Mark M Tanaka

Summary

Affiliation: University of New South Wales
Country: Australia

Publications

  1. ncbi request reprint Coevolution of pathogens and cultural practices: a new look at behavioral heterogeneity in epidemics
    Mark M Tanaka
    Department of Biological Sciences, Stanford University, California 94305, USA
    Theor Popul Biol 62:111-9. 2002
  2. pmc Sequential Monte Carlo without likelihoods
    S A Sisson
    School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
    Proc Natl Acad Sci U S A 104:1760-5. 2007
  3. pmc From traditional medicine to witchcraft: why medical treatments are not always efficacious
    Mark M Tanaka
    Evolution and Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 4:e5192. 2009
  4. pmc A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis
    R Zachariah Aandahl
    School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia
    PLoS Comput Biol 8:e1002573. 2012
  5. pmc Conditions for the evolution of gene clusters in bacterial genomes
    Sara Ballouz
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
    PLoS Comput Biol 6:e1000672. 2010
  6. pmc Evolution of variation in presence and absence of genes in bacterial pathways
    Andrew R Francis
    School of Computing, Engineering and Mathematics, University of Western Sydney, Penrith 2751, Locked Bag 1797, Australia
    BMC Evol Biol 12:55. 2012
  7. pmc Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction
    Steven Hamblin
    School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, The University of New South Wales, Kensington, NSW, Australia
    BMC Evol Biol 13:170. 2013
  8. doi request reprint Escaping an evolutionary lobster trap: drug resistance and compensatory mutation in a fluctuating environment
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, New South Wales 2052 Australia
    Evolution 65:1376-87. 2011
  9. doi request reprint High affinity extremes in combinatorial libraries and repertoires
    Mark M Tanaka
    Evolution and Ecology Research Centre, University of New South Wales, Kensington NSW 2052, Australia
    J Theor Biol 261:260-5. 2009
  10. pmc An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    BMC Infect Dis 6:92. 2006

