Associate Professor Mark Tanaka
PhD Stanford University
Role: 
ARC QEll Fellow
Field of Research: 
Mathematical and Computational Biology
Contact details:
Phone: 
9385-2038
Office: 

Room: 138 Link Wing, Biological Sciences, UNSW, Kensington 2052

 

image_of_mark_tanaka

Research & Current Projects

Research

We are a research group at the University of New South Wales (UNSW), in Sydney, Australia. We use mathematical, computational and statistical methods to understand biological systems — in particular, evolutionary processes. Some topics we have been interested in recently include 1) Evolutionary dynamics of viruses and bacteria. 2) Using approximate Bayesian computation and other methods to analyse molecular data collected from epidemiological studies. We have developed spolTools , a website for analysing and visualising Mycobacterium tuberculosis spoligotypes. 3) Cultural transmission of behavioural traits that influence health and disease. Our research is supported by Discovery Grants from the Australian Research Council.

Education
  • PhD  Stanford University
  • BSc (Hons) University of Sydney

Professional history

  • Associate Professor, School of BABS, 2012 - current
  • Senior Lecturer, UNSW, 2007-2011
  • Lecturer, UNSW,  2002-2007
  • Postdoctoral researcher, Emory University, Atlanta, 2000-2002

Selected awards and grants

  • Moran Medal, Australian Academy of Science (jointly with Dr S. A. Sisson) 2011
  • QEII Fellowship (Australian Research Council) 2009-2013
  • Australian Research Council Discovery Grants: 2011-2013, 2009-2013 and 2005-2007
  • Scientific Visits to Europe, Australian Academy of Science, 2006

Editorial boards

  • PLoS Computational Biology, Associate Editor, 2010-present

Publications

Selected Journals

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, vol. 280, no. 1750, pp. 20122047 - 1-9, http://dx.doi.org/10.1098/rspb.2012.2047; http://rspb.royalsocietypublishing.org/content/280/1750/20122047.long

Francis, AR & Tanaka, M, 2012, 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, vol. 12, no. 55, pp. 1 - 11, doi: 10.1186/1471-2148-12-55

Kidd, M, Chen,Z, Wang, Y, Jackson, KJ, Zhang, L, Boyd, S.D., 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, vol. 188, no. 3, pp. 1333 - 1340, http://www.jimmunol.org/content/early/2011/12/28/jimmunol.1102097.full.pdf+html

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, vol. 12, no. 4, pp. 811 - 818, http://dx.doi.org/10.1016/j.meegid.2011.05.018

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, vol. 8, no. 6, pp. e1002573, http://dx.doi.org/10.1371/journal.pcbi.1002573

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, vol. 286, no. 26, pp. 23397 - 23406, http://dx.doi.org/10.1074/jbc.M111.252098

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, vol. 77, no. 3, pp. 768 - 775

Tanaka, M & Valckenborgh, F, 2011, 'Escaping an evolutionary lobster trap: Drug resistance and compensatory mutation in a fluctuating environment', Evolution, vol. 65, no. 5, pp. 1376 - 1387, http://dx.doi.org/10.1111/j.1558-5646.2011.01223.x

Tanaka, M & Reyes, JF, 2011, 'VNTR mutation in Mycobacterium tuberculosis: Lower rates for less variable loci', Infection Genetics and Evolution, vol. 11, no. 6, pp. 1192 - 1192, http://dx.doi.org/10.1016/j.meegid.2011.03.013

Reyes, JF & Tanaka, M, 2010, 'Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis', Infection Genetics and Evolution, vol. 10, no. 7, pp. 1046 - 1051, http://dx.doi.org/10.1016/j.meegid.2010.06.016

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, vol. 267, no. 4, pp. 565 - 572, http://dx.doi.org/10.1016/j.jtbi.2010.09.031

