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Professor Mark Tanaka

Professor Mark Tanaka

Professor
Science
School of Biotech & Biomolecular Science

I am a mathematical and computational biologist at the University of New South Wales (UNSW) in the School of Biotechnology and Biomolecular Sciences (BABS). At UNSW I am also a member of the Evolution & Ecology Research Centre (E&ERC). I received my BSc(Hons) in genetics from the University of Sydney and my PhD in mathematical biology from Stanford University. My postdoctoral work at Emory University was in the area of microbial evolution.

A major component of my research programme concerns understanding how microbes including pathogens evolve. My research has considered topics such as mutation rates in pathogens and how they evolve; how antimicrobial resistance arises and the consequences of the fitness cost of resistance; the life-cycle of viruses; features of bacterial genomes such as mobile genes and gene clusters; and how microbes alter their environments and thus their own evolutionary trajectory. Another component of my research concerns analysis of genetic data from pathogen isolates collected in molecular epidemiology studies. My research group develops mathematical models which we use to make inferences from genetic and genomic data. I am also interested in human cultural evolution and modelling the interaction between behaviour and disease/health.

For more information about us please visit our lab website.

Professional service roles and affiliations

  • PLoS Computational Biology, Associate Editor
  • Theoretical Population Biology, Associate Editor
  • Genetics Society of AustralAsia, Society for Mathematical Biology, Member
  • Acting Head of School, BABS, 2018-2019
  • Deputy Head of School (Research Director), BABS, 2016-2018.
E-mail
m.tanaka@unsw.edu.au
Location
Room: 2111 Biological Sciences E26
  • Book Chapters | 2018
    Rodrigues G; Francis A; Sisson S; Tanaka M, 2018, 'Inferences on the acquisition of multidrug resistance in Mycobacterium tuberculosis using molecular epidemiological data', in Sisson S; Fan Y; Beaumont M (ed.), Approximate Bayesian Computation Likelihood-Free Methods for Complex Models, Chapman & Hall
    Book Chapters | 2017
    Pečerska J; Wood J; Tanaka MM; Stadler T, 2017, 'Mathematical models for the epidemiology and evolution of mycobacterium tuberculosis', in Strain Variation in the Mycobacterium tuberculosis Complex: Its Role in Biology, Epidemiology and Control, Springer, pp. 281 - 307, http://dx.doi.org/10.1007/978-3-319-64371-7_15
  • Journal articles | 2023
    Luo L; Payne M; Wang Q; Kaur S; Rathnayake IU; Graham R; Gall M; Draper J; Martinez E; Octavia S; Tanaka MM; Jennison AV; Sintchenko V; Lan R, 2023, 'Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.03014-22
    Journal articles | 2022
    Aogo RA; Tanaka MM; Penington CJ, 2022, 'Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract', Journal of Theoretical Biology, 548, pp. 111194, http://dx.doi.org/10.1016/j.jtbi.2022.111194
    Journal articles | 2022
    Kaur S; Payne M; Luo L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2022, 'MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens', Database, 2022, http://dx.doi.org/10.1093/database/baac094
    Journal articles | 2022
    Loo SL; Tanaka MM, 2022, 'The role of a programmatic immune response on the evolution of pathogen traits', Journal of Theoretical Biology, 534, pp. 110962, http://dx.doi.org/10.1016/j.jtbi.2021.110962
    Journal articles | 2022