Collaborators

Detail Information

Publications36

  1. ncbi request reprint Coevolution of pathogens and cultural practices: a new look at behavioral heterogeneity in epidemics
    Mark M Tanaka
    Department of Biological Sciences, Stanford University, California 94305, USA
    Theor Popul Biol 62:111-9. 2002
    ..We find that behaviors increasing the risk of infection can also evolve when they are inherently favored or when there is sufficient clustering of contacts between like behaviors...
  2. pmc Sequential Monte Carlo without likelihoods
    S A Sisson
    School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
    Proc Natl Acad Sci U S A 104:1760-5. 2007
    ..Here we propose a sequential Monte Carlo sampler that convincingly overcomes these inefficiencies. We demonstrate its implementation through an epidemiological study of the transmission rate of tuberculosis...
  3. pmc From traditional medicine to witchcraft: why medical treatments are not always efficacious
    Mark M Tanaka
    Evolution and Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 4:e5192. 2009
    ..These models also illuminate a broader range of phenomena, including the spread of innovations, medical treatment of animals, foraging behaviour, and self-medication in non-human primates...
  4. pmc A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis
    R Zachariah Aandahl
    School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia
    PLoS Comput Biol 8:e1002573. 2012
    ..From this procedure we find that the linear model performs better than the constant model. The general framework we use allows the possibility of extending the analysis to more complex models in the future...
  5. pmc Conditions for the evolution of gene clusters in bacterial genomes
    Sara Ballouz
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
    PLoS Comput Biol 6:e1000672. 2010
    ..Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters...
  6. pmc Evolution of variation in presence and absence of genes in bacterial pathways
    Andrew R Francis
    School of Computing, Engineering and Mathematics, University of Western Sydney, Penrith 2751, Locked Bag 1797, Australia
    BMC Evol Biol 12:55. 2012
    ..A challenge is to understand why there would be variation in gene presence within pathways if they confer a benefit only when complete...
  7. pmc Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction
    Steven Hamblin
    School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, The University of New South Wales, Kensington, NSW, Australia
    BMC Evol Biol 13:170. 2013
    ..To illustrate this concept we focus on Baculoviridae, a family of invertebrate viruses that have evolved to modify the feeding behaviour of their lepidopteran hosts and liquefy their cadavers as part of the course of infection...
  8. doi request reprint Escaping an evolutionary lobster trap: drug resistance and compensatory mutation in a fluctuating environment
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, New South Wales 2052 Australia
    Evolution 65:1376-87. 2011
    ..This stochastic tunneling effect occurs when sufficient time is allowed by the rates of environmental fluctuation...
  9. doi request reprint High affinity extremes in combinatorial libraries and repertoires
    Mark M Tanaka
    Evolution and Ecology Research Centre, University of New South Wales, Kensington NSW 2052, Australia
    J Theor Biol 261:260-5. 2009
    ..The design of libraries may benefit from considering how this plateau is reached as the library size is increased...
  10. pmc An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    BMC Infect Dis 6:92. 2006
    ..An unresolved problem is the effective quantification of the extent of transmission using genetic variation data from such pathogen isolates...
  11. ncbi request reprint The control of copy number of IS6110 in Mycobacterium tuberculosis
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    Mol Biol Evol 21:2195-201. 2004
    ..Specifically, our analysis points to the interaction of separate copies of the element causing lethal effects. We discuss the implications of these findings for genome evolution and molecular epidemiology...
  12. pmc Evidence for positive selection on Mycobacterium tuberculosis within patients
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
    BMC Evol Biol 4:31. 2004
    ..The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients...
  13. pmc The evolution of mutator genes in bacterial populations: the roles of environmental change and timing
    Mark M Tanaka
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Genetics 164:843-54. 2003
    ..In this manner, mutators can increase in frequency over successive selective sweeps. We discuss the implications and predictions of these theoretical results in relation to antibiotic resistance and the evolution of mutation rates...
  14. pmc Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    Genetics 173:1511-20. 2006
    ..I. 0.64, 1.82); and reproductive value 3.4 (95% C.I. 1.4, 79.7). These figures suggest a rapidly spreading epidemic, consistent with observations of the resurgence of tuberculosis in the United States in the 1980s and 1990s...
  15. doi request reprint Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping
    Fabio Luciani
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia
    Infect Genet Evol 8:182-90. 2008
    ..This study illustrates the utility of examining the full distribution of genotype cluster sizes from a given region, in the light of population genetic models...
  16. doi request reprint The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012
    John Sebastian Eden
    Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
    Virology 450:106-13. 2014
    ..Adaptive changes at known blockade epitopes in the viral capsid were also identified that likely contributed to their emergence. ..
  17. pmc Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes
    Josephine F Reyes
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
    BMC Bioinformatics 9:496. 2008
    ..Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates...
  18. ncbi request reprint Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
    Infect Genet Evol 5:35-43. 2005
    ..We also discuss some interpretations and modifications of existing indices. Although our focus is tuberculosis, the methods we discuss are generally applicable to any directly transmissible clonal pathogen...
  19. pmc Recombination within the pandemic norovirus GII.4 lineage
    John Sebastian Eden
