Phylogenomics of recombinant bacteria

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• Nick Goldman, EMBL-European Bioinformatics Institute
• Tuesday 06 February 2018, 13:00-14:00
• MR3 Centre for Mathematical Sciences.

If you have a question about this talk, please contact Dr Vivien Gruar.

This talk has been canceled/deleted

Recombination helps bacteria survive and adapt to a changing environment, for example allowing bacteria to quickly acquire antimicrobial resistance. Recombination also confounds and complicates the reconstruction of bacterial evolution using phylogenetics, because it causes different genes to have different evolutionary histories.

Within this project students will be able to pursue any of the following aims:

• Reconstructing the evolutionary and epidemiological history of highly recombining bacterial human pathogens (e.g. N. gonorrhoeae and H. pylori) using different phylogenetic methods (both bacterial-specific and non) to account for recombination, and using new large genomic datasets.

• Simulating recombinant bacterial evolution to test the efficiency of different evolutionary models and phylogenetic methods.

• Developing new models and algorithm for reconstructing the evolutionary history of highly-recombinant bacteria from genomic datasets, in particular based on hidden Markov models.

Some of these tasks require interest in the evolutionary history and epidemiology of bacteria, and the ability to work with large datasets and several different software distributions; other tasks require ability to code (different languages might work, such as C++, python, or Java), problem solving, and some basic mathematical concepts (preferably from probability and statistics) and skills.

This talk is part of the Cambridge Mathematics Placements Seminars series.

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