Select Publications

Journal articles

Eden J-S;Chisholm RH;Bull RA;White PA;Holmes EC;Tanaka MM, 2017, 'Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants.', Virus Evol, vol. 3, pp. vex018, http://dx.doi.org/10.1093/ve/vex018

Serdoz S;Egri-Nagy A;Sumner J;Holland BR;Jarvis PD;Tanaka MM;Francis AR, 2017, 'Maximum likelihood estimates of pairwise rearrangement distances', Journal of Theoretical Biology, vol. 423, pp. 31 - 40, http://dx.doi.org/10.1016/j.jtbi.2017.04.015

Octavia S;Wang Q;Tanaka MM;Sintchenko V;Lan R, 2017, 'Genomic heterogeneity of Salmonella enterica serovar Typhimurium bacteriuria from chronic infection', Infection, Genetics and Evolution, vol. 51, pp. 17 - 20, http://dx.doi.org/10.1016/j.meegid.2017.03.004

Fu S;Octavia S;Wang Q;Tanaka MM;Tay CY;Sintchenko V;Lan R, 2016, 'Evolution of variable number tandem repeats and its relationship with genomic diversity in Salmonella typhimurium', Frontiers in Microbiology, vol. 7, http://dx.doi.org/10.3389/fmicb.2016.02002

Mahendran V;Liu F;Riordan SM;Grimm MC;Tanaka MM;Zhang L, 2016, 'Examination of the effects of Campylobacter concisus zonula occludens toxin on intestinal epithelial cells and macrophages', Gut Pathogens, vol. 8, http://dx.doi.org/10.1186/s13099-016-0101-9

Chisholm RH;Trauer JM;Curnoed D;Tanaka MM, 2016, 'Controlled fire use in early humans might have triggered the evolutionary emergence of tuberculosis', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, pp. 9051 - 9056, http://dx.doi.org/10.1073/pnas.1603224113

Murray V;Chen JK;Tanaka MM, 2016, 'The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells', Molecular Biology Reports, vol. 43, pp. 639 - 651, http://dx.doi.org/10.1007/s11033-016-3998-7

Chisholm RH;Tanaka MM, 2016, 'The emergence of latent infection in the early evolution of Mycobacterium tuberculosis', Proceedings of the Royal Society B: Biological Sciences, vol. 283, http://dx.doi.org/10.1098/rspb.2016.0499

Chan CH S;Sanders LP;Tanaka MM, 2016, 'Modelling the role of immunity in reversion of viral antigenic sites', Journal of Theoretical Biology, vol. 392, pp. 23 - 34, http://dx.doi.org/10.1016/j.jtbi.2015.12.008

Peck KM;Chan CH S;Tanaka MM, 2015, 'Connecting within-host dynamics to the rate of viral molecular evolution.', Virus Evol, vol. 1, pp. vev013, http://dx.doi.org/10.1093/ve/vev013

Wu Y;Aandahl RZ;Tanaka MM, 2015, 'Dynamics of bacterial insertion sequences: Can transposition bursts help the elements persist? Theories and models', BMC Evolutionary Biology, vol. 15, http://dx.doi.org/10.1186/s12862-015-0560-5

Octavia S;Wang Q;Tanaka MM;Sintchenko V;Lan R, 2015, 'Genomic variability of serial human isolates of salmonella enterica serovar typhimurium associated with prolonged carriage', Journal of Clinical Microbiology, vol. 53, pp. 3507 - 3514, http://dx.doi.org/10.1128/JCM.01733-15

Fu S;Octavia S;Tanaka MM;Sintchenko V;Lan R, 2015, 'Defining the core genome of salmonella enterica serovar typhimurium for genomic surveillance and epidemiological typing', Journal of Clinical Microbiology, vol. 53, pp. 2530 - 2538, http://dx.doi.org/10.1128/JCM.03407-14

Octavia S;Wang Q;Tanaka MM;Kaur S;Sintchenko V;Lan R, 2015, 'Delineating community outbreaks of Salmonella enterica serovar typhimurium by use of whole-genome sequencing: Insights into genomic variability within an outbreak', Journal of Clinical Microbiology, vol. 53, pp. 1063 - 1071, http://dx.doi.org/10.1128/JCM.03235-14

Tanaka MM;Althouse BM;Bergstrom CT, 2014, 'Timing of antimicrobial use influences the evolution of antimicrobial resistance during disease epidemics.', Evol Med Public Health, vol. 2014, pp. 150 - 161, http://dx.doi.org/10.1093/emph/eou027

