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1. Journal articles

  1. Wan Y., Mills E., Leung R.C.Y., Vieira A., Zhi X., Croucher N.J., Woodford N., Jauneikaite E., Ellington M.J., Sriskandan S. (2021). Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microbial Genomics. 2021;7(12). DOI: 10.1099/mgen.0.000702.

  2. Boonyasiri A., Myall A.C., Wan Y., Bolt F., Ledda A., Mookerjee S., Weiße A.Y., Turton J.F., Abbas H., Prakapaite R., Sabnis A., Abdolrasouli A., Malpartida-Cardenas K., Miglietta L., Donaldson H., Gilchrist M., Hopkins K.L., Ellington M.J., Otter J.A., Larrouy-Maumus G., Edwards A.M., Rodriguez-Manzano J., Didelot X., Barahona M., Holmes A.H., Jauneikaite E., Davies F. (2021). Integrated patient network and genomic plasmid analysis reveal a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. medRxiv 2021.10.28.21265436. DOI: 10.1101/2021.10.28.21265436. (Note: A. B., A.C. M., and Y. W. are co-first authors.)

  3. Myall A.C., Peach R.L., Wan Y., Mookerjee S., Jauneikaite E., Bolt F., Price J.R., Davies F., Wiesse A.Y., Holmes A., Barahona M. (2021). Characterising contact in disease outbreaks via a network model of spatial-temporal proximity. medRxiv DOI: 2021.04.07.21254497.

  4. Wan, Y., Wick, R.R., Zobel, J., Ingle, D.J., Inouye, M., Holt, K.E (2020). 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). DOI: 10.1186/s12864-020-07019-6.

  5. 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.

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

  7. Chen, Q., Zhang, X., Wan, Y., Zobel, J., & Verspoor, K. (2017). Sequence Clustering Methods and Completeness of Biological Database Search. In BAI@ IJCAI (pp. 8-14).

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

  9. 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.

2. Conference or workshop presentations

  1. Wan Y., Mills E., Leung R.C.Y., Vieira A., Jauneikaite E., Zhi X., Croucher N.J., Woodford N., Ellington M.J., Sriskandan S. Poster [P002]: Nitrofurantoin-resistant Escherichia coli in the UK: genetic basis, diversity, and undetected occurrences. Annual Conference Online 2021. 26 Apr 2021. London, UK. Microbial Society.
  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.
  3. Wan Y., Wick R., Ingle D., Inouye M., Zobel J., Holt K. poster [POA-341]: Network analysis of bacterial genes to predict horizontal co-transfer and mobile genetic elements. SMBE2018 Conference, Yokohama, Japan. 8–12 Jul 2018.
  4. 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.
  5. 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.