• The University of Western Australia (M002), 35 Stirling Highway,

    6009 Perth

    Australia

Accepting PhD Students

  • 1828 Citations
  • 15 h-Index
20012019
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Research Output 2001 2019

  • 1828 Citations
  • 15 h-Index
  • 43 Article
  • 3 Review article
  • 2 Conference paper
  • 1 Chapter
2019
Helicobacter
Western Australia
Helicobacter pylori
Breath Tests
Urea
Open Access
Metronidazole
Helicobacter pylori
Proteins
biotin carboxylase
Sequence Alignment

An updated view on bacterial glycogen structure

Wang, L. & Wise, M. J., 1 Jan 2019, In : Microbiology Australia. 40, 4, p. 195-199 5 p.

Research output: Contribution to journalReview article

Open Access
Bacterial Structures
Glycogen
Bacterial Physiological Phenomena
Vibrio cholerae
Mycobacterium tuberculosis
4 Citations (Scopus)

Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

Wang, L., Liu, Q., Wu, X., Huang, Y., Wise, M. J., Liu, Z., Wang, W., Hu, J. & Wang, C., 1 Dec 2019, In : Scientific Reports. 9, 1, 1034.

Research output: Contribution to journalArticle

Open Access
Archaea
Computational Biology
Energy Metabolism
Polyhydroxyalkanoates
Polyphosphates

Determining parameters for non-linear models of multi-loop free energy change

Ward-Graham, M., Sun, H., Datta, A., Wise, M. J. & Mathews, D., 1 Nov 2019, In : Bioinformatics. 35, 21, p. 4298-4306

Research output: Contribution to journalArticle

Nonlinear Dynamics
Free energy
Nonlinear Model
Free Energy
Linear Models

Gastric Helicobacter pylori infection perturbs human oral microbiota

Chua, E. G., Chong, J. Y., Lamichhane, B., Webberley, K. M., Marshall, B. J., Wise, M. J. & Tay, C. Y., 28 Jan 2019, In : PEERJ. 7, 14 p., e6336.

Research output: Contribution to journalArticle

Open Access
Helicobacter pylori
Microbiota
Helicobacter Infections
Urea
mouth
3 Citations (Scopus)

Molecular Structure of Glycogen in Escherichia coli

Wang, L., Liu, Q., Tan, X., Wang, Z., Wang, M., Wise, M. J., Li, C., Ma, C., Li, E., Deng, B., Du, Y., Tang, D. & Gilbert, R. G., 4 Jun 2019, In : Biomacromolecules. 20, 7, p. 2821-2829

Research output: Contribution to journalArticle

Glycogen
Escherichia coli
Molecular structure
Glucose
Polymers

Structural, biomechanical and hemodynamic assessment of the bladder wall in healthy subjects

Volikova, A. I., Marshall, B. J., Yin, J. M. A., Goodwin, R., Ee-Pan Chow, P. & Wise, M. J., 1 Jan 2019, In : Research and Reports in Urology. 11, p. 233-245 13 p.

Research output: Contribution to journalArticle

Open Access
Healthy Volunteers
Urinary Bladder
Hemodynamics
Routine Diagnostic Tests
Urologic Diseases
3 Citations (Scopus)

Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria

Wang, L., Liu, Q., Hu, J., Asenso, J., Wise, M. J., Wu, X., Ma, C., Chen, X., Yang, J. & Tang, D., 14 Jan 2019, In : Frontiers in Microbiology. 9, 12 p., 3354.

Research output: Contribution to journalArticle

Open Access

Systematic analysis of metabolic pathway distributions of bacterial energy reserves

Wang, L., Yang, J., Huang, Y., Liu, Q., Xu, Y., Piao, X. & Wise, M. J., 1 Aug 2019, In : G3: Genes, Genomes, Genetics. 9, 8, p. 2489-2496 8 p.

Research output: Contribution to journalArticle

Open Access
Metabolic Networks and Pathways
Energy Metabolism
Bacterial Genomes
Polyphosphates
Proteome

The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039

Lamichhane, B., Chua, E-G., Wise, M. J., Laming, C., Marshall, B. J. & Tay, C-Y., 20 Feb 2019, In : Gut Pathogens. 11, 1, p. 7 284.

Research output: Contribution to journalArticle

Open Access
Helicobacter pylori
Genome
Methyltransferases
DNA Restriction-Modification Enzymes
Somalia
2018

A Faster Algorithm for Maximum Induced Matchings on Circle Graphs

Ward-Graham, M. H., Gozzard, A., Wise, M. J. & Datta, A., Aug 2018, In : Journal of Graph Algorithms and Applications. 22, 2, p. 389-396 8 p.

