By Professor Mark Tanaka

Book Chapters

Chowdhury TK; Park LAF; Stone G; Tanaka MM; Francis A, 2023, 'Estimating the relative contribution of transmission to the prevalence of drug resistance in tuberculosis', in Data Driven Science for Clinically Actionable Knowledge in Diseases, pp. 64 - 91, http://dx.doi.org/10.1201/9781003292357-3

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, http://dx.doi.org/10.1007/978-3-319-64371-7_15

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, http://dx.doi.org/10.1093/ofid/ofad676

Yu P; Pooladvand P; Tanaka MM; Wahl LM, 2024, 'Extinctions Caused by Host-Range Expansion', SIAM Journal on Applied Dynamical Systems, 23, pp. 1677 - 1703, http://dx.doi.org/10.1137/23M1605582

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

Aogo RA; Tanaka MM; Penington CJ, 2022, 'Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract', Journal of Theoretical Biology, 548, http://dx.doi.org/10.1016/j.jtbi.2022.111194

Xiong X; Loo SL; Tanaka MM, 2022, 'Gut mutualists can persist in host populations despite low fidelity of vertical transmission', Evolutionary Human Sciences, 4, http://dx.doi.org/10.1017/ehs.2022.38

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

Loo SL; Tanaka MM, 2022, 'The role of a programmatic immune response on the evolution of pathogen traits', Journal of Theoretical Biology, 534, http://dx.doi.org/10.1016/j.jtbi.2021.110962

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

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

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, http://dx.doi.org/10.1098/rspb.2022.0439

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

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, http://dx.doi.org/10.1099/MGEN.0.000605

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, http://dx.doi.org/10.1099/MGEN.0.000310

Tanaka MM; Godfrey-Smith P; Kerr B, 2020, 'The dual landscape model of adaptation and niche construction', Philosophy of Science, 87, pp. 478 - 498, http://dx.doi.org/10.1086/708692

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

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, http://dx.doi.org/10.2807/1560-7917.ES.2020.25.20.1900519

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, http://dx.doi.org/10.1186/s40168-020-00809-w

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

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

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

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, http://dx.doi.org/10.1093/ve/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', , http://dx.doi.org/10.1101/559666

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, http://dx.doi.org/10.1038/s41426-018-0065-6

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

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, http://dx.doi.org/10.1038/s41598-017-06079-1

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

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

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

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, 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, 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, 283, pp. 20160499, http://dx.doi.org/10.1098/rspb.2016.0499

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

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, 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, 8, pp. 18, http://dx.doi.org/10.1186/s13099-016-0101-9

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, 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, 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, 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, 53, pp. 1063 - 1071, http://dx.doi.org/10.1128/JCM.03235-14

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

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

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

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, http://dx.doi.org/10.1016/j.jtbi.2013.09.026

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

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

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

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, http://dx.doi.org/10.1016/j.epidem.2013.08.002

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

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