    Tanaka MM; Wahl LM, 2022, 'Surviving environmental change: When increasing population size can increase extinction risk', Proceedings of the Royal Society B: Biological Sciences, 289, pp. 20220439, http://dx.doi.org/10.1098/rspb.2022.0439
    Journal articles | 2022
    Wahl LM; Tanaka MM, 2022, 'Hazardous Loss of Genetic Diversity through Selective Sweeps in Asexual Populations', American Naturalist, 199, pp. 313 - 329, http://dx.doi.org/10.1086/717813
    Journal articles | 2022
    Xiong X; Loo SL; Tanaka MM, 2022, 'Gut mutualists can persist in host populations despite low fidelity of vertical transmission', Evolutionary Human Sciences, 4, pp. 1 - 28, http://dx.doi.org/10.1017/ehs.2022.38
    Journal articles | 2022
    Xu Z; Hu D; Luu LDW; Octavia S; Keil AD; Sintchenko V; Tanaka MM; Mooi FR; Robson J; Lan R, 2022, 'Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis', Emerging Microbes and Infections, 11, pp. 1460 - 1473, http://dx.doi.org/10.1080/22221751.2022.2077129
    Journal articles | 2021
    Luo L; Payne M; Kaur S; Hu D; Cheney L; Octavia S; Wang Q; Tanaka MM; Sintchenko V; Lan R, 2021, 'Elucidation of global and national genomic epidemiology of salmonella enterica serovar enteritidis through multilevel genome typing', Microbial Genomics, 7, http://dx.doi.org/10.1099/MGEN.0.000605
    Journal articles | 2021
    Payne M; Octavia S; Luu LDW; Sotomayor-Castillo C; Wang Q; Tay ACY; Sintchenko V; Tanaka MM; Lan R, 2021, 'Enhancing genomics-based outbreak detection of endemic salmonella enterica serovar typhimurium using dynamic thresholds', Microbial Genomics, 7, http://dx.doi.org/10.1099/MGEN.0.000310
    Journal articles | 2021
    Xiong X; Loo SL; Zhang L; Tanaka MM, 2021, 'Modelling the effect of birth and feeding modes on the development of human gut microbiota', Proceedings of the Royal Society B: Biological Sciences, 288, pp. 20201810, http://dx.doi.org/10.1098/rspb.2020.1810
    Journal articles | 2020
    Aandahl RZ; Bhatia S; Vaudagnotto N; Street AG; Francis AR; Tanaka MM, 2020, 'MERCAT: Visualising molecular epidemiology data combining genetic markers and drug resistance profiles', Infection, Genetics and Evolution, 77, pp. 104043, http://dx.doi.org/10.1016/j.meegid.2019.104043
    Journal articles | 2020
    Jayasundara D; Lee E; Octavia S; Lan R; Tanaka MM; Wood JG, 2020, 'Emergence of pertactin-deficient pertussis strains in Australia can be explained by models of vaccine escape', Epidemics, 31, pp. 100388, http://dx.doi.org/10.1016/j.epidem.2020.100388
    Journal articles | 2020
    Lai YW; Ridone P; Peralta G; Tanaka MM; Baker MAB, 2020, 'Evolution of the stator elements of rotary prokaryote motors', Journal of Bacteriology, 202, http://dx.doi.org/10.1128/JB.00557-19
    Journal articles | 2020
    Loo SL; Ong A; Kyaw W; Thibaut LM; Lan R; Tanaka MM, 2020, 'Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination', Applied and Environmental Microbiology, 87, pp. 1 - 16, http://dx.doi.org/10.1128/AEM.02002-20
    Journal articles | 2020
    Payne M; Kaur S; Wang Q; Hennessy D; Luo L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2020, 'Multilevel genome typing: Genomics-guided scalable resolution typing of microbial pathogens', Eurosurveillance, 25, http://dx.doi.org/10.2807/1560-7917.ES.2020.25.20.1900519
    Journal articles | 2020
    Tanaka MM; Godfrey-Smith P; Kerr B, 2020, 'The dual landscape model of adaptation and niche construction', Philosophy of Science, 87, pp. 478 - 498, http://dx.doi.org/10.1086/708692
    Journal articles | 2020
    Zhang E; Thibaut LM; Terauds A; Raven M; Tanaka MM; Van Dorst J; Wong SY; Crane S; Ferrari BC, 2020, 'Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: A tale of two oases', Microbiome, 8, pp. 37, http://dx.doi.org/10.1186/s40168-020-00809-w