Research output: Contribution to journalArticle

Open Access
Circle Graph
Induced Matching
Fast Algorithm
Computational chemistry
Bioinformatics
10 Citations (Scopus)

Distribution patterns of polyphosphate metabolism pathway and its relationships with bacterial durability and virulence

Wang, L., Yan, J., Wise, M. J., Liu, Q., Asenso, J., Huang, Y., Dai, S., Liu, Z., Du, Y. & Tang, D., 24 Apr 2018, In : Frontiers in Microbiology. 9, APR, 782.

Research output: Contribution to journalArticle

Open Access
Polyphosphates
Virulence
Virulence Factors
Proteome
Life Style
4 Citations (Scopus)

Genomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations

Al Suwayyid, B. A., Coombs, G. W., Speers, D. J., Pearson, J., Wise, M. J. & Kahler, C. M., 27 Feb 2018, In : BMC Genomics. 19, 1, 165.

Research output: Contribution to journalArticle

Open Access
Metagenomics
Neisseria gonorrhoeae
Western Australia
Epidemiology
Gonorrhea
2 Citations (Scopus)

Optimized M9 minimal salts medium for enhanced growth rate and glycogen accumulation of Escherichia coli DH5α

Wang, L., Liu, Q., Du, Y., Tang, D. & Wise, M. J., 1 Sep 2018, In : Microbiology and Biotechnology Letters. 46, 3, p. 194-200 7 p.

Research output: Contribution to journalArticle

Glycogen
Salts
Escherichia coli
Growth
Bacteria
2017
3 Citations (Scopus)

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best

Ward, M., Datta, A., Wise, M. & Matthews, D., 21 Aug 2017, In : Nucleic Acids Research. 45, 14, p. 8541-8550 10 p.

Research output: Contribution to journalArticle

Open Access
RNA
Polymers
Physics
3 Citations (Scopus)

Quantum changes in Helicobacter pylori gene expression accompany host-adaptation

Chua, E-G., Wise, M. J., Khosravi, Y., Seow, S-W., Amoyo, A. A., Pettersson, S., Peters, F., Tay, C-Y., Perkins, T. T., Loke, M-F., Marshall, B. J. & Vadivelu, J., Feb 2017, In : DNA Research. 24, 1, p. 37-49 13 p.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence

Wang, L., Liu, Z., Dai, S., Yan, J. & Wise, M. J., 3 Nov 2017, In : Frontiers in Microbiology. 8, p. 1-14 14 p., 2167.

Research output: Contribution to journalArticle

Open Access
2016
2 Citations (Scopus)

dCITE: Measuring necessary cladistic information can help you reduce polytomy artefacts in trees

Wise, M. J., 1 Nov 2016, In : PLoS One. 11, 11, e0166991.

Research output: Contribution to journalArticle

Open Access
Entropy
entropy
Artifacts
Genes
phylogeny

Human milk composition and function in the infant

Geddes, D., Kakulas, F., Wise, M. & Hartmann, P., 1 Jul 2016, Fetal and Neonatal Physiology . Polin, R. A., Abman, S. H., Rowitch, D. H., Benitz, W. E. & Fox, W. W. (eds.). 5th ed. Philadelphia: Elsevier, Vol. 1. p. 273-280 8 p.

Research output: Chapter in Book/Conference paperChapter

2015
3 Citations (Scopus)
163 Downloads (Pure)

Consistent gene expression profiles in MexTAg transgenic mouse and wild type mouse asbestos-induced mesothelioma

Robinson, C., Dick, I., Wise, M., Holloway, A., Diyagama, D., Robinson, B., Creaney, J. & Lake, R., 18 Dec 2015, In : BMC Cancer. 15, 14 p., 983.

Research output: Contribution to journalArticle

Open Access
File
Asbestos
Mesothelioma
Transcriptome
Transgenic Mice
Viral Tumor Antigens
5 Citations (Scopus)

Influence of in situ progressive N-terminal is still controversial truncation of glycogen branching enzyme in Escherichia coli DH5α on glycogen structure, accumulation, and bacterial viability

Wang, L., Regina, A., Butardo, V. M., Kosar-Hashemi, B., Larroque, O., Kahler, C. & Wise, M., 2015, In : BMC Microbiology. 15, 96, p. 1-14

Research output: Contribution to journalArticle

Open Access
1,4-alpha-Glucan Branching Enzyme
Microbial Viability
Glycogen
Escherichia coli
Desiccation
8 Citations (Scopus)

Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity

Ariff, A., Wise, M., Kahler, C., Tay, A. C. Y., Peters, F., Perkins, T. & Chang, B., 24 Oct 2015, In : BMC Genomics. 16, 1, p. 1-19 19 p., 860.

