Prof Murray Cox staff profile picture

Contact details +64 (06) 356 9099  ext. 84747

Prof Murray Cox PhD, BSc (Hons)

Professor in Computational Biology

Institute of Fundamental Sciences

My research group addresses fundamental questions in contemporary genomics: the study of an organism's entire complement of DNA. The ability to integrate new genetic technologies with sophisticated computational analysis remains a key bottleneck in advancing the biological sciences. My research group leverages national and international connections to address outstanding biological questions at the interface of genomics, computer science and statistics.

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Professional

Contact details

  • Ph: +64-6-356 9099 x84747
    Location: 5.04, Science Tower D
    Campus: Turitea

Qualifications

  • Doctor of Philosophy - University of Otago (2003)
  • Bachelor of Sciences with Honours - University of Otago (2000)

Prizes and Awards

  • Higher degree. Awarded a Doctor of Science (DSc) by the University of Otago (2017), for excellence in ‘reconstructing social prehistory from genomic data in the Indo-Pacific region’. The DSc is the highest recognition of scientific achievement awarded by the university. - University of Otago (2017)
  • Medals and awards. Awarded the 2014 Life Technologies Award for Excellence in Molecular Biology, recognizing ‘research excellence using molecular based techniques, particularly published research in high-ranking international journals’. Also, awarded the 2015 Massey University Research Medal (Team), given to the top research team at Massey University and awarded to the Bio-Protection Research Unit for excellence in ‘decoding the molecular basis of fungal-plant interactions’. - Life Technologies Ltd; Massey University (2014)

Research Expertise

Research Interests

I am particularly interested in modeling genome dynamics — firstly, establishing how genetic variation is distributed within and between individuals, and secondly, determining how this diversity changes over evolutionary time.

My work draws heavily on genetics with a solid foundation in biochemistry, statistics, computer science and anthropology. I design and implement novel algorithms and statistics, largely in the fields of coalescent theory, demographic inference and systems biology. These tools are currently being applied to several ongoing projects, including i) reconstructing human prehistory in the Pacific region, ii) determining how the transcriptome evolves, and iii) developing new methods of demographic inference. These projects typically utilize the latest next generation sequencing technologies.

More broadly, I am interested in the interface between biology, statistics and computer science, especially where large genetic datasets can be applied to address questions of outstanding biological importance.

Thematics

Health and Well-being

Area of Expertise

Field of research codes
Biological Sciences (060000): Evolutionary Biology (060300)

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 6 6

Current Projects

Project Title: When genomes collide: How allopolyploids respond to genome shock?

Date Range: 2015 - 2018

Funding Body: Royal Society of New Zealand

Project Team:

Completed Projects

Project Title: Revealing the mosaic genome structure of spatially admixed populations

The Pacific region provides a natural model system to study complex admixture. While Melanesian groups first settled the region ~45,000 years ago, individuals of Asian descent are relative newcomers, arriving less than 5,000 years ago. However, with rare exceptions, the relative proportions of Asian-Melanesian ancestry are not known. In 2010, I published the first spatial survey of genetic ancestry in the Pacific. In a unique and ongoing NZ-US-Indonesian collaboration, I screened a panel of ancestry informative markers in 1,430 individuals from 60 populations spanning mainland Asia to Melanesia. This pilot study produced the first snapshot of Asian-Melanesian ancestry across the Pacific region. In contrast with prior expectations, I discovered that Asian ancestry does not decline gradually across the entirety of Island Southeast Asia, but instead falls rapidly within a small area of eastern Indonesia.
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Date Range: 2012 - 2015

Funding Body: Marsden Fund - Full

Project Team:

Project Title: Research Medal 2010 - Early Career

Massey's 'Early Career' medal is awarded to the university's top young scientist in recognition of their research and scientific leadership. In 2010, this medal was awarded to Murray Cox for his research in computational biology, an emerging field at the interface of biology, computer science and statistics. Murray's research is focused on two areas - human demographic inference, which aims to reconstruct the historical movements of human populations, particularly in the Indo-Pacific region; and genome evolution, which explores how an individual's entire DNA complement changes through time. The medal was awarded on the basis of Murray's international publication record in these two areas.
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Date Range: 2010 - 2012