Ballouz, S, Lan, R, Francis, AR & Tanaka, M, 2010, 'Conditions for the evolution of gene clusters in bacterial genomes.', PLoS Computational Biology, vol. 6, no. 2, pp. e1000672 - e1000672, http://dx.doi.org/10.1371/journal.pcbi.1000672

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 - Biological Sciences, vol. 106, no. 34, pp. 14711 - 14715, http://dx.doi.org/10.1073/pnas.0902437106

Tanaka, M, Kendal, J & Laland, K, 2009, 'From traditional medicine to witchcraft: Why medical treatments are not always efficacious', PLoS One, vol. 4

Tanaka, M, 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

Tanaka, M, Sisson, SA & King, GC, 2009, 'High affinity extremes in combinatorial libraries and repertoires', Journal of Theoretical Biology, vol. 261, no. 2, pp. 260 - 265

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, no. 1-2, pp. 67 - 80, http://dx.doi.org/10.1016/j.jim.2007.09.016

Luciani, F, Francis, AR & Tanaka, M, 2008, 'Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping', Infection Genetics and Evolution, vol. 8, no. 2, pp. 182 - 190, http://dx.doi.org/10.1016/j.meegid.2007.12.004

Reyes, JF, Francis, AR & Tanaka, M, 2008, 'Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes', BMC bioinformatics, vol. 9, pp. 496 - 511

Tang, C, Reyes, JF, Luciani, F, Francis, AR & Tanaka, M, 2008, 'spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex', Bioinformatics, vol. 24, no. 20, pp. 2414 - 2415, http://dx.doi.org/10.1093/bioinformatics/btn434

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, vol. 277, pp. 197 - 204

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 - Biological Sciences, vol. 104, pp. 1760 - 1765

Bull, RA, Tanaka, M & White, PA, 2007, 'Norovirus recombination', Journal of General Virology, vol. 88, pp. 3347 - 3359

Tanaka, M, Phong, R & Francis, AR, 2006, 'An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates', BMC Infectious Diseases, vol. 6

Tanaka, M, Francis, AR, Luciani, F & Sisson, SA, 2006, 'Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data', Genetics, vol. 173, no. 3, pp. 1511 - 1520, http://dx.doi.org/10.1534/genetics.106.055574

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 - Biological Sciences, vol. 103, pp. 15266 - 15271

Regoes, R, Crotty, S, Antia, R & Tanaka, M, 2005, 'Optimal replication of poliovirus within cells', American Naturalist, vol. 165, pp. 364 - 373

Bull, RA, Hansman, G, Clancy, LE, Tanaka, M, Rawlinson, WD & White, PA, 2005, 'Norovirus recombination in ORF1/ORF2 overlap', Emerging Infectious Diseases, vol. 11, pp. 1079 - 1085

Tanaka, M & Francis, AR, 2005, 'Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information', Infection Genetics and Evolution, vol. 5, pp. 35 - 43

Tanaka, M, Rosenberg, NA & Small, P, 2004, 'The control of copy number of IS6110 in Mycobacterium tuberculosis', Molecular Biology and Evolution, vol. 21, pp. 2195 - 2201

Tanaka, M, 2004, 'Evidence for positive selection on Mycobacterium tuberculosis within patients', BMC Evolutionary Biology, vol. 4, pp. 31 - 31, http://www.sciencedirect.com/science/article/B6WVB-4DDXPVK-1DJ/2/f334506a35b611ad027df1d4402c8566

Tanaka, M & Francis, AB, 2004, 'Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information', Infection Genetics and Evolution, vol. 5, pp. 35 - 43, http://www.sciencedirect.com/science/article/B6W8B-4CXDMDG-1/2/02df10eab777b62abf2b00b8740b94e3

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, vol. 68, pp. 109 - 114

Tanaka, M, Bergstrom, CT & Levin, B, 2003, 'The Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing', Genetics, vol. 164, pp. 843 - 854

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, vol. 63, pp. 347 - 363