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Associate Professor Michael Charleston

School of Information Technologies

J12 - The School of Information Technologies
The University of Sydney

Telephone +61 2 9351 4459
Fax +61 2 9351 3838

Website School of Information Technologies

Imaging, Visualisation and Information Technologies

Teaching and supervision

COMP3456 - Computational Methods for Life Sciences
COMP5456 - Computational Methods for Life Sciences
INFO1103 - Introduction to Programming
INFO3220 - Object Oriented Design

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Themes

Biomedical engineering and technology

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Selected grants

2010

  • Modelling disease evolution and emergence; Charleston M; Australian Research Council (ARC)/Discovery Projects (DP).

2009

  • Heterarchical modelling of nutritional ecology: from individuals to communities; Couzin I, Simpson S, Raubenheimer D, Couzin I, Charleston M, Sword G; Australian Research Council/Discovery Projects (DP).

2007

  • The origin and evolution of the animal phyla inferred from analysis of multiple gene data; Charleston M, Jermiin L; Australian Research Council (ARC)/Discovery.

2006

  • Advanced Bioinformatics Teaching Facility; Arthur J, Triccas J, Jermiin L, Charleston M, Yang Y, Britton W; University of Sydney (Sesqui)/Teaching Equipment Grant.
  • A grid-enabled meta server for protein threading; Charleston M, Zomaya A, Viglas A, Zhou B; Australian Research Council (ARC)/Discovery Project.
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Selected publications

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Book Chapters

  • Shankar, G., Charleston, M., Murray, M., Hibbs, D. (2007). A structural and phylogenetic analysis of cytochrome P450. In Damjana Rozman (Eds.), Proceedings of the 15th International Conference on Cytochromes P450: Biochemistry, Biophysics and Functional Genomics, (pp. 75-80). Bologna, Italy: Medimond.
  • Charleston, M., Galvani, A. (2006). A cophylogenetic perspective on host-pathogen evolution. In Zhilan Feng, Ulf Dieckmann, Simon Levin (Eds.), Disease Evolution Models, Concepts, and Data Analyses, (pp. 145-160). USA: American Mathematical Society.
  • Charleston, M., Perkins, S. (2003). Lizards, malaria, and jungles in the Caribbean. In Page, R.D.M. (Eds.), TANGLED TREES: PHYLOGENY, COSPECIATION AND COEVOLUTION, (pp. 65-92). United States: The University of Chicago Press.
  • Charleston, M. (2002). Principles of cophylogenetic maps. In Lassig, M. & Valleriani, A. (Eds.), Biological Evolution and Statistical Physics, (pp. 122-147). United States: Springer.

