After training in Computer Science (at Charles University in Prague), I became interested in interdisciplinary research where I can apply my computational background to important questions in biology and medicine. During my DPhil (at University of Oxford), I developed my interest in mutagenesis, epigenomics, and cancer research. We showed that:
- 5-hydroxymethylcytosine is protective against mutations (in contrast with the pro-mutagenicity of the major DNA modification 5-methylcytosine),
- DNA replication leaves a detectable footprint in most mutational processes,
- the widely accepted explanation of mutational signature 1, one of the two most widespread mutational patterns, is contradicted by observations in sequencing data of cancer patients, implicating involvement of an independent replication-linked mechanism.
In my postdoctoral research (at University of California Davis), I studied mutations in the non-coding genome – and how they contribute to cancer and other diseases. We also used epigenome editing to dissect the fascinating mechanisms of how different epigenetic marks in the non-coding genome regulate gene expression.
Throughout my past research, I have worked on many international collaborative projects with clinicians, experimental scientists, and computer scientists. For example, in a collaboration with researchers from Google Brain and Charles University in Prague, we were the first to show a human-level deep-learning AI for language translation.
In summer 2023, I have started my group at the Oxford branch of Ludwig Cancer Research to study the mechanisms of how mutagenesis and epigenomics together and independently cause cancer.
Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements.
Tomkova M. et al, (2023), Nucleic acids research, 51
Transforming machine translation: a deep learning system reaches news translation quality comparable to human professionals.
Popel M. et al, (2020), Nature communications, 11
Mutational signature distribution varies with DNA replication timing and strand asymmetry
Tomkova M. et al, (2018), Genome Biology, 19
DNA Replication and associated repair pathways are involved in the mutagenesis of methylated cytosine
Tomkova M. et al, (2018), DNA Repair, 62, 1 - 7
5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA
Tomkova M. et al, (2016), eLife, 5
Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma.
Carroll TM. et al, (2023), Cancer cell, 41, 1222 - 1241.e7