Therefore, phylogenetic inference based on the structure of phage virion proteins may provide a deeper insight into their evolutionary history. Currently, the methods for structure-guided phylogeny are not well developed. The purpose of this project is to optimize the method for maximum likelihood phylogenetic inference on protein structure and use it to reveal new evolutionary connections within tailed phages. The work will involve general bioinformatics methods, including bash-scripting, database search tools, multiple sequence alignment tools and phylogenetic software. The candidate will gain extensive theoretical background and practical skills to work in the field of evolutionary biology.
Recommended literature:
- Weinheimer AR, Ha AD, Aylward FO. Towards a unifying phylogenomic framework for tailed phages. PLoS Genet. 2025 Feb 5;21(2):e1011595. doi: 10.1371/journal.pgen.1011595. PMID: 39908317; PMCID: PMC11835377.
- Mifsud JCO, Suchard MA, Holmes EC, Lemey P. Recent advances in the inference of deep viral evolutionary history. J Virol. 2025 Sep 23;99(9):e0029225. doi: 10.1128/jvi.00292-25. Epub 2025 Aug 22. PMID: 40844272; PMCID: PMC12456133.
- Ng WM, Stelfox AJ, Bowden TA. Unraveling virus relationships by structure-based phylogenetic classification. Virus Evol. 2020 Feb 12;6(1):veaa003. doi: 10.1093/ve/veaa003. PMID: 32064119; PMCID: PMC7015158.
- Moi D, Bernard C, Steinegger M, Nevers Y, Langleib M, Dessimoz C. Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses. Nat Struct Mol Biol. 2025 Oct 10. doi: 10.1038/s41594-025-01649-8. Epub ahead of print. PMID: 41073779.
Research area: Structural biology, virology
Keywords: Tailed bacteriophages; Viral evolution; Structural phylogeny; Protein fold conservation; Structure-guided classification
Funding of the PhD candidate:
The student will be supported by the ERC consolidator grant Phage infection of bacterial biofilm (101043452). In the academic year 2026/27 the net income of the CEITEC PhD School student is expected to be at least CZK 29,400 (approx. EUR 1215)
Requirements for candidate:
The prospective student should be interested in learning techniques of structural phylogeny. Previous experience with molecular biology, programming, scripting, and data analyses is a plus.
Start date: February 2027 or sooner
Sign-up link: https://www.ceitec.eu/structure-guided-phylogeny-of-tailed-bacteriophages/t11641
Where to apply
Website: https://www.ceitec.eu/structure-guided-phylogeny-of-tailed-bacteriophages/t11641
Work Location(s)
Number of offers available: 1
Company/Institute: CEITEC MU
Country: Czech Republic
City: Brno
Postal Code: 625 00
Street: Kamenice 753/5
