2015


• Seumois G*, Chavez L* et al. Epigenomic analysis of primary human T cells reveals novel genes and enhancers associated with Th2 memory differentiation and asthma susceptibility. Nature Immunology 2014 (featured by the  Epigenome Roadmap)


Chavez, L*, Huang, Y* et al. Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea. PNAS 2014


• Huang, Y*, Chavez, L* et al. Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. PNAS 2014


• Lienhard M, Grimm C, Morkel M, Herwig R, Chavez L. MEDIPS: genome wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 2014


• Jeong M, (…) Chavez L, Ko M et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nature Genetics 2014


• Ko M, An J, Bandukwala HS, Chavez L et al. Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX. Nature 2013


• Grimm C, Chavez L et al. DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet. 2013


• Gerasimova A, Chavez L et al. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One 2013


Chavez, L., Jozefczuk, J., et al. Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Research 2010
*equal contribution