ETD

Archivio digitale delle tesi discusse presso l'Università di Pisa

Tesi etd-05042017-115310


Tipo di tesi
Tesi di dottorato di ricerca
Autore
BARUCCO, MARA
URN
etd-05042017-115310
Titolo
Measuring genomic variations associated with bacterial population structure
Settore scientifico disciplinare
FIS/03
Corso di studi
FISICA
Relatori
tutor Prof. Leporini, Dino
relatore Dott. Muzzi, Alessandro
Parole chiave
  • meningo
  • GWAS
  • GBS
  • clustering methods
  • bacterial population
  • NTHi
  • whole genome sequencing
Data inizio appello
01/06/2017
Consultabilità
Completa
Riassunto
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.
In this context is inserted my PhD thesis work: in the necessity of evaluate and quantify
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.
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