    Journal articles | 2019
    Russo AG; Kelly AG; Tuipulotu DE; Tanaka MM; White PA, 2019, 'Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes', Virus Evolution, 5, http://dx.doi.org/10.1093/ve/vez010
    Journal articles | 2019
    Zhang E; Thibaut L; Terauds A; Wong S; van Dorst J; Tanaka M; Ferrari B, 2019, 'Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica', , http://dx.doi.org/10.1101/559666
    Journal articles | 2018
    Chisholm RH; Connelly BD; Kerr B; Tanaka MM, 2018, 'The role of pleiotropy in the evolutionary maintenance of positive niche construction', American Naturalist, 192, pp. 35 - 48, http://dx.doi.org/10.1086/697471
    Journal articles | 2018
    Liu F; Ma R; Tay CYA; Octavia S; Lan R; Chung HKL; Riordan SM; Grimm MC; Leong RW; Tanaka MM; Connor S; Zhang L, 2018, 'Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease', Emerging Microbes and Infections, 7, http://dx.doi.org/10.1038/s41426-018-0065-6
    Journal articles | 2017
    Eden JS; Chisholm RH; Bull RA; White PA; Holmes EC; Tanaka MM, 2017, 'Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants', Virus Evolution, 3, http://dx.doi.org/10.1093/ve/vex018
    Journal articles | 2017
    Fu S; Hiley L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2017, 'Comparative genomics of Australian and international isolates of Salmonella Typhimurium: Correlation of core genome evolution with CRISPR and prophage profiles', Scientific Reports, 7, http://dx.doi.org/10.1038/s41598-017-06079-1
    Journal articles | 2017
    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, 51, pp. 17 - 20, http://dx.doi.org/10.1016/j.meegid.2017.03.004
    Journal articles | 2017
    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, 423, pp. 31 - 40, http://dx.doi.org/10.1016/j.jtbi.2017.04.015
    Journal articles | 2016
    Chan CHS; Sanders LP; Tanaka MM, 2016, 'Modelling the role of immunity in reversion of viral antigenic sites', Journal of Theoretical Biology, 392, pp. 23 - 34, http://dx.doi.org/10.1016/j.jtbi.2015.12.008
    Journal articles | 2016
    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, 283, http://dx.doi.org/10.1098/rspb.2016.0499
    Journal articles | 2016
    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, 113, pp. 9051 - 9056, http://dx.doi.org/10.1073/pnas.1603224113
    Journal articles | 2016
    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, 7, http://dx.doi.org/10.3389/fmicb.2016.02002
    Journal articles | 2016
    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, 8, http://dx.doi.org/10.1186/s13099-016-0101-9
    Journal articles | 2016
    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, 43, pp. 639 - 651, http://dx.doi.org/10.1007/s11033-016-3998-7
    Journal articles | 2015
    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, 53, pp. 2530 - 2538, http://dx.doi.org/10.1128/JCM.03407-14
    Journal articles | 2015
    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, 53, pp. 1063 - 1071, http://dx.doi.org/10.1128/JCM.03235-14
    Journal articles | 2015
    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, 53, pp. 3507 - 3514, http://dx.doi.org/10.1128/JCM.01733-15
    Journal articles | 2015
    Peck KM; Chan CHS; Tanaka M, 2015, 'Connecting within-host dynamics to the rate of viral molecular evolution', Virus Evolution, 1, pp. vev013 - vev013, http://dx.doi.org/10.1093/ve/vev013
    Journal articles | 2015
    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, 15, http://dx.doi.org/10.1186/s12862-015-0560-5
    Journal articles | 2014
