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Tesi etd-05042017-115310


Thesis type
Tesi di dottorato di ricerca
Author
BARUCCO, MARA
URN
etd-05042017-115310
Title
Measuring genomic variations associated with bacterial population structure
Settore scientifico disciplinare
FIS/03
Corso di studi
FISICA
Commissione
tutor Prof. Leporini, Dino
relatore Dott. Muzzi, Alessandro
Parole chiave
  • GWAS
  • whole genome sequencing
  • GBS
  • NTHi
  • meningo
  • bacterial population
  • clustering methods
Data inizio appello
01/06/2017;
Consultabilità
parziale
Data di rilascio
01/06/2020
Riassunto analitico
This PhD thesis work is fruit of a collaboration between the Department of Physics “Enrico Fermi” of the University of Pisa and the gsk Vaccines Center in Siena - GSK Vaccines, Siena. It falls within the context of bacterial population genomics, with a particular interest in applications to species able to cause severe diseases such as meningitis.<br>In this context is inserted my PhD thesis work: in the necessity of evaluate and quantify<br>variations among bacterial genomes belonging to the same species in order to analyse and reconstruct the population structure of that species. During my PhD I developed a pipeline that can measure polymorphisms mutation rates, on a whole genome level, for big datasets of genomes (up to 4000 genomes). On the basis of these rates it is possible to reconstruct phylogenetic trees of the species, to observe recombination event among strains and to perform studies of association between genomic features and phenotypical or epidemiological classifications<br>
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