Research output: Contribution to journalArticle

Open Access
Prophages
Moraxella (Branhamella) catarrhalis
Genes
Bacteriophages
Virulence
2014
21 Citations (Scopus)

Comparative analysis of the full genome of the Helicobacter pylori isolate, Sahul64, identifies genes of high divergence

Lu, W., Wise, M., Tay, A. C. Y., Windsor, H., Marshall, B., Peacock, C. & Perkins, T., 2014, In : Journal of Bacteriology. 196, 5, p. 1073-1083

Research output: Contribution to journalArticle

Open Access
Helicobacter pylori
Genome
Genomic Islands
Genes
Virulence
2013

Anhydrobiosis: The curious case of the bdelloid rotifer

Boschetti, C., Crisp, A., Micklem, G., Wise, M. & Tunnacliffe, A., 2013, In : Cryobiology and Cryotechnology. 59, 1, p. 29-34 6 p.

Research output: Contribution to journalArticle

A Preliminary Study on the Effects of Barnstars on Wikipedia Editing

Lim, K. H., Datta, A. & Wise, M., 2013, The 9th International Symposium on Wikis and Open Collaboration. New York, USA: Association for Computing Machinery (ACM), Vol. N/A. p. 2pp

Research output: Chapter in Book/Conference paperConference paper

2 Citations (Scopus)

Mean Protein Evolutionary Distance: A Method for Comparative Protein Evolution and Its Application

Wise, M., 2013, In : PLoS One. 8, 4, p. 10pp

Research output: Contribution to journalArticle

Open Access
2012
15 Citations (Scopus)

Coexpression of nuclear receptors and histone methylation modifying genes in the testis: Implications for endocrine disruptor modes of action

Anderson, A. M., Carter, K., Anderson, D. & Wise, M., 2012, In : PLoS One. 7, 4, p. 11pp

Research output: Contribution to journalArticle

Open Access
88 Citations (Scopus)

Intrinsically disordered proteins as molecular shields

Chakrabortee, S., Tripathi, R., Watson, M., Kaminski Schierle, G. S., Kurniawan, D. P., Kaminski, C. F., Wise, M. & Tunnacliffe, A., 2012, In : Molecular Biosystems. 8, p. 210-219

Research output: Contribution to journalArticle

6 Citations (Scopus)

Predicting pseudoknotted structures across two RNA sequences

Sperschneider, J., Datta, A. & Wise, M., 2012, In : Bioinformatics. 28, 23, p. 3058-3065

Research output: Contribution to journalArticle

Open Access
2011
36 Citations (Scopus)

Glycogen with short average chain length enhances bacterial durability

Wang, L. & Wise, M., 2011, In : Naturwissenschaften. 98, p. 719-729

Research output: Contribution to journalReview article

durability
glycogen
energy
biochemistry
microbiology
33 Citations (Scopus)

Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins

Sperschneider, J., Datta, A. & Wise, M., 2011, In : RNA. 17, 1, p. 27-38

Research output: Contribution to journalArticle

60 Citations (Scopus)

Role of Pro-oncogenic Protein Disulfide Isomerase (PDI) Family Member Anterior Gradient 2 (AGR2) in the Control of Endoplasmic Reticulum Homeostasis

Higa, A., Mulot, A., Delom, F., Bouchecareilh, M., Nguyen, D. T., Boismenu, D., Wise, M. & Chevet, E., 2011, In : Journal of Biological Chemistry. 286, p. 44855-44868

Research output: Contribution to journalArticle

2010
32 Citations (Scopus)

Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae

Reardon, W., Chakrabortee, S., Pereira, T. C., Tyson, T., Banton, M. C., Dolan, K. M., Culleton, B. A., Wise, M., Burnell, A. M. & Tunnacliffe, A., 2010, In : B M C Molecular Biology. 11, 6, p. Article number 6, 18pp

Research output: Contribution to journalArticle

Open Access
2009
43 Citations (Scopus)