Journals

  • Hoyal Cuthill, J., Charleston, M. (2012). Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies. PLoS One, 7(5), 1-11.
  • do Nascimento, F., Gongora, J., Charleston, M., Tristem, M., Lowdon, S., Moran, C. (2011). Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species. BMC Evolutionary Biology, 11(1), 139-1-139-13.
  • Ho, J., Charleston, M. (2011). Network modelling of gene regulation. Biophysical Reviews, 3(1), 1-13.
  • Sadi, S., Kuo, F., Ho, J., Charleston, M., Chen, T. (2011). Verification of phylogenetic inference programs using metamorphic testing. Journal of Bioinformatics and Computational Biology, 9(6), 729-747.
  • Yoo, P., Ho, Y., Ng, J., Charleston, M., Saksena, N., Yang, P., Zomaya, A. (2010). Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles. BMC Genomics, 11 Suppl 4(S22), 1-10.
  • Simpson, S., Raubenheimer, D., Charleston, M., Clissold, F. (2010). Modelling nutritional interactions: from individuals to communities. Trends in Ecology and Evolution, 25(1), 53-60.
  • Sumner, J., Charleston, M. (2010). Phylogenetic estimation with partial likelihood tensors. Journal of Theoretical Biology, 262, 413-424.
  • Ho, J., Stefani, M., dos Remedios, C., Charleston, M. (2009). A model selection approach to discover age-dependent gene expression patterns using quantile regression models. BMC Genomics, 10(Suppl 3), S16-1-S16-18.
  • Ramsden, C., Holmes, E., Charleston, M. (2009). Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence. Molecular Biology and Evolution, 26(1), 143-153.
  • Firth, C., Charleston, M., Duffy, S., Shapiro, B., Holmes, E. (2009). Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2. Journal of Virology, 83(24), 12813-12821.
  • Estigoy, C., Ponten, F., Odeberg, J., Herbert, B., Guilhaus, M., Charleston, M., Ho, J., Cameron, D., dos Remedios, C. (2009). Intercalated discs: multiple proteins perform multiple functions in non-failing and failing human hearts. Biophysical Reviews, 1(1), 43-49.
  • Libeskind-Hadas, R., Charleston, M. (2009). On the Computational Complexity of Reticulate Cophylogeny Reconstruction Problem. Journal of Computational Biology, 16(1), 105-117.
  • Ho, J., Stefani, M., dos Remedios, C., Charleston, M. (2008). Differential variability analysis of gene expression and its application to human diseases. Bioinformatics, 24(doi:10.1093/bioinformatics/btn142), i390-i398.
  • Ho, Y., Abecasis, A., Theys, K., Deforche, K., Dwyer, D., Charleston, M., Vandamme, A., Saksena, N. (2008). HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments. Virology Journal, 5(14), 1-10.
  • Ho, J., Koundinya, R., Caetano, T., dos Remedios, C., Charleston, M. (2008). Inferring differential leukocyte activity from antibody microarrays using a latent variable model. Genome Informatics, 21(1), 126-137.
  • Sumner, J., Charleston, M., Jermiin, L., Jarvis, P. (2008). Markov invariants, plethysms, and phylogenetics. Journal of Theoretical Biology, 253(3), 601-615.
  • Al Mazari, A., Zomaya, A., Charleston, M., Salem, H., Maher, A., Garsia, R. (2007). Lability of Antiretroviral Drug Resistance Mutations - Correlates with Immunological and Virologial Responses. Current HIV Research, 5(4), 430-439.
  • Etherington, G., Ring, S., Charleston, M., Dicks, J., Rayward-Smith, V., Roberts, I. (2006). Tracing the origin and co-phylogeny of caliciviruses. Journal of General Virology, 87(5), 1229-1235.
  • Jermiin, L., Poladian, L., Charleston, M. (2005). Evolution: Is the "Big Bang" in Animal Evolution Real? Science, 310(5756), 1910-1911.
  • Mu, J., Joy, D., Duan, J., Huang, Y., Carlton, J., Walker, J., Barnwell, J., Beerli, P., Charleston, M., Pybus, O., et al (2005). Host Switch Leads to Emergence of Plasmodium vivax Malaria in Humans. Molecular Biology and Evolution, 22(8), 1686-1693.
  • Charleston, M., Perkins, S. (2005). Traversing the tangle: Algorithms and applications for cophylogenetic studies. Journal of Biomedical Informatics, 39(1), 62-71.
  • Jackson, A., Charleston, M. (2004). A Cophylogenetic Perspective of RNA-virus Evolution. Molecular Biology and Evolution, 21(1), 45-57.
  • Charleston, M. (2003). Recent results in cophylogeny mapping. ADVANCES IN PARASITOLOGY, 54, 303-330.
  • Charleston, M., Charleston, M. (2002). Preferential Host Switching by Primate Lentiviruses Can Account for Phylogenetic Similarity with the Primate Phylogeny. Systematic Biology, 51(3), 528-535.
  • Charleston, M., Robertson, D. (2002). Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology, 51(3), 528-535.
  • Charleston, M. (2001). Hitch-hiking: A parallel heuristic search strategy, applied to the phylogeny problem. Journal of Computational Biology, 8(1), 79-91.
  • Penny, D., McComish, B., Charleston, M., Hendy, M. (2001). Mathematical Elegance With Biochemical Realism: The Covarion Model of Molecular Evolution. Journal of Molecular Evolution, 53(6), 711-723.
  • Pybus, O., Charleston, M., Gupta, S., Rambaut, A., Holmes, E., Harvey, P. (2001). The Epidemic Behavior of the Hepatitis C Virus. Science, 292(5525), 2323-2325.

