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Next-generation sequencing technology enables routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens. However, few whole genome sequencing-based genotyping pipelines are available for practical applications. Here, we present the whole genome sequencing-based single nucleotide polymorphism (SNP) genotyping method and apply to the evolutionary analysis of methicillin-resistant Staphylococcus aureus. The SNP genotyping method calls genome variants using next-generation sequencing reads of whole genomes and calculates the pair-wise Jaccard distances of the genome variants. The method may reveal the high-resolution whole genome SNP profiles and the structural variants of different isolates of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) strains. The phylogenetic analysis of whole genomes and particular regions may monitor and track the evolution and the transmission dynamic of bacterial pathogens. The computer programs of the whole genome sequencing-based SNP genotyping method are available to the public at https://github.com/cyinbox/NGS.
We calculate the mutual information function for each of the 24 chromosomes in the human genome. The same correlation pattern is observed regardless the individual functional features of each chromosome. Moreover, correlations of different scale leng
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure. A signifi
The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the
Anti-staphylococcal penicillins (ASPs) are recommended as first-line agents in methicillin-susceptible Staphylococcus aureus (MSSA) bacteraemia. Concerns about their safety profile have contributed to the increased use of cefazolin. The comparative c
The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China