Comparative analysis of transcriptomic and translatomic responses to viral infection in human and mosquito cells
Supervisors
Juana Díez
UPF, 1st supervisor
Manuel Irimia
CRG, 2nd supervisor
Objectives
To investigate how viral codon usage patterns predict host-cell responses and adaptation. The project will focus on coronaviruses and other viruses, exploring whether viral codon enrichment links to virus-induced cell stress pathways, and developing tools to anticipate the evolution and impact of emerging viruses
Methodology
The student will perform a large-scale computational analysis of codon usage across all human virus genomes. This will involve comparative transcriptomics, genomics, and translatomics analyses, calculating standard codon usage metrics and examining compositional features such as dinucleotide usage. These signatures will be analyzed in a phylogenetic framework to identify evolutionary shifts. The student will also have the opportunity to validate computational predictions experimentally in cell culture by testing infectivity, cellular responses, and translation efficiency of viruses with distinct codon profiles.
Required Skills
A background in virology, RNA biology, or evolutionary biology is required. Substantial experience in computational methods is recommended, including familiarity with command line tools and some programming language (e.g., python). Some familiarity with phylogenetic methods is encouraged. We are particularly interested in candidates with a creative and open scientific mindset, and who value a collaborative approach to research.
Expected Results
The project is expected to open a new view in virus evolution, defining codon usage signatures of viral adaptation, revealing convergent evolution across virus families, identifying predictive models linking codon bias to host responses. It will also help understand why different viruses give rise to different infection outcomes.
Planned Secondments
GIMM (Morais) in year 2 (2 months) to receive training on software for high-level transcriptomic analyses and
statistical methods.
CNRS (Walczak) in year 3 (1 month) to build models on DC’s data.
UCD (Teeling) in year 3 (1 week) to learn about bat immune research, and bat’s exceptional viral responses.
Enrolment in doctoral programs
PhD in Biomedicine from Universitat Pompeu Fabra
References
Muscolino, E and Díez J. Viral Codon Usage and the Host Transfer RNA. Annu Rev Virol. 2025. doi: 10.1146/annurev-virology-092623-105418. Epub 2025 Apr 23.