International PhD Programme research topics
When you apply for the EMBL International PhD Programme, you are asked to select two EMBL research units and to indicate up to four research areas that interest you. A variety of backgrounds - such as biology, chemistry, computational science, mathematics and statistics - are relevant to PhD projects at EMBL-EBI. As well as purely computational projects, there may also be possibilities to incorporate some experimental biology in collaborating laboratories.
The following Group Leaders at EMBL-EBI are hoping to recruit PhD students in the ongoing round.
We are interested in the development of computational tools to characterize the patterns of mutations and genome instability processes in human cancers through the analysis of genome sequencing data from clinical samples and preclinical models. Our research areas include the discovery of biomarkers of drug response, inference of the molecular mechanisms underlying cancer evolution, early detection of cancer, and the identification of the somatic alterations predictive of response and resistance to immunotherapies. We are also interested in the application of artificial intelligence to model drug response using genomically characterized preclinical models to uncover new vulnerabilities of cancer.
Computational comparative genomics
The order Rodentia underwent an extraordinary adaptive radiation during the Cenozoic and accounts for nearly half of all known mammalian diversity containing over 2,000 species. Rodents spread over almost every landmass on earth and occupy almost all terrestrial ecosystems from rainforests, deserts, and arctic tundra. Murid rodents have a rate of chromosomal rearrangement that has been estimated to be between three times and hundreds of times faster than in primates.
For over a century, mice have been used to model human disease, leading to many fundamental discoveries about mammalian biology and the development of new therapies. Mouse genetics research has been further catalysed by a plethora of genomic resources developed in the last 20 years, including the genome sequence of C57BL/6J and more recently the first draft reference genomes for 16 additional laboratory strains. Collectively, the comparison of these genomes highlights the extreme diversity that exists at loci associated with the immune system, pathogen response, and key sensory functions, which form the foundation for dissecting phenotypic traits in vivo.
We are interested in the structure, function, and mechanisms of gene regulation in the most diverse loci in the mouse genome. The selective pressures driving diversity and CNVs includes host-pathogen coevolution (e.g., red queen hypothesis), kin selection, mating preference, and even selective sweeps due to strong positive selection. Many of these genes have direct orthologues in the human genome and are therefore important for understanding health and disease, drug development, and vaccine development.
Decoding phenotypes using single cell genomics
The Papatheodorou group develops computational approaches to unravel the molecular basis of phenotypes in health and disease at the cell type level, by integrating bulk and single-cell “omics” data of different modalities.