Hamblin SR;White PA;Tanaka MM, 2014, 'Viral niche construction alters hosts and ecosystems at multiple scales', Trends in Ecology and Evolution, vol. 29, pp. 594 - 599, http://dx.doi.org/10.1016/j.tree.2014.08.005

Aandahl RZ;Stadler T;Sisson SA;Tanaka MM, 2014, 'Exact vs. approximate computation: Reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters', Genetics, vol. 196, pp. 1227 - 1230, http://dx.doi.org/10.1534/genetics.113.158808

Eden JS;Hewitt J;Lim KL;Boni MF;Merif J;Greening G;Ratcliff RM;Holmes EC;Tanaka MM;Rawlinson WD;White PA, 2014, 'The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012', Virology, vol. 450-451, pp. 106 - 113, http://dx.doi.org/10.1016/j.virol.2013.12.005

Egri-Nagy A;Gebhardt V;Tanaka MM;Francis AR, 2014, 'Group-theoretic models of the inversion process in bacterial genomes', Journal of Mathematical Biology, vol. 69, pp. 243 - 265, http://dx.doi.org/10.1007/s00285-013-0702-6

Wu Y;Saddler CA;Valckenborgh F;Tanaka MM, 2014, 'Dynamics of evolutionary rescue in changing environments and the emergence of antibiotic resistance', Journal of Theoretical Biology, vol. 340, pp. 222 - 231, http://dx.doi.org/10.1016/j.jtbi.2013.09.026

Chan CH S;Hamblin S;Tanaka MM, 2013, 'The effects of linkage on comparative estimators of selection', BMC Evolutionary Biology, vol. 13, http://dx.doi.org/10.1186/1471-2148-13-244

Saddler CA;Wu Y;Valckenborgh F;Tanaka MM, 2013, 'Epidemiological control of drug resistance and compensatory mutation under resistance testing and second-line therapy', Epidemics, vol. 5, pp. 164 - 173, http://dx.doi.org/10.1016/j.epidem.2013.08.002

Hamblin S;Tanaka MM, 2013, 'Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction', BMC Evolutionary Biology, vol. 13, http://dx.doi.org/10.1186/1471-2148-13-170

Regoes RR;Hamblin S;Tanaka MM, 2013, 'Viral mutation rates: Modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed', Proceedings of the Royal Society B: Biological Sciences, vol. 280, http://dx.doi.org/10.1098/rspb.2012.2047

Eden JS;Tanaka MM;Boni MF;Rawlinson WD;White PA, 2013, 'Recombination within the pandemic norovirus GII.4 lineage', Journal of Virology, vol. 87, pp. 6270 - 6282, http://dx.doi.org/10.1128/JVI.03464-12

Francis AR;Tanaka MM, 2012, 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, vol. 12, http://dx.doi.org/10.1186/1471-2148-12-55

Aandahl RZ;Reyes JF;Sisson SA;Tanaka MM, 2012, 'A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis', PLoS Computational Biology, vol. 8, http://dx.doi.org/10.1371/journal.pcbi.1002573

Kidd MJ;Chen Z;Wang Y;Jackson KJ;Zhang L;Boyd SD;Fire AZ;Tanaka MM;Gaëta BA;Collins AM, 2012, 'The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements', Journal of Immunology, vol. 188, pp. 1333 - 1340, http://dx.doi.org/10.4049/jimmunol.1102097

Reyes JF;Chan CH S;Tanaka MM, 2012, 'Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis', Infection, Genetics and Evolution, vol. 12, pp. 811 - 818, http://dx.doi.org/10.1016/j.meegid.2011.05.018

Ch apos Ng SL;Octavia S;Xia Q;Duong A;Tanaka MM;Fukushima H;Lan R, 2011, 'Population structure and evolution of pathogenicity of yersinia pseudotuberculosis', Applied and Environmental Microbiology, vol. 77, pp. 768 - 775, http://dx.doi.org/10.1128/AEM.01993-10

Tanaka MM;Valckenborgh F, 2011, 'Escaping an evolutionary lobster trap: Drug resistance and compensatory mutation in a fluctuating environment', Evolution, vol. 65, pp. 1376 - 1387, http://dx.doi.org/10.1111/j.1558-5646.2011.01223.x

Leshchyns'ka I;Tanaka MM;Schachner M;Sytnyk V, 2011, 'Immobilized pool of NCAM180 in the postsynaptic membrane is homeostatically replenished by the flux of NCAM180 from extrasynaptic regions', Journal of Biological Chemistry, vol. 286, pp. 23397 - 23406, http://dx.doi.org/10.1074/jbc.M111.252098

