B.Sc. Project: Evaluation of TNFa -238 and -308 polymorphisms frequency in Vietnamese population

• PCR-RFLP to detect SNPs at nucleotide positions –238 and – 308 in the promoter region of human TNF-α gene that involve in immunity against infectious diseases including typhoid fever and malaria.

Molecular Detection of Drug Resistance in Mycobacterium tuberculosis

• Biohazard Category 3 containment experience, subbing, archiving and extracting DNA
  from M. tb cultures routinely.
• Molecular typing (spoligotyping) of M. tb.
• Used sequencing to discover resistant mutants against TB first line drugs (rifampicin and
  isoniazid) and fluoroquinolones.

Thesis Title: Analysis of IncHI1 plasmids in Salmonella enterica serovar Typhi

• Set up Plasmid Multi-Locus Sequence Typing for IncHI1 plasmids
• Transposon Directed Illumina Sequencing (TraDIS - Transposon mutant library combined with Illumina sequencing) using 1.1 million mutant library to identify genetic elements contributing to the stability of IncHI1 plasmids in S. Typhi.
• Site-specific mutagenesis (using suicide vector) to generate knock-out mutants that de-stabilise IncHI1 plasmids.
• Used phenotype arrays and gene expression arrays to identify the effect of different IncHI1 plasmids on S. Typhi phenotypes and their global gene expression.

Antibiotic resistance, Plasmid biology and Virulence of uropathogenic E. coli

Responsibilities: Leading and managing research projects, analyzing research data, writing manuscripts and supervising students.

Skills:

• Analysis of whole genome sequences and other big biological datasets.
• Targeted mutagenesis of clinical UPEC isolates using lambda-red recombinase.
• Transposon directed insertion-site sequencing (TraDIS).
• Illumina and Nanopore sequencing platforms.
• RNA sequencing.
• Urinary tract infection mouse models: C57BL/6 and C3H/HeJ.
• Confocal and fluorescent microscopy.
• Phenotypic assays relevant to characterized uropathogens.

• Development and implement of bioinformatic pipelines for commercial services.
• Supporting R&D activities including study design, manuscript writing and publication.
• Consultation on building a data science team for R&D.
• Hardware and software consultation for high-throughput data analysis.