    School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
    J Virol 87:6270-82. 2013
    ..4 variants. Lastly, this study highlights the many challenges in the identification of true recombination events and proposes that guidelines be applied for identifying NoV recombinants...
  20. doi request reprint Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis
    Josephine F Reyes
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    Infect Genet Evol 12:811-8. 2012
    ..However, deep phylogenetic inferences using spoligotypes or VNTRs with a small number of loci are likely to be unreliable...
  21. doi request reprint spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex
    Chaka Tang
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia
    Bioinformatics 24:2414-5. 2008
    ....
  22. pmc The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis
    Fabio Luciani
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
    Proc Natl Acad Sci U S A 106:14711-5. 2009
    ..For instance, projections using our estimates suggest that the prevalence of tuberculosis may decline with successful treatment, but the proportion of cases associated with resistance is likely to increase...
  23. ncbi request reprint Norovirus recombination
    Rowena A Bull
    School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney 2052, Australia
    J Gen Virol 88:3347-59. 2007
    ..A total of 20 NoV recombinant types were identified in circulation worldwide. The recombination point is the ORF1/2 overlap in all isolates except one, which demonstrated a double recombination event within the polymerase region...
  24. doi request reprint Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis
    Josephine F Reyes
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    Infect Genet Evol 10:1046-51. 2010
    ..These findings confirm the high level of discrimination observed using multilocus VNTR typing, and suggest that caution should be taken not to underestimate the extent of recent transmission when using this marker...
  25. pmc Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis
    Shear Lane Ch'ng
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Appl Environ Microbiol 77:768-75. 2011
    ..The differences in pathogenicity among Y. pseudotuberculosis strains are likely due to the variable presence and instability of the virulence factors...
  26. ncbi request reprint Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis
    Noah A Rosenberg
    Department of Biological Sciences, University of Southern California, 1042 W 36th Place DRB 289, Los Angeles, CA 90089, USA
    Theor Popul Biol 63:347-63. 2003
    ..0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology...
  27. doi request reprint Dynamics of evolutionary rescue in changing environments and the emergence of antibiotic resistance
    Yue Wu
    School of Biotechnology and Biomolecular Sciences, and Evolution and Ecology Research Centre, University of New South Wales, NSW 2052 Australia
    J Theor Biol 340:222-31. 2014
    ..Finally, we use the model to show how niche construction, whereby organisms are the source of environmental change, produces more complex dynamics. ..
  28. pmc Detecting emerging strains of tuberculosis by using spoligotypes
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
    Proc Natl Acad Sci U S A 103:15266-71. 2006
    ..Importantly, the strains that are identified as emerging are not simply those with the largest number of cases. The use of this method should facilitate the targeting of individual genotypes in intervention programs...
  29. doi request reprint Exact vs. approximate computation: Reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters
    R Zachariah Aandahl
    School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052 Australia
    Genetics 196:1227-30. 2014
    ..This demonstrates the value of approximate analyses in validating exact methods. ..
  30. doi request reprint The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements
    Marie J Kidd
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
    J Immunol 188:1333-40. 2012
    ..Together with data highlighting the extent of haplotypic variation within the population, this suggests that there may be substantial variability in the available Ab repertoires of different individuals...
  31. pmc The effects of linkage on comparative estimators of selection
    Carmen H S Chan
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    BMC Evol Biol 13:244. 2013
    ..These methods, however, rely on the assumption that a change in frequency of one mutation will not affect changes in frequency of other mutations...
  32. doi request reprint Epidemiological control of drug resistance and compensatory mutation under resistance testing and second-line therapy
    Clare A Saddler
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia Evolution and Ecology Research Centre, The University of New South Wales, NSW 2052, Australia
    Epidemics 5:164-73. 2013
    ..When double resistance is possible, the boundary is affected by the relative strengths of resistance against the two drugs in the double-resistant-compensated strain. ..
  33. pmc Norovirus recombination in ORF1/ORF2 overlap
    Rowena A Bull
    School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
    Emerg Infect Dis 11:1079-85. 2005
    ..We provide evidence to support the theory of the role of subgenomic RNA promoters as recombination hotspots and describe a simple mechanism of how recombination might occur in NoV...
  34. ncbi request reprint Method for assessing the similarity between subsets of the T cell receptor repertoire
    Vanessa Venturi
    Department of Haematology, Prince of Wales Hospital, Kensington NSW 2052, Australia
    J Immunol Methods 329:67-80. 2008
    ....
  35. doi request reprint Trade-offs in resource allocation in the intracellular life-cycle of hepatitis C virus
    Alison K McLean
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    J Theor Biol 267:565-72. 2010
    ..The most productive strategy is a form of the Free Movement model in which genomes are allocated entirely to the replication-translation cycle while allowing some genomes to be packaged through reallocation...
  36. ncbi request reprint The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T
    Lamia Zaghloul
    FEMS Microbiol Lett 277:197-204. 2007
    ..Of the genes disrupted by ISs, those involved in signal transduction, intracellular trafficking, and cell motility are most commonly targeted, suggesting selection against genes in these categories...