Conferences

  • Al Mazari, A., Zomaya, A., Charleston, M., Garsia, R. (2007). A Novel Algorithm for Adaptive and Neutral Evolutionary Patterns Associated with HIV Drug Resistance. 2007 IEEE/ACS International Conference on Computer Systems and Applications (AICCSA 2007). (IEEE) Institute of Electrical and Electronics Engineers.
  • Al Mazari, A., Zomaya, A., Charleston, M., Salem, H., Maher, A., Garsia, R. (2006). Immunological and Virological Responses Correlated with Evolution of Resistance in Patients Treated with Antiretroviral Agents. 18th Annual ASHM Conference.
  • Shankar, G., Charleston, M., Murray, M., Hibbs, D. (2006). Phylogenetic analysis of cytochrome P450 structures. BIOINFORMATICS AUSTRALIA 2006, Sydney: NSW Office for Science and Medical Research.

2012

  • Hoyal Cuthill, J., Charleston, M. (2012). Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies. PLoS One, 7(5), 1-11.

2011

  • do Nascimento, F., Gongora, J., Charleston, M., Tristem, M., Lowdon, S., Moran, C. (2011). Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species. BMC Evolutionary Biology, 11(1), 139-1-139-13.
  • Ho, J., Charleston, M. (2011). Network modelling of gene regulation. Biophysical Reviews, 3(1), 1-13.
  • Sadi, S., Kuo, F., Ho, J., Charleston, M., Chen, T. (2011). Verification of phylogenetic inference programs using metamorphic testing. Journal of Bioinformatics and Computational Biology, 9(6), 729-747.

2010

  • Yoo, P., Ho, Y., Ng, J., Charleston, M., Saksena, N., Yang, P., Zomaya, A. (2010). Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles. BMC Genomics, 11 Suppl 4(S22), 1-10.
  • Simpson, S., Raubenheimer, D., Charleston, M., Clissold, F. (2010). Modelling nutritional interactions: from individuals to communities. Trends in Ecology and Evolution, 25(1), 53-60.
  • Sumner, J., Charleston, M. (2010). Phylogenetic estimation with partial likelihood tensors. Journal of Theoretical Biology, 262, 413-424.

2009

  • Ho, J., Stefani, M., dos Remedios, C., Charleston, M. (2009). A model selection approach to discover age-dependent gene expression patterns using quantile regression models. BMC Genomics, 10(Suppl 3), S16-1-S16-18.
  • Ramsden, C., Holmes, E., Charleston, M. (2009). Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence. Molecular Biology and Evolution, 26(1), 143-153.
  • Firth, C., Charleston, M., Duffy, S., Shapiro, B., Holmes, E. (2009). Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2. Journal of Virology, 83(24), 12813-12821.
  • Estigoy, C., Ponten, F., Odeberg, J., Herbert, B., Guilhaus, M., Charleston, M., Ho, J., Cameron, D., dos Remedios, C. (2009). Intercalated discs: multiple proteins perform multiple functions in non-failing and failing human hearts. Biophysical Reviews, 1(1), 43-49.
  • Libeskind-Hadas, R., Charleston, M. (2009). On the Computational Complexity of Reticulate Cophylogeny Reconstruction Problem. Journal of Computational Biology, 16(1), 105-117.

2008

  • Ho, J., Stefani, M., dos Remedios, C., Charleston, M. (2008). Differential variability analysis of gene expression and its application to human diseases. Bioinformatics, 24(doi:10.1093/bioinformatics/btn142), i390-i398.
  • Ho, Y., Abecasis, A., Theys, K., Deforche, K., Dwyer, D., Charleston, M., Vandamme, A., Saksena, N. (2008). HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments. Virology Journal, 5(14), 1-10.
  • Ho, J., Koundinya, R., Caetano, T., dos Remedios, C., Charleston, M. (2008). Inferring differential leukocyte activity from antibody microarrays using a latent variable model. Genome Informatics, 21(1), 126-137.
  • Sumner, J., Charleston, M., Jermiin, L., Jarvis, P. (2008). Markov invariants, plethysms, and phylogenetics. Journal of Theoretical Biology, 253(3), 601-615.