    Aandahl RZ; Stadler T; Sisson SA; Tanaka MM, 2014, 'Exact vs. approximate computation: Reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters', Genetics, 196, pp. 1227 - 1230, http://dx.doi.org/10.1534/genetics.113.158808
    Journal articles | 2014
    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, 450-451, pp. 106 - 113, http://dx.doi.org/10.1016/j.virol.2013.12.005
    Journal articles | 2014
    Egri-Nagy A; Gebhardt V; Tanaka MM; Francis AR, 2014, 'Group-theoretic models of the inversion process in bacterial genomes', Journal of Mathematical Biology, 69, pp. 243 - 265, http://dx.doi.org/10.1007/s00285-013-0702-6
    Journal articles | 2014
    Hamblin SR; White PA; Tanaka MM, 2014, 'Viral niche construction alters hosts and ecosystems at multiple scales', Trends in Ecology and Evolution, 29, pp. 594 - 599, http://dx.doi.org/10.1016/j.tree.2014.08.005
    Journal articles | 2014
    Tanaka MM; Althouse BM; Bergstrom CT, 2014, 'Timing of antimicrobial use influences the evolution of antimicrobial resistance during disease epidemics', Evolution, Medicine and Public Health, 2014, pp. 150 - 161, http://dx.doi.org/10.1093/emph/eou027
    Journal articles | 2014
    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, 340, pp. 222 - 231, http://dx.doi.org/10.1016/j.jtbi.2013.09.026
    Journal articles | 2013
    Chan CHS; Hamblin S; Tanaka MM, 2013, 'The effects of linkage on comparative estimators of selection', BMC Evolutionary Biology, 13, http://dx.doi.org/10.1186/1471-2148-13-244
    Journal articles | 2013
    Eden J-S; Tanaka M; Boni MF; Rawlinson WD; White PA, 2013, 'Recombination within the pandemic norovirus GII.4 lineage', Journal of Virology, 87, pp. 6270 - 6282, http://dx.doi.org/10.1128/JVI.03464-12
    Journal articles | 2013
    Hamblin S; Tanaka MM, 2013, 'Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction', BMC Evolutionary Biology, 13, http://dx.doi.org/10.1186/1471-2148-13-170
    Journal articles | 2013
    Regoes RR; Hamblin S; Tanaka M, 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 of London Series B - Biological Sciences, 280, pp. 1 - 9, http://dx.doi.org/10.1098/rspb.2012.2047
    Journal articles | 2013
    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, 5, pp. 164 - 173, http://dx.doi.org/10.1016/j.epidem.2013.08.002
    Journal articles | 2012
    Aandahl R; Reyes JF; Sisson SA; Tanaka M, 2012, 'A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis', PLoS Computational Biology, 8, pp. e1002573, http://dx.doi.org/10.1371/journal.pcbi.1002573
    Journal articles | 2012
    Francis AR; Tanaka M, 2012, 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, 12, pp. 1 - 11, http://dx.doi.org/10.1186/1471-2148-12-55
    Journal articles | 2012
    Kidd M; Chen Z; Wang Y; Jackson KJ; Zhang L; Boyd SD; Fire AZ; Tanaka M; Gaeta BA; Collins AM, 2012, 'The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements', The Journal Of Immunology, 188, pp. 1333 - 1340, http://dx.doi.org/10.4049/jimmunol.1102097
    Journal articles | 2012
    Reyes JF; Chan C; Tanaka M, 2012, 'Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis', Infection Genetics and Evolution, 12, pp. 811 - 818, http://dx.doi.org/10.1016/j.meegid.2011.05.018
    Journal articles | 2011
    Leshchyns'ka I; Tanaka M; Schachner M; Sytnyk V, 2011, 'Immobilized pool of NCAM180 in the postsynaptic membrane is homeostatically replenished by the flux of NCAM180 from extrasynaptic regions', The Journal of Biological Chemistry, 286, pp. 23397 - 23406, http://dx.doi.org/10.1074/jbc.M111.252098
    Journal articles | 2011
