The University of Western Australia

UWA Staff Profile

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Michael J. Wise

Assoc/Prof Michael J. Wise

Associate Professor
Computer Science and Software Engineering

Contact details
Computer Science and Software Engineering
The University of Western Australia (M002)
35 Stirling Highway
+61 8 6488 3452
+61 8 6488 1089
Professor Michael Wise completed a double degree in Engineering and Arts and a PhD in electrical engineering at the University of New South Wales. He then worked for the University Technology, Sydney for two years before lecturing in Computer Science at the University of Sydney. Here he created computer software for use in plagiarism detection until the discovery that his programs had a secondary use in gene sequence alignment prompted him to shift his research to bioinformatics. Prof Wise was subsequently employed a Senior Research Fellow at Pembroke College in Cambridge. In 2004 he moved to The University of Western Australia, where he has an 80% appointment with the School of Biomedical, Biomolecular and Chemical Sciences and a 20% appointment with Computer Sciences.
Key research
Bioinformatics, Computational Biology, Microbial Informatics, Research/Publication Ethics
1. Michael J. Wise, ‘‘Mean Protein Evolutionary Distance: A Method for Comparative Protein
Evolution and its Application’’, PLoS One 8 (2013) (To appear).
2. Jana Sperschneider, Amitava Datta and Michael J. Wise, ‘‘Predicting Pseudoknotted Structures
Across two RNA Sequences’’, Bioinformatics 28:3058-3065 (2012).
3. Alison May Anderson, Kim W Carter, Denise Anderson and Michael J Wise, ‘‘Multi-Study
Coexpression Analysis Sheds new Light on the Susceptibility of Histone Methylation Marks to
Endocrine Disruption’’, PLoS One 7:e34158 (2012).
4. Sohini Chakrabortee, Rashmi Tripathi, Matthew Watson, Gabriele S. Kaminski Schierle, Davy
P. Kurniawan, Clemens F. Kaminski, Michael J. Wise and Alan Tunnacliffe, ‘‘Intrinsically
Disordered Proteins as Molecular Shields’’, Mol. BioSyst 8:210-219 (2012).
5. Arisa Higa, Audrey Mulot, Frdric Delom, Marion Bouchecareilh, Duc Thang Nguyn, Daniel
Boismenu, Michael J. Wise and Eric Chevet, ‘‘Role of the Pro-Oncogenic Protein Disulfide
Isomerase (PDI)-Family Member Anterior Gradient 2 (AGR2) in the Control of Endoplasmic
Reticulum Homeostasis’’, J Biol Chem 286:44855-44868 (2011).
6. Liang Wang and Michael J. Wise, ‘‘Glycogen with Short Average Chain Length Enhances
Bacterial Durability’’, Naturwissenschaften 98:719-729 (2011).
7. Jana Sperschneider, Amitava Datta and Michael J. Wise, ``Heuristic RNA Pseudoknot Prediction Including Intramolecular Kissing Hairpins'', RNA (2010) (Epub Nov. 22. doi:10.1261/rna.2394511
8. Wesley Reardon, Sohini Chakrabortee, Tiago Campos Pereira, Trevor Tyson, Matthew C Banton, Katharine M Dolan, Bridget A Culleton, Michael J Wise, Ann M Burnell and Alan Tunnacliffe, ``Expression Profiling and Cross-Species Rna Interference (RNAi) of Desiccation-Induced Transcripts in the Anhydrobiotic Nematode Aphelenchus avenae'', BMC Molecular Biology 11(6) (2010)
9. Michael J. Wise, ``Not So HoT - Heads or Tails is Not Able to Reliably Compare Multiple Sequence Alignments'', Cladistics 26:438-443 (2010)
10. Simon Bahrndorff, Alan Tunnacliffe, Michael J. Wise, Brian McGee, Martin Holmstrup and Volker Loeschcke, ``Bioinformatics and Protein Expression Analyses Implicate LEA Proteins in the Drought Response of Collembola'', Journal of Insect Physiology 55:210-217 (2009)
11. Tanya Golubchik, Michael J. Wise, Simon Easteal and Lars S. Jermiin, ``Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments'', Molecular Biology and Evolution 24:2433-2442 (2007)
12. Alan Tunnacliffe and Michael J Wise, ``The Continuing Conundrum of the LEA Proteins'', Naturwissenschaften 94:791-812 (2007)
13. Yair Benita, Michael J. Wise, Martin C. Lok, Ian Humphery-Smith and Ronald S. Oosting, ``Analysis of High-Throughput Protein Expression in Escherichia coli'', Molecular and Cellular Proteomics 5:1567-1580 (2006)
14. Maximilian J Telford, Michael J Wise and Vivek Gowri-Shankar, ``Consideration of RNA Secondary Structure Significantly Improves Likelihood-Based Estimates of Phylogeny: Examples from the Bilateria'', Molecular Biology and Evolution 22:1129-1136 (2005)
15. Michael J. Wise and Alan Tunnacliffe, ``POPP the Question: What do LEA proteins do?'', Trends in Plant Science 9:13-17 (2004)
16. Michael J. Wise, ``LEAping to Conclusions: A Computational Reanalysis of Late Embryogenesis Abundant Proteins and Their Possible Roles'', BMC Bioinformatics 4(52) (2003)
17. Yair Benita, Ronald S. Oosting, Martin C. Lok, Michael J. Wise and Ian Humphery-Smith, ``Regionalized GC Content of Template DNA as a Predictor of PCR Success'', Nucleic Acids Research 31(e99) (2003)
18. Xiao-Qin Xia and Michael J. Wise, ``DiMSim: A Discrete-Event Simulator of Metabolic Networks'', Journal of Chemical Information and Computer Science 43:1011-1019 (2003)
Roles, responsibilities and expertise
Member of UWA Academic Board and Academic Council
Industrial relevance
Prediction of protein function, particular of microbial proteins
International Society for Computational Biology
Association for Computing Machinery
Australian Society for Microbiology
Committee on Publication Ethics
Prof Wise provides lectures for pharmacy, structural biology, molecular biology and microbiology. He also lectures in computer science.
New and noteworthy
Prof Wise was Chair of the Immunisation Alliance of Western Australia from 2010 to 2016
Current projects
A/Professor Wise is primarily interested in microbial informatics. His current research projects include:
1. Discovering the function of microbial (and, sometimes, eukaryote) genes by looking at their genomic contexts: Propinquity analysis. Genes that are found close together n a genome often have related functions. This means that by looking at an unfamiliar gene in the context of the entire genome, we can make educated guesses as to what its function might be.
2. Abiotic stress tolerance, particularly desiccation and cold stress, in plants and microorganisms. Apart from the clear need to make plants more drought tolerant, there appears to be a link between durability of non-vector born bacterial pathogens (i.e. their toughness) and their pathogenicity. This is currently being explored.
3. Software for constructing phylogenetic trees. Contrary to received wisdom, adding more taxa to phylogentic trees often decreases their accuracy. This is because not enough variable gene sites remain in the data, so there is not enough information for the programs to differentiate species correctly.
Research profile
Research profile and publications

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Last updated:
Tuesday, 3 November, 2015 2:39 PM