2007

  • Al Mazari, A., Zomaya, A., Charleston, M., Garsia, R. (2007). A Novel Algorithm for Adaptive and Neutral Evolutionary Patterns Associated with HIV Drug Resistance. 2007 IEEE/ACS International Conference on Computer Systems and Applications (AICCSA 2007). (IEEE) Institute of Electrical and Electronics Engineers.
  • Shankar, G., Charleston, M., Murray, M., Hibbs, D. (2007). A structural and phylogenetic analysis of cytochrome P450. In Damjana Rozman (Eds.), Proceedings of the 15th International Conference on Cytochromes P450: Biochemistry, Biophysics and Functional Genomics, (pp. 75-80). Bologna, Italy: Medimond.
  • Al Mazari, A., Zomaya, A., Charleston, M., Salem, H., Maher, A., Garsia, R. (2007). Lability of Antiretroviral Drug Resistance Mutations - Correlates with Immunological and Virologial Responses. Current HIV Research, 5(4), 430-439.

2006

  • Charleston, M., Galvani, A. (2006). A cophylogenetic perspective on host-pathogen evolution. In Zhilan Feng, Ulf Dieckmann, Simon Levin (Eds.), Disease Evolution Models, Concepts, and Data Analyses, (pp. 145-160). USA: American Mathematical Society.
  • Al Mazari, A., Zomaya, A., Charleston, M., Salem, H., Maher, A., Garsia, R. (2006). Immunological and Virological Responses Correlated with Evolution of Resistance in Patients Treated with Antiretroviral Agents. 18th Annual ASHM Conference.
  • Shankar, G., Charleston, M., Murray, M., Hibbs, D. (2006). Phylogenetic analysis of cytochrome P450 structures. BIOINFORMATICS AUSTRALIA 2006, Sydney: NSW Office for Science and Medical Research.
  • Etherington, G., Ring, S., Charleston, M., Dicks, J., Rayward-Smith, V., Roberts, I. (2006). Tracing the origin and co-phylogeny of caliciviruses. Journal of General Virology, 87(5), 1229-1235.

2005

  • Jermiin, L., Poladian, L., Charleston, M. (2005). Evolution: Is the "Big Bang" in Animal Evolution Real? Science, 310(5756), 1910-1911.
  • Mu, J., Joy, D., Duan, J., Huang, Y., Carlton, J., Walker, J., Barnwell, J., Beerli, P., Charleston, M., Pybus, O., et al (2005). Host Switch Leads to Emergence of Plasmodium vivax Malaria in Humans. Molecular Biology and Evolution, 22(8), 1686-1693.
  • Charleston, M., Perkins, S. (2005). Traversing the tangle: Algorithms and applications for cophylogenetic studies. Journal of Biomedical Informatics, 39(1), 62-71.

2004

  • Jackson, A., Charleston, M. (2004). A Cophylogenetic Perspective of RNA-virus Evolution. Molecular Biology and Evolution, 21(1), 45-57.

2003

  • Charleston, M., Perkins, S. (2003). Lizards, malaria, and jungles in the Caribbean. In Page, R.D.M. (Eds.), TANGLED TREES: PHYLOGENY, COSPECIATION AND COEVOLUTION, (pp. 65-92). United States: The University of Chicago Press.
  • Charleston, M. (2003). Recent results in cophylogeny mapping. ADVANCES IN PARASITOLOGY, 54, 303-330.

2002

  • Charleston, M., Charleston, M. (2002). Preferential Host Switching by Primate Lentiviruses Can Account for Phylogenetic Similarity with the Primate Phylogeny. Systematic Biology, 51(3), 528-535.
  • Charleston, M., Robertson, D. (2002). Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology, 51(3), 528-535.
  • Charleston, M. (2002). Principles of cophylogenetic maps. In Lassig, M. & Valleriani, A. (Eds.), Biological Evolution and Statistical Physics, (pp. 122-147). United States: Springer.

2001

  • Charleston, M. (2001). Hitch-hiking: A parallel heuristic search strategy, applied to the phylogeny problem. Journal of Computational Biology, 8(1), 79-91.
  • Penny, D., McComish, B., Charleston, M., Hendy, M. (2001). Mathematical Elegance With Biochemical Realism: The Covarion Model of Molecular Evolution. Journal of Molecular Evolution, 53(6), 711-723.
  • Pybus, O., Charleston, M., Gupta, S., Rambaut, A., Holmes, E., Harvey, P. (2001). The Epidemic Behavior of the Hepatitis C Virus. Science, 292(5525), 2323-2325.
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