Wee Wei Yee, Gavin

Assistant Lecturer
School of Science

wee.weiyee@monash.edu
+603 5514 5619
Room 4-8-26
https://orcid.org/0000-0001-8965-0680

Dr Wei Yee Wee received his B.Sc. in Bioinformatics from Multimedia University (MMU) in 2012. After graduation, he continue with his Ph.D in Bioinformatics in University of Malaya and continue to work as Post Doctoral Research Fellow under Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya after he gained his Ph.D. He has gained many years of experience in the field of bioinformatics research. Currently, he is an assistant lecturer in the School of Sciences and engages in education and research through contribution to multidisciplinary research projects, research funding and research publication in ISI Journals. He has a proven record in publication and published around 24 high impact papers since 2012. He has also take part in setup, design, establishment and maintenance of new bioinformatics laboratory.

Dr Wei Yee Wee has been involved in variety of Next Generation Sequencing (NGS) projects such as whole genome and transcriptome analysis on eukaryotic genomes, bacteria genome and metagenomics. He is familiar with Bioinformatics analysis such as genome assembly, genome annotation, genes comparative study, identification of SNP variants and prediction on the effect of the SNP variants, differential gene expression analysis, pan-genome analysis, phylogenetic tree analysis, prophage identification. He also develop useful Bioinformatics tools and pipelines such as the Pairwise Genome Comparison (PGC) and the Pathogenomics Profilling Tool (PathoProT). PGC is a bioinformatics tool which allow user to perform pairwise genome alignment and visualize the alignment in a circular layout and PathoProT allow user to screen for virulence genes in the genome. These 2 tools have been implemented and integrated into few published database such as VibrioBase and HelicoBase.

Dr Wei Yee Wee current research projects are the whole genome analysis of Mycobacterium cosmeticum and transcriptomic analysis of Bosenbergia rotunda.

Qualifications

  • Doctor of Philosophy, University of Malaya, 2016
  • Bachelor of Science (Honours) in Bioinformatics, Multimedia University (MMU), 2012

Expertise

  • Bioinformatics

Research Interests

Bioinformatics related research project. I am interest in variety of Next Generation Sequencing (NGS) projects such as whole genome and transcriptome analysis on eukaryotic genomes, bacteria genome and metagenomics. Bioinformatics analysis such as genome assembly, genome annotation, genes comparative study, identification of SNP variants and prediction on the effect of the SNP variants, differential gene expression analysis, pan-genome analysis, phylogenetic tree analysis, prophage identification will able to further characterize and unveil more novel biological knowledge by using just dry lab instead of wet lab. I am also interest in develop Bioinformatics tools and pipelines which will allow researcher without Bioinformatics knowledge to have a chance to perform Bioinformatics analysis easily.

Teaching

  • BIO1011 Biology 1

Scholarly Journals

Wee, W. Y., Dutta, A., & Choo, S. W. (2017). Comparative genome analyses of mycobacteria give better insights into their evolution. PloS one, 12(3), e0172831.

Choo, S. W., Rayko, M., Tan, T. K., Hari, R., Komissarov, A., Wee, W. Y., ... & Wilson, R. K. (2016). Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research, 26(10), 1312-1322.

Wee, W. Y., Ang, M. Y., Dutta, A., Dymock, D., Paterson, I. C., & Choo, S. W. (2016). Comparative Genome Analysis of Fusobacterium nucleatum. Genome Biology and Evolution, 8(9), 2928-2938.

Wee, W. Y., Tan, T. K., Jakubovics, N. S., & Choo, S.W. (2016). Whole-genome sequencing and comparative analysis of Mycobacterium brisbanense reveals a possible soil origin and capability in fertiliser synthesis. PLOS ONE.

Choo, S.W., Dutta, A., Wong, G. J., Wee, W. Y., Ang, M. Y., & Siow, C.C. (2016). Comparative genomic analysis reveals a possible novel Non-Tuberculous Mycobacterium species with high pathogenic potential. PLOS ONE.

Yusoff, A.M., Tan, T. K., Hari, R, Koepfli, K.P., Wee, W. Y., Antunes, A., Sitam, F.T., … & Choo, S.W. (2016). De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. Scientific Reports.

Tan, S. Y., Dutta, A., Jakubovics, N. S., Ang, M. Y., Siow, C. C., Mutha, N. V., Wee, W. Y.,...& Choo, S. W. (2015). YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. BMC bioinformatics, 16(1), 1.

Teo, W. F. A., Wee, W. Y., Choo, S. W., & Tan, G. Y. A. (2015). Draft genome sequence of a marine actinobacteria Sciscionella strain SE31. Marine genomics, 20, 11-12.

