Minh Duy Phan, PhD

University of Cambridge, U.K. Computer Science and Molecular Biology

EDUCATION

ABOUT ME

CURRENT RESEARCH THEMES

My research has focused on development and implementation of high-throughput functional genomics to investigate genes involved in bacterial virulence and the biology of multidrug resistance plasmids. I am one of the original inventors of the transposon directed insertion-site sequencing (TraDIS) technique at the Wellcome Trust Sanger Institute, Cambridge, UK (Genome Research) and successfully transferred the methodology to the University of Queensland, Australia, establish it as the first in Australia capable of performing this innovative technology. I have applied TraDIS to study multiple pathogens, including Salmonella Typhi and Typhimurim, uropathogenic E. coli (UPEC), Klebsiella pneumoniae and Mycobacterium tuberculosis. In UPEC, I used TraDIS to to study multiple aspects of uropathogenic E. coli virulence, including serum resistance (PLoS Genetics), zinc resistance (PNAS), capsule regulation (MBio), polymixins resistance (JAC), cefotaxime resistance (JAC), and motility (PLoS One). A focus of my recent research has been the study of multidrug resistance plasmids. My works shed lights on the genetic requirement for plasmid replication and conjugation, including IncF plasmids (PloS One), IncC plasmids (Nature Microbiology) and I-complex plasmids (PLoS Genetics). Since 2017, my research has expanded to using next-generation sequencing to understand the population genetics of Vietnamese population (Human Mutation, Scientific reports), as well as cancer genomics (BMC cancer, Frontiers in Oncology, Bioinformatics).

OTHER ACTIVITIES

  • BacPath (2011, 2013, 2015, 2017)
  • Australian Society of Microbiology (2018)
  • International Society of Plasmid Biology (2014, 2018, 2021)
  • Infectious Disease Genomics & Global Health (2013)
  • EMBO|EMBL Symposium New Approaches and Concepts in Microbiology (2013)
  • Lorne Infection and Immunity (2012)
  • Antibiotic Resistance Mechanisms – Workshop for Researchers (2007, 2008 and 2009)
  • Society for General Microbiology meeting (2008)
  • Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) 47th (2007)
  • Vietnam School of Development (2021)
  • Tan Tan University (2021)
  • Curator of the plasmid MLST schemes for IncHI1 and IncC plasmids.
  • Serve as reviewer for MGEN, mBio, Microbiology Spectrum, PLoS Neglected Tropical Diseases, J Antimicrobial Chemotherapy, Antiomicrobial Agents & Chemotherapy, BMC Infectious Diseases, Scientific Reports, PLoS One and J Infection in Developing Countries.
  • Vice-chair of Australian Society of Microbiology Queensland branch (2018 – 2020).

RESEARCH EXPERIENCE

2003
2003
B.Sc. student
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Vietnam and University of Natural Sciences, Vietnam National University, Ho Chi Minh City, Vietnam

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.
2003 - 2005
Research Assistant
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Vietnam

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.
2006
2006 - 2009
Ph.D. candidate
Wellcome Trust Sanger Institute, UK and the University of Cambridge

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.
2010
06/2010 – 01/2023
Research Fellow
Schembri Laboratory, School of Chemistry and Molecular Biosciences, UQ, Australia

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.
03/2017 - Present
Gene Solutions, Vietnam
R&D scientific advisor/Co-head of Data Department
  • 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.
2023
01/2023 - Present
Research Fellow
Schembri Laboratory, Institute for Molecular Bioscience, UQ, Australia

PUBLICATIONS

SPOT-MAS video