I head the computational genomics group at the Ludwig Institute for Cancer Research.
The main focus of my group is to understand the causes and consequences of mutation rate heterogeneity. In previous work, I established that epigenetic marks in the form of histone modifications have a profound influence on the mutational landscape in cancer cells. More recently, my lab analysed the influence of different DNA modifications on mutability, and described how DNA replication changes the distribution of mutations in cancer genomes. This has important implications for our understanding of cancer development. For example, it allows us to identify new carcinogenic mechanisms that might be preventable.
We are also interested in developing novel genomic methods in the area of single-cell technology. For example, as part of ongoing collaboration we have created tools to assess the robustness of single-cell transcriptome measurements, and built tools to process epigenetic sequencing data using a brand-new, Oxford-developed technology called TAPS.
Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.
Liu Y. et al, (2019), Nature biotechnology, 37, 424 - 429
Mutational signature distribution varies with DNA replication timing and strand asymmetry
Tomkova M. et al, (2018), Genome Biology, 19
BEARscc determines robustness of single-cell clusters using simulated technical replicates
Severson DT. et al, (2018), Nature Communications, 9
5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA
Tomkova M. et al, (2016), eLife, 5
Chromatin organization is a major influence on regional mutation rates in human cancer cells
Schuster-Böckler B. and Lehner B., (2012), Nature, 488, 504 - 507
Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution
Louphrasitthiphol P. et al, (2020), Molecular Cell
Author Correction: The effects of mutational processes and selection on driver mutations across cancer types.
Temko D. et al, (2020), Nature communications, 11