Tanaka MM;Reyes JF, 2011, 'VNTR mutation in Mycobacterium tuberculosis: Lower rates for less variable loci', Infection, Genetics and Evolution, vol. 11, pp. 1192, http://dx.doi.org/10.1016/j.meegid.2011.03.013

Tanaka MM;Reyes JF, 2011, 'Mutation rate of VNTR loci in Mycobacterium tuberculosis: Response to Supply et al.', Infection, Genetics and Evolution, vol. 11, pp. 1189 - 1190, http://dx.doi.org/10.1016/j.meegid.2011.01.014

Reyes JF;Tanaka MM, 2010, 'Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis', Infection, Genetics and Evolution, vol. 10, pp. 1046 - 1051, http://dx.doi.org/10.1016/j.meegid.2010.06.016

McLean AK;Luciani F;Tanaka MM, 2010, 'Trade-offs in resource allocation in the intracellular life-cycle of hepatitis C virus', Journal of Theoretical Biology, vol. 267, pp. 565 - 572, http://dx.doi.org/10.1016/j.jtbi.2010.09.031

Ballouz S;Francis AR;Lan R;Tanaka MM, 2010, 'Conditions for the evolution of gene clusters in bacterial genomes', PLoS Computational Biology, vol. 6, http://dx.doi.org/10.1371/journal.pcbi.1000672

Sisson SA;Fan Y;Tanaka MM, 2009, 'Sequential Monte Carlo without likelihoods (Proceedings of the National Academy of Sciences of the United States of America (2007) 104, 6, (1760-1765) DOI:10.1073/pnas.0607208104)', Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 16889, http://dx.doi.org/10.1073/pnas.0908847106

Tanaka MM;Kendal JR;Laland KN, 2009, 'From traditional medicine to witchcraft: Why medical treatments are not always efficacious', PLoS ONE, vol. 4, http://dx.doi.org/10.1371/journal.pone.0005192

Tanaka MM;Sisson SA;King GC, 2009, 'High affinity extremes in combinatorial libraries and repertoires', Journal of Theoretical Biology, vol. 261, pp. 260 - 265, http://dx.doi.org/10.1016/j.jtbi.2009.07.041

Tanaka MM;Cristescu R;Cooper DW, 2009, 'Effective population size of koala populations under different population management regimes including contraception', Wildlife Research, vol. 36, pp. 601 - 609, http://dx.doi.org/10.1071/WR08160

Luciani F;Sisson SA;Jiang H;Francis AR;Tanaka MM, 2009, 'The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis', Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 14711 - 14715, http://dx.doi.org/10.1073/pnas.0902437106

Reyes JF;Francis AR;Tanaka MM, 2008, 'Models of deletion for visualizing bacterial variation: An application to tuberculosis spoligotypes', BMC Bioinformatics, vol. 9, http://dx.doi.org/10.1186/1471-2105-9-496

Luciani F;Francis AR;Tanaka MM, 2008, 'Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping', Infection, Genetics and Evolution, vol. 8, pp. 182 - 190, http://dx.doi.org/10.1016/j.meegid.2007.12.004

Venturi V;Kedzierska K;Tanaka MM;Turner SJ;Doherty PC;Davenport MP, 2008, 'Method for assessing the similarity between subsets of the T cell receptor repertoire', Journal of Immunological Methods, vol. 329, pp. 67 - 80, http://dx.doi.org/10.1016/j.jim.2007.09.016

Tang C;Reyes JF;Luciani F;Francis AR;Tanaka MM, 2008, 'spolTools: Online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex', Bioinformatics, vol. 24, pp. 2414 - 2415, http://dx.doi.org/10.1093/bioinformatics/btn434

Bull RA;Tanaka MM;White PA, 2007, 'Norovirus recombination', Journal of General Virology, vol. 88, pp. 3347 - 3359, http://dx.doi.org/10.1099/vir.0.83321-0

Zaghloul L;Tang C;Chin HY;Bek EJ;Lan R;Tanaka MM, 2007, 'The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T', FEMS Microbiology Letters, vol. 277, pp. 197 - 204, http://dx.doi.org/10.1111/j.1574-6968.2007.00957.x

Sisson SA;Fan Y;Tanaka MM, 2007, 'Sequential Monte Carlo without likelihoods', Proceedings of the National Academy of Sciences of the United States of America, vol. 104, pp. 1760 - 1765, http://dx.doi.org/10.1073/pnas.0607208104

Tanaka MM;Phong R;Francis AR, 2006, 'An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates', BMC Infectious Diseases, vol. 6, http://dx.doi.org/10.1186/1471-2334-6-92


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