    Octavia S; Ch''ng SL; Xia Q; Duong A; Tanaka M; Fukushima H; Lan R, 2011, 'Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis', Applied and Environmental Microbiology, 77, pp. 768 - 775, http://dx.doi.org/10.1128/AEM.01993-10
    Journal articles | 2011
    Tanaka M; Reyes JF, 2011, 'Mutation rate of VNTR loci in Mycobacterium tuberculosis: Response to Supply et al.', Infection Genetics and Evolution, 11, pp. 1189 - 1190, http://dx.doi.org/10.1016/j.meegid.2011.01.014
    Journal articles | 2011
    Tanaka M; Reyes JF, 2011, 'VNTR mutation in Mycobacterium tuberculosis: Lower rates for less variable loci', Infection Genetics and Evolution, 11, pp. 1192 - 1192, http://dx.doi.org/10.1016/j.meegid.2011.03.013
    Journal articles | 2011
    Tanaka M; Valckenborgh F, 2011, 'Escaping an evolutionary lobster trap: Drug resistance and compensatory mutation in a fluctuating environment', Evolution, 65, pp. 1376 - 1387, http://dx.doi.org/10.1111/j.1558-5646.2011.01223.x
    Journal articles | 2010
    Ballouz S; Lan R; Francis AR; Tanaka M, 2010, 'Conditions for the evolution of gene clusters in bacterial genomes.', PLoS Computational Biology, 6, pp. e1000672 - e1000672, http://dx.doi.org/10.1371/journal.pcbi.1000672
    Journal articles | 2010
    Mclean A; Luciani F; Tanaka M, 2010, 'Trade-offs in resource allocation in the intracellular life-cycle of hepatitis C virus', Journal of Theoretical Biology, 267, pp. 565 - 572, http://dx.doi.org/10.1016/j.jtbi.2010.09.031
    Journal articles | 2010
    Reyes JF; Tanaka M, 2010, 'Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis', Infection Genetics and Evolution, 10, pp. 1046 - 1051, http://dx.doi.org/10.1016/j.meegid.2010.06.016
    Journal articles | 2009
    Luciani F; Sisson SA; Jiang H; Francis AR; Tanaka M, 2009, 'The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis', Proceedings of the National Academy of Sciences of the United States of America, 106, pp. 14711 - 14715, http://dx.doi.org/10.1073/pnas.0902437106
    Journal articles | 2009
    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, 106, pp. 16889, http://dx.doi.org/10.1073/pnas.0908847106
    Journal articles | 2009
    Tanaka M; Cristescu R; Cooper DW, 2009, 'Effective population size of koala populations under different population management regimes including contraception', Wildlife Research, 36, pp. 601 - 609, http://dx.doi.org/10.1071/WR08160
    Journal articles | 2009
    Tanaka M; Kendal J; Laland K, 2009, 'From traditional medicine to witchcraft: Why medical treatments are not always efficacious', PLoS One, 4, http://dx.doi.org/10.1371/journal.pone.0005192
    Journal articles | 2009
    Tanaka M; Sisson SA; King GC, 2009, 'High affinity extremes in combinatorial libraries and repertoires', Journal of Theoretical Biology, 261, pp. 260 - 265, http://dx.doi.org/10.1016/j.jtbi.2009.07.041
    Journal articles | 2008
    Luciani F; Francis AR; Tanaka M, 2008, 'Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping', Infection Genetics and Evolution, 8, pp. 182 - 190, http://dx.doi.org/10.1016/j.meegid.2007.12.004
    Journal articles | 2008
    Reyes JF; Francis AR; Tanaka M, 2008, 'Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes', BMC bioinformatics, 9, pp. 496 - 511, http://dx.doi.org/10.1186/1471-2105-9-496
    Journal articles | 2008
    Tang C; Reyes JF; Luciani F; Francis AR; Tanaka M, 2008, 'spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex', Bioinformatics, 24, pp. 2414 - 2415, http://dx.doi.org/10.1093/bioinformatics/btn434
    Journal articles | 2008
    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, 329, pp. 67 - 80, http://dx.doi.org/10.1016/j.jim.2007.09.016
