The University of Western Australia
Professor Michael Wise
Professor
Contact details
| Address | Biochemistry and Molecular Biology The University of Western Australia (M310) 35 Stirling Highway CRAWLEY WA 6009 Australia |
|---|---|
| Phone | 6488 4410 / 9346 4869 |
| Fax | 6488 1148 |
| michael.wise@uwa.edu.au | |
| Personal homepage | http://www.pam1.bcs.uwa.edu.au/~michaelw |
Location
Room 209, Molecular and Chemical Sciences Building, Crawley campus
Biography
Associate 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. A/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. He combines his academic and political interests in his role as Deputy Chair of The Immunisation Alliance of WA.
Key research
- Bioinformatics, Computational Biology, Systems Biology
Major research interests
- Aggregation-prone proteins
- Bioinformatics of anhydrobiosis in plants, animals and microfauna
- Evaluation of bioinformatics methodologies
- Low complexity/natively unfolded proteins
- Microbial informatics
Qualifications
BA BEng PhD N.S.W.
Publications
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)
Alan Tunnacliffe and Michael J Wise, ‘‘The Continuing Conundrum of the LEA Proteins’’, Naturwissenschaften 94:791-812 (2007) (IF 2.0; ISI Citations 2).
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)
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)
Michael J. Wise and Alan Tunnacliffe, ‘‘POPP the Question: What do LEA proteins do?’’, Trends in Plant Science 9:13-17 (2004)
Michael J. Wise, ‘‘LEAping to Conclusions: A Computational Reanalysis of Late Embryogenesis Abundant Proteins and Their Possible Roles’’, BMC Bioinformatics 4(52) (2003)
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)
Michael J. Wise, ‘‘Alignment Algorithms Revisited: Alignment Algorithms for Use in Low Similarity Protein Comparisons’’, European Control Conference, Cambridge, U.K. (September 1-4, 2003).
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)
Michael J. Wise, ‘‘The POPPs: Clustering and Searching Using Peptide Probability Profiles’’, Bioinformatics S18:38-45 (2002) (IF 5.7; ISI Citations 6).
John M. Kenney, David Knight, Michael J. Wise and Fritz Vollrath, ‘‘Amyloidogenic Nature of Spider Silk’’, European Journal of Biochemistry 269:4159-4163 (2002)
Michael J. Wise, ‘‘0j.py: A Software Tool for Low Complexity Proteins and Protein Domains’’, Bioinformatics S17:288-295 (2001)
Michael J. Wise and A. Mark Osborn, ‘‘TRUFFLER: Programs to Study Microbial Community Composition and Flux from Fluorescent DNA Fingerprinting Data’’, 2nd IEEE
International Symposium on Bioinformatics and Bioengineering, Bethesda, MD, U.S.A.:129-135 (November 4-6, 2001) (ISI Citations 1).
Michael J. Wise, ‘‘Protein Annotators’ Assistant’’, Trends in Biochemical Sciences 25(5):252-253 (May 2000)
Michael J. Wise, ‘‘Protein Annotators’ Assistant: A Novel Application of Information Retrieval Techniques’’, Journal of the American Society for Information Science (JASIS)
51(12):1131-1136, John Wiley (October 2000)
Peter A. Meric and Michael J. Wise, ‘‘Quantitative, Scalable Discrete-Event Simulation of Metabolic Pathways’’, Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB’99), Heidelberg, Germany, ed. Thomas Lengauer, Reinhard Schneider, Peer Bork et al:187-194, AAAI Press (August 6-10, 1999).
Michael J. Wise, Tim Littlejohn and Ian Humphery-Smith, ‘‘Better Cutters for Protein Mass Fingerprinting: Preliminary Findings’’, Fifth International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece:340-343, AAAI Press (June 21-25, 1997).
Michael J. Wise, Tim Littlejohn and Ian Humphery-Smith, ‘‘Peptide-mass Fingerprinting and the Ideal Covering Set for Protein Characterisation’’, Electrophoresis 18(8):1399-1409 (1997)
Michael J Wise, ‘‘Neweyes: A System for Comparing Biological Sequences Using the Running Karp-Rabin Greedy String-Tiling Algorithm’’, Third International Conference on
Intelligent Systems for Molecular Biology, Cambridge, England., ed. Christopher Rawlings, Dominic Clark, Russ Altman et. al.:393−401, AAAI Press (July 16-19, 1995).
