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.Barakat A Al Suwayyid, Geoffrey W Coombs, David J Speers, Julie Pearson,
Michael J Wise and Charlene M Kahler, ‘‘Genomic Epidemiology and Population
Structure of Neisseria gonorrhoeae from Remote Highly Endemic Western
Australian Populations’’, BMC Genomics 19 (2018) (In press).

2. Liang Wang, Zhanzhong Liu, Shiyun Dai, Jiawei Yan and Michael J. Wise, ‘‘The
Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of
Durability and Virulence’’, Front Microbiol 8:2167 (2017).

3. Max Ward, Amitava Datta, Michael Wise and David H. Mathews, ‘‘Advanced
Multi-Loop Algorithms for RNA Secondary Structure Prediction Reveal that the
Simplest Model is Best’’, Nucleic Acids Res 45:8541-8550 (2017).

4. Eng-Guan Chua, Michael J. Wise, Yalda Khosravi, Shih-Wee Seow, Arlaine A.
Amoyo, Sven Pettersson, Fanny Peters, Chin-Yen Tay, Timothy T. Perkins, Mun-
Fai Loke, Barry J. Marshall and Jamuna Vadivelua, ‘‘Quantum Changes in
Helicobacter pylori Gene Expression Accompany Host-Adaptation’’, DNA Res
24:37-49 (2017).

5. Michael J. Wise, ‘‘Measuring Necessary Cladistic Information can help you
Reduce Polytomy Artefacts in Trees’’, PLoS One 11:e0166991 (2016).

6. D. T. Geddes, F. Hassiotou, M. J. Wise and P. E. Hartmann, ‘‘Human Milk
Composition and Function in the Infant’’, Fetal and Neonatal Physiology (5e), ed.
Richard Polin, Steven Abman, David Rowitch and William Benitz, pp. 273-280,
Elsevier (2016).

7. Cleo Robinson, Ian M. Dick, Michael J. Wise, Andrew Holloway, Dileepa
Diyagama, Bruce W. S. Robinson, Jenette Creaney and Richard A. Lake,
‘‘Consistent Gene Expression Profiles in MexTAg Transgenic Mouse and Wild
Type Mouse Asbestos-Induced Mesothelioma’’, BMC Cancer 15:983 (2015).

8. Amir Ariff, Michael J Wise, Charlene M Kahler, Chin Yen Tay, Fanny Peters,
Timothy T Perkins and Barbara J Chang, ‘‘Novel Moraxella catarrhalis
Prophages Display Hyperconserved Non-Structural Genes Despite their Genomic
Diversity’’, BMC Genomics 16:860 (2015).

9. Liang Wang, Ahmed Regina, Vito M. Butardo Jr., Behjat Kosar-Hashemi, Oscar
Larroque, Charlene M. Kahler and Michael J. Wise, ‘‘Influence of In Situ
Progressive N-Terminal Truncation of Glycogen Branching Enzyme in
Escherichia coli DH5a on Glycogen Structure, Accumulation, and Bacterial
Viability’’, BMC Microbiology 15:96 (2015).

10. Wei Lu, Michael J. Wise, Chin Yen Tay, Helen M. Windsor, Barry J. Marshall,
Christopher Peacock and Tim Perkins, ‘‘Comparative Analysis of the Full
Genome of Helicobacter pylori Isolate Sahul64 Identifies Genes of High
Divergence’’, J. Bacteriol. 196:1073-1083 (2014).

11. Michael J. Wise, ‘‘Mean Protein Evolutionary Distance: A Method for
Comparative Protein Evolution and its Application’’, PLoS One 8:e61276 (2013).

12. Chiara Boschetti, Alastair Crisp, Gos Micklem, Michael J. Wise and Alan
Tunnacliffe, ‘‘Anhydrobiosis: The Curious Case of the Bdelloid Rotifer’’,
Cyrobiology and Cryotechnology 59:29-34, Japan Society for Cyrobiology and
Cryotechnology (2013).

13. Jana Sperschneider, Amitava Datta and Michael J. Wise, ‘‘Predicting
Pseudoknotted Structures Across two RNA Sequences’’, Bioinformatics
28:3058-3065 (2012).

14. Alison M. Anderson, Kim W. Carter, Denise Anderson and Michael J. Wise,
‘‘Coexpression of Nuclear Receptors and Histone Methylation Modifying Genes
in the Testis: Implications for Endocrine Disruptor Modes of Action’’, PLoS One
7:e34158 (2012).

15. 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).

16. 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).

17. Liang Wang and Michael J. Wise, ‘‘Glycogen with Short Average Chain Length
Enhances Bacterial Durability’’, Naturwissenschaften 98:719-729 (2011).

18. Jana Sperschneider, Amitava Datta and Michael J. Wise, ‘‘Heuristic RNA
Pseudoknot Prediction Including Intramolecular Kissing Hairpins’’, RNA
17:27-38 (2011).
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 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

The University of Western Australia

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