    Journal articles | 2007
    Bull RA; Tanaka M; White PA, 2007, 'Norovirus recombination', Journal of General Virology, 88, pp. 3347 - 3359, http://dx.doi.org/10.1099/vir.0.83321-0
    Journal articles | 2007
    Sisson SA; Fan Y; Tanaka M, 2007, 'Sequential Monte Carlo without likelihoods', Proceedings of the National Academy of Sciences of the United States of America, 104, pp. 1760 - 1765, http://dx.doi.org/10.1073/pnas.0607208104
    Journal articles | 2007
    Zaghloul L; Tang C; Chin H; Bek EJ; Lan R; Tanaka M, 2007, 'The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T', FEMS Microbiology Letters, 277, pp. 197 - 204, http://dx.doi.org/10.1111/j.1574-6968.2007.00957.x
    Journal articles | 2006
    Tanaka M; Francis AR; Luciani F; Sisson SA, 2006, 'Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data', Genetics, 173, pp. 1511 - 1520, http://dx.doi.org/10.1534/genetics.106.055574
    Journal articles | 2006
    Tanaka M; Francis AR, 2006, 'Detecting emerging strains of tuberculosis by using spoligotypes', Proceedings of the National Academy of Sciences of the United States of America, 103, pp. 15266 - 15271, http://dx.doi.org/10.1073/pnas.0603130103
    Journal articles | 2006
    Tanaka M; Phong R; Francis AR, 2006, 'An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates', BMC Infectious Diseases, 6, http://dx.doi.org/10.1186/1471-2334-6-92
    Journal articles | 2005
    Bull RA; Hansman G; Clancy LE; Tanaka M; Rawlinson WD; White PA, 2005, 'Norovirus recombination in ORF1/ORF2 overlap', Emerging Infectious Diseases, 11, pp. 1079 - 1085, http://dx.doi.org/10.3201/eid1107.041273
    Journal articles | 2005
    Regoes R; Crotty S; Antia R; Tanaka M, 2005, 'Optimal replication of poliovirus within cells', American Naturalist, 165, pp. 364 - 373, http://dx.doi.org/10.1086/428295
    Journal articles | 2005
    Tanaka M; Francis AR, 2005, 'Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information', Infection Genetics and Evolution, 5, pp. 35 - 43, http://dx.doi.org/10.1016/j.meegid.2004.06.001
    Journal articles | 2004
    Tanaka M; Rosenberg NA; Small P, 2004, 'The control of copy number of IS6110 in Mycobacterium tuberculosis', Molecular Biology and Evolution, 21, pp. 2195 - 2201, http://dx.doi.org/10.1093/molbev/msh234
    Journal articles | 2004
    Tanaka M, 2004, 'Evidence for positive selection on Mycobacterium tuberculosis within patients', BMC Evolutionary Biology, 4, pp. 31 - 31, http://dx.doi.org/10.1186/1471-2148-4-31
    Journal articles | 2003
    Cotsapas C; Chan EK; Kirk MF; Tanaka M; Little PF, 2003, 'Genetic variation and the control of transcription', Cold Spring Harbor Symposia on Quantitative Biology, 68, pp. 109 - 114, http://dx.doi.org/10.1101/sqb.2003.68.109
    Journal articles | 2003
    Rosenberg NA; Tsolaki AG; Tanaka M, 2003, 'Estimating change rates of genetic markers suing serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis', Theoretical Population Biology, 63, pp. 347 - 363, http://dx.doi.org/10.1016/S0040-5809(03)00010-8
    Journal articles | 2003
    Tanaka M; Bergstrom CT; Levin B, 2003, 'The Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing', Genetics, 164, pp. 843 - 854
    Journal articles | 2002
    Tanaka MM; Kumm J; Feldman MW, 2002, 'Coevolution of Pathogens and Cultural Practices: A New Look at Behavioral Heterogeneity in Epidemics', Theoretical Population Biology, 62, pp. 111 - 119, http://dx.doi.org/10.1006/tpbi.2002.1585
    Journal articles | 2001
    Tanaka MM; Rosenberg NA, 2001, 'Optimal estimation of transposition rates of insertion sequences for molecular epidemiology', Statistics in Medicine, 20, pp. 2409 - 2420, http://dx.doi.org/10.1002/sim.910
