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1. Journal articles

Microbial genomic epidemiology

  1. Wan, Y., Gorrie, C. L., Jenney, A., Mirceta, M., & Holt, K. E. (2015). Draft genome sequence of a clinical isolate of Serratia marcescens, strain AH0650_Sm1. Genome announcements, 3(5), e01007-15.


  1. Wan, Y., Wick, R.R., Zobel, J., Ingle, D.J., Inouye, M., Holt, K.E. GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. BMC Genomics 21, 658 (2020).

  2. Chen, Q., Wan, Y., Zhang, X., Lei, Y., Zobel, J., & Verspoor, K. (2018). Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality (JDIQ), 9(3), 17.

  3. Chen, Q., Zhang, X., Wan, Y., Zobel, J. & Verspoor, K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. Journal of Computational Biology, (2018). doi:10.1089/cmb.2018.0198.

  4. Chen, Q., Wan, Y., Lei, Y., Zobel, J., & Verspoor, K. (2016, December). Evaluation of CD-HIT for constructing non-redundant databases. In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on. (pp. 703-706). IEEE.

2. Conference or workshop presentations

Microbial genomic epidemiology

  1. Wan Y., Wick R., Ingle D., Inouye M., Zobel J., Holt K. poster presentation [POA-341]: Network analysis of bacterial genes to predict horizontal co-transfer and mobile genetic elements. SMBE2018 Conference, Yokohama, Japan. 8–12 Jul 2018.
  2. Wan Y., Wick R., Ingle D., Inouye M., Zobel J., Holt K. 10-minute oral presentation: A network approach for detecting horizontal co-transfer of antimicrobial resistance genes in bacteria. ABACBS-2018 Conference, Parkville, VIC, Australia. 27–28 Nov 2018.


  1. Wan Y., Joo E., Jung C. Poster presentation: Integrative analysis of DNA methylation and gene expression in breast cancer. ABiC 2014 Conference, Parkville, VIC, Australia. 11–12 Oct 2014.
  2. Wan Y. A comparison of three approaches to prokaryotic genome annotation. MESB19 course, Gothenburg, Sweden, 25–29 Aug 2019. DOI: 10.13140/RG.2.2.21120.79365.

3. Doctor of Philosophy


Wan, Y. Detecting horizontal co-transfer of antimicrobial resistance genes in bacteria: a network approach. (The University of Melbourne, 2019).

This is the final version of my PhD thesis, which was submitted to the University of Melbourne on 9 August 2019.


I presented the work for my thesis on Friday 17 August 2018 in Bio21 Institute to the Department of Biochemistry and Molecular Biology in which I enrolled. A poster of the oration can be accessed via this link.