Alan Tunnacliffe and Michael J Wise, ‘‘The Continuing Conundrum of the LEA Proteins’’, Naturwissenschaften 94:791-812 (2007) (IF 2.0; ISI Citations 2).
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)
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)
Michael J. Wise and Alan Tunnacliffe, ‘‘POPP the Question: What do LEA proteins do?’’, Trends in Plant Science 9:13-17 (2004)
Michael J. Wise, ‘‘LEAping to Conclusions: A Computational Reanalysis of Late Embryogenesis Abundant Proteins and Their Possible Roles’’, BMC Bioinformatics 4(52) (2003)
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)
Michael J. Wise, ‘‘Alignment Algorithms Revisited: Alignment Algorithms for Use in Low Similarity Protein Comparisons’’, European Control Conference, Cambridge, U.K. (September 1-4, 2003).
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)
Michael J. Wise, ‘‘The POPPs: Clustering and Searching Using Peptide Probability Profiles’’, Bioinformatics S18:38-45 (2002) (IF 5.7; ISI Citations 6).
John M. Kenney, David Knight, Michael J. Wise and Fritz Vollrath, ‘‘Amyloidogenic Nature of Spider Silk’’, European Journal of Biochemistry 269:4159-4163 (2002)
Michael J. Wise, ‘‘0j.py: A Software Tool for Low Complexity Proteins and Protein Domains’’, Bioinformatics S17:288-295 (2001)
Michael J. Wise and A. Mark Osborn, ‘‘TRUFFLER: Programs to Study Microbial Community Composition and Flux from Fluorescent DNA Fingerprinting Data’’, 2nd IEEE
International Symposium on Bioinformatics and Bioengineering, Bethesda, MD, U.S.A.:129-135 (November 4-6, 2001) (ISI Citations 1).
Michael J. Wise, ‘‘Protein Annotators’ Assistant’’, Trends in Biochemical Sciences 25(5):252-253 (May 2000)
Michael J. Wise, ‘‘Protein Annotators’ Assistant: A Novel Application of Information Retrieval Techniques’’, Journal of the American Society for Information Science (JASIS)
51(12):1131-1136, John Wiley (October 2000)
Peter A. Meric and Michael J. Wise, ‘‘Quantitative, Scalable Discrete-Event Simulation of Metabolic Pathways’’, Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB’99), Heidelberg, Germany, ed. Thomas Lengauer, Reinhard Schneider, Peer Bork et al:187-194, AAAI Press (August 6-10, 1999).
Michael J. Wise, Tim Littlejohn and Ian Humphery-Smith, ‘‘Better Cutters for Protein Mass Fingerprinting: Preliminary Findings’’, Fifth International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece:340-343, AAAI Press (June 21-25, 1997).
Michael J. Wise, Tim Littlejohn and Ian Humphery-Smith, ‘‘Peptide-mass Fingerprinting and the Ideal Covering Set for Protein Characterisation’’, Electrophoresis 18(8):1399-1409 (1997)
Michael J Wise, ‘‘Neweyes: A System for Comparing Biological Sequences Using the Running Karp-Rabin Greedy String-Tiling Algorithm’’, Third International Conference on
Intelligent Systems for Molecular Biology, Cambridge, England., ed. Christopher Rawlings, Dominic Clark, Russ Altman et. al.:393−401, AAAI Press (July 16-19, 1995).
Future research
Simulation of metabolic and general reaction pathway networks; analysis of low complexity/natively unfolded proteins; keyword clusting of proteins
Industrial relevance
In silico toxicology; prediction of protein function
Memberships
International Society for Computational Biology
Assocation for Computing Machinery
Assocation for Computing Machinery
Teaching
A/Prof Wise guest lectures for pharmacy, structural biology, molecular biology, genetics and microbiology. His primary teaching commitments are:
CITS3200 Professional Computing (Unit Co-ordinator)
SCIE2203 Bioinformatics (Crawley and Singapore Campus)
MICR8838 Research Project
CITS3200 Professional Computing (Unit Co-ordinator)
SCIE2203 Bioinformatics (Crawley and Singapore Campus)
MICR8838 Research Project
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.
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