Bioinformatics and protein expression analyses implicate LEA proteins in the drought response of Collembola

Bahrndorff, S., Tunnacliffe, A., Wise, M., Mcgee, B., Holmstrup, M. & Loeschcke, V., 2009, In : Journal of Insect Physiology. 55, 3, p. 210-217

Research output: Contribution to journalArticle

Droughts
Collembola
Computational Biology
bioinformatics
Embryonic Development
7 Citations (Scopus)

No so HoT - heads or tails is not able to reliably compare multiple sequence alignments

Wise, M., 2009, In : Cladistics. 26, 4, p. 1-6

Research output: Contribution to journalArticle

sequence alignment
tail
alignment
phylogeny
methodology
2007
74 Citations (Scopus)

Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments

Golubchik, T., Wise, M., Easteal, S. & Jermin, L. S., 2007, In : Molecular Biology and Evolution. 24, 11, p. 2433-2442

Research output: Contribution to journalArticle

Sequence Alignment
sequence alignment
alternative splicing
Recombinant DNA
alignment
464 Citations (Scopus)

The continuing conundrum of the LEA proteins

Tunnacliffe, A. & Wise, M., 2007, In : Naturwissenschaften. 94, 10, p. 791-812

Research output: Contribution to journalArticle

embryogenesis
protein
proteins
water stress
biophysics
2006
13 Citations (Scopus)

Analysis of High Throughput Protein Expression in Escherichia coli

Benita, Y., Wise, M., Lok, M. C., Humphrey-Smith, I. & Oosting, R. S., 2006, In : Molecular and Cellular Proteomics. 5, p. 1567-1580

Research output: Contribution to journalArticle

Escherichia coli
Throughput
Proteins
Inclusion Bodies
Pipelines
2005
101 Citations (Scopus)

Consideration of RNA Secondary Structure Significantly Improves Likelihood-Based Estimates of Phylogeny: Examples from the Bilateria

Telford, M. J., Wise, M. & Gowrie-Shankar, V., 2005, In : Molecular Biology and Evolution. 22, 4, p. 1129-1136

Research output: Contribution to journalArticle

secondary structure
Phylogeny
Ribosomal RNA
phylogeny
ribosomal RNA
2004
290 Citations (Scopus)

POPP the question: what do LEA proteins do?

Wise, M. & Tunnacliffe, A., 2004, In : Trends in Plant Science. 9, 1, p. 13-17

Research output: Contribution to journalReview article

2003
7 Citations (Scopus)

DiMSim: A Discrete-Event Simulator of Metabolic Networks

Xia, X. & Wise, M., 2003, In : Journal of Chemical Information and Modeling. 43, 3, p. 1011-1019

Research output: Contribution to journalArticle

Metabolites
Simulators
event
Stoichiometry
Differential equations
191 Citations (Scopus)
Embryogenesis
Embryonic Development
Proteins
Protein
tryptophan-leucine
91 Citations (Scopus)

Regionalized GC content of template DNA as a predictor of PCR success

Benita, Y., Oosting, R. S., Lok, M. C., Wise, M. & Humphrey-Smith, I., 2003, In : Nucleic Acids Research. 31, 16, p. 1-7

Research output: Contribution to journalArticle

Base Composition
Polymerase Chain Reaction
DNA
Recombinant Proteins
Open Reading Frames
2002
158 Citations (Scopus)

Amyloidogenic nature of spider silk

Kenney, J. M., Knight, D., Wise, M. & Vollrath, F., 2002, In : The F E B S Journal. 269, p. 4159-4163

Research output: Contribution to journalArticle

20 Citations (Scopus)

The POPPs: clustering and searching using peptide probability profiles

Wise, M., 2002, In : Bioinformatics. 18, p. S38-S45

Research output: Contribution to journalArticle

2001
15 Citations (Scopus)

0j.py: a software tool for low complexity proteins and protein domains

Wise, M., 2001, In : Bioinformatics. 17, p. S288-S295

Research output: Contribution to journalArticle

4 Citations (Scopus)

TRUFFLER: programs to study microbial community composition and flux from fluorescent DNA fingerprinting data

Wise, M. & Osborn, A. M., 2001, Proceedings of the IEEE 2nd International Symposium on Bioinformatics and Bioengineering. Bourbakis, N. G. (ed.). Bethesda, MD, USA ed. United States: IEEE, Institute of Electrical and Electronics Engineers, Vol. 2001. p. 129-135

Research output: Chapter in Book/Conference paperConference paper