    Journal articles | 2000
    Rhee JT; Tanaka MM; Behr MA; Agasino CB; Paz EA; Hopewell PC; Small PM, 2000, 'Use of multiple markers in population-based molecular epidemiologic studies of tuberculosis', International Journal of Tuberculosis and Lung Disease, 4, pp. 1111 - 1119
    Journal articles | 2000
    Tanaka MM; Small PM; Salamon H; Feldman MW, 2000, 'The dynamics of repeated elements: Applications to the epidemiology of tuberculosis', Proceedings of the National Academy of Sciences of the United States of America, 97, pp. 3532 - 3537, http://dx.doi.org/10.1073/pnas.97.7.3532
    Journal articles | 1999
    Field D; Magnasco MO; Moxon ER; Metzgar D; Tanaka MM; Wills C; Thaler DS, 1999, 'Contingency loci, mutator alleles, and their interactions. Synergistic strategies for microbial evolution and adaptation in pathogenesis', Annals of the New York Academy of Sciences, 870, pp. 378 - 381, http://dx.doi.org/10.1111/j.1749-6632.1999.tb08907.x
    Journal articles | 1999
    Tanaka MM; Feldman MW, 1999, 'Theoretical considerations of cross-immunity, recombination and the evolution of new parasitic strains', Journal of Theoretical Biology, 198, pp. 145 - 163, http://dx.doi.org/10.1006/jtbi.1999.0906
    Journal articles | 1997
    Tanaka MM; Liang XM; Gray YHM; Sved JA, 1997, 'The accumulation of P-element-induced recombinants in the germline of male Drosophila melanogaster', Genetics, 147, pp. 1769 - 1782
    Journal articles | 1996
    Gray YHM; Tanaka MM; Sved JA, 1996, 'P-element-induced recombination in Drosophila melanogaster: Hybrid element insertion', Genetics, 144, pp. 1601 - 1610
  • Preprints | 2022
    Kaur S; Payne M; Luo L; Octavia S; Tanaka M; Sintchenko V; Lan R, 2022, MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens, , http://dx.doi.org/10.1101/2022.06.14.496187
    Preprints | 2022
    Luo L; Payne M; Wang Q; Kaur S; Rathnayake I; Graham R; Gall M; Draper J; Martinez E; Octavia S; Tanaka M; Jennison A; Sintchenko V; Lan R, 2022, Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis, , http://dx.doi.org/10.1101/2022.05.18.492204
    Preprints | 2022
    Xu Z; Hu D; Wai Luu LD; Octavia S; Keil A; Sintchenko V; Tanaka M; Mooi F; Robson J; Lan R, 2022, Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis, , http://dx.doi.org/10.1101/2022.01.05.475016
    Preprints | 2021
    Zhang E; Czechowski P; Terauds A; Wong SY; Chelliah DS; Raven M; Tanaka MM; Ferrari BC, 2021, Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills, , http://dx.doi.org/10.1101/2021.09.22.461446
    Preprints | 2020
    Francis A; Guo Y; Hurley P; Obst O; Park L; Tanaka M; Thomson R; Wang XR, 2020, Projected ICU and Mortuary load due to COVID-19 in Sydney, , http://dx.doi.org/10.1101/2020.03.31.20049312
    Preprints | 2020
    Luo L; Payne M; Kaur S; Hu D; Cheney L; Octavia S; Wang Q; Tanaka M; Sintchenko V; Lan R, 2020, Elucidation of global and local genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing, , http://dx.doi.org/10.1101/2020.06.30.169953
    Preprints | 2016
    Serdoz S; Egri-Nagy A; Sumner J; Holland BR; Jarvis PD; Tanaka MM; Francis AR, 2016, Maximum likelihood estimates of pairwise rearrangement distances, , http://dx.doi.org/10.48550/arxiv.1602.03962
    Preprints | 2015
    Chan CHS; Sanders LP; Tanaka MM, 2015, Modelling the role of immunity in reversion of viral antigenic sites, , http://dx.doi.org/10.1101/027995
    Preprints | 2014
    Egri-Nagy A; Gebhardt V; Tanaka MM; Francis AR, 2014, Group-theoretic models of the inversion process in bacterial genomes, , http://dx.doi.org/10.48550/arxiv.1401.0567

