Associate Professor Michael Charleston

PhD
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

Personal page

Research interests

Associate Professor Michael Charleston's research in bioinformatics is increasing our understanding of how biological entities evolve, co-evolve and interact - from genes interacting with each other at timescales of milliseconds, through organisms interacting within ecosystems at timescales of days, to species rising and falling at evolutionary timescales of millions of years.

"My work combines elements of computer science, mathematics, statistics and biology in the multidisciplinary 'super-field' of bioinformatics. Biology forms the motivation for my research, providing questions that are interesting and challenging from all four areas.

"My main focus is on evolutionary biology, answering questions such as: 'What are the evolutionary relationships among these species?', 'How fast is this virus evolving?', 'How have these parasites evolved with their host species?', 'Where did this pathogen come from' and even 'What risk of emergent disease does this non-human pathogen present?'

"I find bioinformatics a completely fascinating area, absolutely full of amazing discoveries to be made. I'm very fortunate to be working in a research area in which I can answer really cool biological questions with real impact, and tackle puzzling problems about evolution, metabolism, epidemiology and ecology, coupled with challenging problems from computer science that need clever algorithms. And who doesn't like big problems?

"It's important to know these things, because nothing in biology makes sense unless it's considered within the context of evolution. If we don't understand how the living world works, we can't hope to last in it or preserve it for very long."

Teaching and supervision

COMP3456 - Computational Methods for Life Sciences

COMP5456 - Computational Methods for Life Sciences

INFO1103 - Introduction to Programming

INFO3220 - Object Oriented Design

Themes

Biomedical engineering and technology

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 (ARC)/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 Projects (DP).

2006

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

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. (2013). A simple model explains the dynamics of preferential host switching among mammal rna viruses. Evolution, 67(4), 980-990. [More Information]
  • Lichtenstein, I., Charleston, M., Caetano, T., Gamble, J., Vadas, M. (2013). Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies. BMC Bioinformatics, 14(1), 1-22. [More Information]
  • Hoyal Cuthill, J., Charleston, M. (2012). Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies. PLoS One, 7(5), 1-11. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • Sumner, J., Charleston, M. (2010). Phylogenetic estimation with partial likelihood tensors. Journal of Theoretical Biology, 262, 413-424. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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

  • Gluga, R., Kay, J., Lister, R., Simon, S., Charleston, M., Harland, J., Teague, D. (2013). A conceptual model for reflecting on expected learning vs. demonstrated student performance. Fifteenth Australasian Computing Education Conference, Adelaide: ACS Publications.
  • 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.

2013

  • Gluga, R., Kay, J., Lister, R., Simon, S., Charleston, M., Harland, J., Teague, D. (2013). A conceptual model for reflecting on expected learning vs. demonstrated student performance. Fifteenth Australasian Computing Education Conference, Adelaide: ACS Publications.
  • Hoyal Cuthill, J., Charleston, M. (2013). A simple model explains the dynamics of preferential host switching among mammal rna viruses. Evolution, 67(4), 980-990. [More Information]
  • Lichtenstein, I., Charleston, M., Caetano, T., Gamble, J., Vadas, M. (2013). Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies. BMC Bioinformatics, 14(1), 1-22. [More Information]

2012

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

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. [More Information]
  • 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. [More Information]

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. [More Information]
  • 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. [More Information]
  • Sumner, J., Charleston, M. (2010). Phylogenetic estimation with partial likelihood tensors. Journal of Theoretical Biology, 262, 413-424. [More Information]

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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]
  • 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. [More Information]

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. [More Information]

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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