Computational tools for molecular epidemiology and computational genomics of Neisseria meningitidis

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dc.contributor.author Katz, Lee Scott en_US
dc.date.accessioned 2012-02-17T19:25:35Z
dc.date.available 2012-02-17T19:25:35Z
dc.date.issued 2010-11-17 en_US
dc.identifier.uri http://hdl.handle.net/1853/42934
dc.description.abstract Neisseria meningitidis is a gram negative, and sometimes encapsulated, diplococcus that causes devastating disease worldwide. For the worldwide genetic surveillance of N. meningitidis, the gold standard for profiling the bacterium uses genetic loci found around the genome. Unfortunately, the software for analyzing the data for these profiles is difficult to use for a variety of reasons. This thesis shows my suite of tools called the Meningococcus Genome Informatics Platform for the analysis of these profiling data. To better understand N. meningitidis, the CDC Meningitis Laboratory and other world class laboratories have adopted a whole genome approach. To facilitate this approach, I have developed a computational genomics assembly and annotation pipeline called the CG-Pipeline. It assembles a genome, predicts locations of various features, and then annotates those features. Next, I developed a comparative genomics browser and database called NBase. Using CG-Pipeline and NBase, I addressed two open questions in N. meningitidis research. First, there are N. meningitidis isolates that cause disease but many that do not cause disease. What is the genomic basis of disease associated versus asymptomatically carried isolates of N. meningitidis? Second, some isolates' capsule type cannot be easily determined. Since isolates are grouped into one of many serogroups based on this capsule, which aids in epidemiological studies and public health response to N. meningitidis, often an isolate cannot be grouped. Thus the question is what is the genomic basis of nongroupability? This thesis addresses both of these questions on a whole genome level. en_US
dc.publisher Georgia Institute of Technology en_US
dc.subject Meningitis en_US
dc.subject SNP en_US
dc.subject Genome en_US
dc.subject Typing en_US
dc.subject Recombination en_US
dc.subject Iinfluenza en_US
dc.subject Bioinformatics en_US
dc.subject Applied bioinformatics en_US
dc.subject Serogroup en_US
dc.subject ST en_US
dc.subject Sequencing projects en_US
dc.subject MLST en_US
dc.subject.lcsh Epidemiology
dc.subject.lcsh Molecular epidemiology
dc.subject.lcsh Genomes
dc.subject.lcsh Genomics
dc.title Computational tools for molecular epidemiology and computational genomics of Neisseria meningitidis en_US
dc.type Dissertation en_US
dc.description.degree PhD en_US
dc.contributor.department Biology en_US
dc.description.advisor Committee Chair: Jordan, I. King; Committee Co-Chair: Mayer, Leonard; Committee Member: Bergman, Nicholas; Committee Member: Choi, Jung; Committee Member: Weitz, Joshua en_US


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