Selected research grants

  • National Health & Medical Research Council Ideas Grant 2022-2024 Transforming genomic surveillance of foodborne Salmonella infections with SalmonellaTracker: a standardised, high resolution and scalable platform. CI: R. Lan, M.Tanaka, S. Octavia, M. Payne
  • Australian Research Council Discovery Project 2021-2023, How can cultural innovations trigger the emergence of new diseases? CI: M. Tanaka, PI: J. Kendal
  • National Health & Medical Research Council Project Grant 2018-2020, Reducing pertussis burden by optimising molecular epidemiological surveillance of epidemic Bordetella pertussis in Australia. CIs: R. Lan, V. Sintchenko, F. Mooi, M. Tanaka
  • Australian Research Council Discovery Project 2017-2019, New models linking microbial natural history and molecular evolution. CIs: M. Tanaka and R. Lan
  • National Health & Medical Research Council Project Grant 2017-2019, Optimising temporal genomic surveillance of Salmonella infections in Australia. CIs: R. Lan, V. Sintchenko, M. Tanaka, S. Octavia
  • National Health & Medical Research Council Project Grant 2017-2019, Assessing acellular pertussis vaccine effectiveness: integrating transmission models, genetics and cohort data to inform policy. CIs: J. Wood, M. Tanaka, R. Lan, P. McIntyre, H. Gidding, P. Campbell
  • Australian Research Council Linkage Project 2016-2018, Elucidating the genetic basis of newly evolved metabolic functions in yeast. CIs: R. Edwards, M. Wilkins, M. Tanaka, P. Attfield, P. Bell
  • Australian Research Council Future Fellowship 2014-2018, How microbes build their environments through evolutionary feedback. CI: M. Tanaka
  • National Health & Medical Research Council  Project Grant 2013-2015, Molecular epidemiology and high resolution surveillance of Salmonella enterica serovar Typhimurium in Australia. CIs: R. Lan, V. Sintchenko, M. Tanaka, S. Octavia
  • Australian Research Council Discovery Project 2011-2013, Understanding mutation and genetic reassortment in viruses: New mathematical models of viral dynamics and evolution. CIs: M. Tanaka, P. White, K. Koelle, R. Regoes
  • Australian Research Council Discovery Project 2009--2013, Mathematical models and bioinformatic analyses of bacterial genome evolution. CIs: M. Tanaka, A. Francis and R. Lan
  • Australian Academy of Science, Scientific Visits to Europe 2006. CI: M. Tanaka
  • Australian Research Council Discovery Project 2005-2007, Evolutionary models and bioinformatic analyses of genetic variation in pathogens. CIs: M. Tanaka and A. Francis.

  • Future Fellowship (Australian Research Council) 2014-2018
  • Moran Medal, Australian Academy of Science (jointly with S. A. Sisson) 2011
  • QEII Fellowship (Australian Research Council) 2009-2013

My Research Supervision

Sara Loo (postdoctoral research associate), Xiyan Xiong (PhD candidate), Chelsea Liang (Hons)

Joint supervisor of PhD students Winton Wu (primary supervisor: Jai Tree), Eden Zhang (primary supervisor: Belinda Ferrari), Lewis Mercer (primary supervisor: Peter White), Jyoti Prakash Gurung (primary supervisor: Matt Baker), Md Imtiazul Islam (primary supervisor: Matt Baker).

My Teaching

  • Coordinator of Microbial Genetics (BABS3021/MICR3621)
  • Lecturer: Genes, Genomes and Evolution (BABS3291), Genetics (BABS2204/2264), Microbiology (MICR2011), Applied Biomolecular Sciences (BABS1202) and other courses.