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Select Publications

Book Chapters

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

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,

Journal articles

Young AM; Tanaka MM; Yuwono C; Wehrhahn MC; Zhang L, 2024, 'Clinical Setting Comparative Analysis of Uropathogens and Antibiotic Resistance: A Retrospective Study Spanning the Coronavirus Disease 2019 Pandemic', Open Forum Infectious Diseases, 11,

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,

Aogo RA; Tanaka MM; Penington CJ, 2022, 'Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract', Journal of Theoretical Biology, 548,

Xiong X; Loo SL; Tanaka MM, 2022, 'Gut mutualists can persist in host populations despite low fidelity of vertical transmission', Evolutionary Human Sciences, 4,

Wahl LM; Tanaka MM, 2022, 'Hazardous Loss of Genetic Diversity through Selective Sweeps in Asexual Populations', American Naturalist, 199, pp. 313 - 329,

Loo SL; Tanaka MM, 2022, 'The role of a programmatic immune response on the evolution of pathogen traits', Journal of Theoretical Biology, 534,

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,

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,

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,

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,

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, pp. 000605,

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, pp. 000310,

Tanaka MM; Godfrey-Smith P; Kerr B, 2020, 'The dual landscape model of adaptation and niche construction', Philosophy of Science, 87, pp. 478 - 498,

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,

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, pp. 1900519,

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,

Lai YW; Ridone P; Peralta G; Tanaka MM; Baker MAB, 2020, 'Evolution of the stator elements of rotary prokaryote motors', Journal of Bacteriology, 202,

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,

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,

Russo AG; Kelly AG; Tuipulotu DE; Tanaka MM; White PA; Enosi Tuipulotu D, 2019, 'Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes', Virus Evolution, 5, pp. vez010,

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', ,

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, pp. 1 - 14,

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,

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, pp. 9733,

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,

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,

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,

Chisholm RH; Trauer JM; Curnoed D; Tanaka MM; Curnoe D, 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,

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,

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, pp. 20160499,

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,

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, pp. 2002,

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, pp. 18,

Wu Y; Aandahl RZ; Tanaka MM; Wu Y, 2015, 'Dynamics of bacterial insertion sequences: Can transposition bursts help the elements persist? Theories and models', BMC Evolutionary Biology, 15, pp. 288,

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,

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,

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,

Peck KM; Chan CHS; Tanaka M, 2015, 'Connecting within-host dynamics to the rate of viral molecular evolution', Virus Evolution, 1, pp. vev013 - vev013,

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,

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,

Wu Y; Saddler CA; Valckenborgh F; Tanaka MM; Wu Y, 2014, 'Dynamics of evolutionary rescue in changing environments and the emergence of antibiotic resistance', Journal of Theoretical Biology, 340, pp. 222 - 231,

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,

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,

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,

Saddler CA; Wu Y; Valckenborgh F; Tanaka MM; Wu Y, 2013, 'Epidemiological control of drug resistance and compensatory mutation under resistance testing and second-line therapy', Epidemics, 5, pp. 164 - 173,

Chan CHS; Hamblin S; Tanaka MM, 2013, 'The effects of linkage on comparative estimators of selection', BMC Evolutionary Biology, 13, pp. 244,

Hamblin S; Tanaka MM, 2013, 'Behavioural manipulation of insect hosts by Baculoviridae as a process of niche construction', BMC Evolutionary Biology, 13, pp. 170,

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,

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