Tan, M. F., Siow, C. C., Dutta, A., Mutha, N. V., Wee, W. Y., Heydari, H., ... & Choo, S. W. (2015). Development of ListeriaBase and comparative analysis of Listeria monocytogenes. BMC genomics, 16(1), 1.

Choo, S. W., Ang, M. Y., Dutta, A., Tan, S. Y., Siow, C. C., Heydari, H., Wee, W. Y.,  ... & Wong, G. J. (2015). MycoCAP-Mycobacterium Comparative Analysis Platform. Scientific reports, 5.

Heydari, H., Siow, C. C., Tan, M. F., Jakubovics, N. S., Wee, W. Y., Mutha, N. V., ... & Choo, S. W. (2014). CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips. PloS one, 9(1), e86318.

Heydari, H., Mutha, N. V., Mahmud, M. I., Siow, C. C., Wee, W. Y., Wong, G. J., ... & Choo, S. W. (2014). StaphyloBase: a specialized genomic resource for the staphylococcal research community. Database, 2014, bau010.

Choo, S. W., Wee, W. Y., Ngeow, Y. F., Mitchell, W., Tan, J. L., Wong, G. J., ... & Xiao, J. (2014). Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential. Scientific reports, 4.

Choo, S. W., Ang, M. Y., Fouladi, H., Tan, S. Y., Siow, C. C., Mutha, N. V., Wee, W. Y.,  ... & Rehvathy, V. (2014). HelicoBase: a Helicobacter genomic resource and analysis platform. BMC genomic s, 15(1), 1.

Ang, M. Y., Heydari, H., Jakubovics, N. S., Mahmud, M. I., Dutta, A., Wee, W. Y., ...& Choo, S. W. (2014). FusoBase: an online Fusobacterium comparative genomic analysis platform. Database, 2014, bau082.

Choo, S. W., Heydari, H., Tan, T. K., Siow, C. C., Beh, C. Y., Wee, W. Y., ... & Yazdi, A. H. (2014). VibrioBase: a model for next-generation genome and annotation database development. The Scientific World Journal, 2014.

Tan, J. L., Ngeow, Y. F., Wee, W. Y., Wong, G. J., Ng, H. F., & Choo, S. W. (2014). Comparative genomic analysis of Mycobacterium iranicum UM_TJL against representative mycobacterial species suggests its environmental origin. Scientific reports, 4.

Khosravi, Y., Rehvathy, V., Wee, W. Y., Wang, S., Baybayan, P., Singh, S., ...& Choo, S. W. (2013). Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives. Gut pathogens, 5(1), 1.

Wee, W. Y., Heydari, H., Lokanathan, N., Hari, R., Yusoff, A. M., Beh, C. Y., ...& Choo, S. W. (2013). MabsBase: a Mycobacterium abscessus genome and annotation database. PloS one, 8(4), e62443.

Ngeow, Y. F., Leong, M. L., Wong, Y. L., Wong, G. J., Tan, J. L., Wee, W. Y., ... & Choo, S. W. (2013). Draft Genome Sequence of Mycobacterium massiliense Strain M159, Showing Phenotypic Resistance to β-Lactam and Tetracycline Antibiotics. Genome announcements, 1(4), e00669-13.

Tan, J. L., Ng, H. F., Wee, W. Y., Ang, M. Y., Wong, G. J., Ngeow, Y. F., & Choo, S. W. (2013). First whole-genome sequence of Mycobacterium iranicum, a newly reported mycobacterial species. Genome announcements, 1(5), e00732-13.

Choo, S. W., Yusoff, A. M., Wong, Y. L., Wee, W. Y., Ong, C. S., Ng, K. P., & Ngeow, Y. F. (2012). Genome analysis of Mycobacterium massiliense strain M172, which contains a putative mycobacteriophage. Journal of bacteriology, 194(18), 5128-5128.

Ngeow, Y. F., Wee, W. Y., Wong, Y. L., Tan, J. L., Ongi, C. S., Ng, K. P., & Choo, S. W. (2012). Genomic analysis of Mycobacterium abscessus strain M139, which has an ambiguous subspecies taxonomic position. Journal of bacteriology, 194(21), 6002-6003.

Research Grants

  • Wee, WY., Jakubovics, NS., 2018, Extracellular DNA as a Target for Oral Biofilm Control, Monash Mobility Grant, RM20k
  • Ayub, Q., Chow, SC., Philips, ME., Wee, WY., Lian, YLA., 2018, Host-Pathogen Genetics In Orang Asli Individuals Infected With Intestinal Nematodes, FRGS Grant.

Postgraduate (Present)

  1. Mohanambal Moorthy (with A/Prof Uma Palanisamy)
  2. Lee Da Yi
  3. Mainul Hasan Sarker (with Dr Song Beng Kah)

Honours (present)

  1. Shusruto Rishik

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