Funding Body: Massey University

Project Team:

Research Outputs

Journal

Burgess, SA., Flint, SH., Lindsay, D., Cox, MP., & Biggs, PJ. (2017). Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiology. 17(1)
[Journal article]Authored by: Biggs, P., Burgess, S., Cox, M., Flint, S.
Brucato, N., Kusuma, P., Beaujard, P., Sudoyo, H., Cox, MP., & Ricaut, FX. (2017). Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Scientific Reports. 7(1)
[Journal article]Authored by: Cox, M.
Kusuma, P., Brucato, N., Cox, MP., Letellier, T., Manan, A., Nuraini, C., . . . Ricaut, FX. (2017). The last sea nomads of the Indonesian archipelago: Genomic origins and dispersal. European Journal of Human Genetics. 25(8), 1004-1010
[Journal article]Authored by: Cox, M.
Dupont, PY., & Cox, MP. (2017). Genomic data quality impacts automated detection of lateral gene transfer in fungi. G3: Genes, Genomes, Genetics. 7(4), 1301-1314
[Journal article]Authored by: Cox, M., Dupont, P.
Schmid, J., Day, R., Zhang, N., Dupont, PY., Cox, MP., Schardl, CL., . . . Zhou, Y. (2017). Host tissue environment directs activities of an Epichloë Endophyte, while it induces systemic hormone and defense responses in its native perennial ryegrass host. Molecular Plant-Microbe Interactions. 30(2), 138-149
[Journal article]Authored by: Cox, M., Dupont, P., Schmid, J., Zhang, N.
Campbell, MA., Ganley, ARD., Gabaldón, T., & Cox, MP. (2016). The case of the missing ancient fungal polyploids. American Naturalist. 188(6), 602-614
[Journal article]Authored by: Cox, M.
Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., . . . Reich, D. (2016). Genomic insights into the peopling of the Southwest Pacific. Nature. 538(7626), 510-513
[Journal article]Authored by: Cox, M.
Pagani, L., Lawson, DJ., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, M., . . . Ekomasova, N. (2016). Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 538(7624), 238-242
[Journal article]Authored by: Cox, M.
Vallée, F., Luciani, A., & Cox, MP. (2016). Reconstructing demography and social behavior during the neolithic expansion from genomic diversity across island southeast asia. Genetics. 204(4), 1495-1506
[Journal article]Authored by: Cox, M.
Mellow, K., Chettri, P., Kabir, S., McDougal, RL., Cox, MP., Stewart, A., . . . Bradshaw, RE. (2016). Molecular markers for quantification of bioactive fungal strains associated with Pinus radiata. New Zealand Plant Protection. 69, 64-67
[Journal article]Authored by: Bradshaw, R., Cox, M.
Brucato, N., Kusuma, P., Cox, MP., Pierron, D., Purnomo, GA., Adelaar, A., . . . Ricaut, FX. (2016). Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo. Molecular Biology and Evolution. 33(9), 2396-2400
[Journal article]Authored by: Cox, M.
Hazelton, ML., & Cox, MP. (2016). Bandwidth selection for kernel log-density estimation. Computational Statistics and Data Analysis. 103, 56-67
[Journal article]Authored by: Cox, M., Hazelton, M.
Cox, MP., Hudjashov, G., Sim, A., Savina, O., Karafet, TM., Sudoyo, H., . . . Lansing, JS. (2016). Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation. Molecular Biology and Evolution. 33(9), 2273-2284
[Journal article]Authored by: Cox, M.
Lange, C., Weld, RJ., Cox, MP., Bradshaw, RE., McLean, KL., Stewart, A., . . . Steyaert, JM. (2016). Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains. PeerJ. 2016(5)
[Journal article]Authored by: Bradshaw, R., Cox, M.
Kusuma, P., Brucato, N., Cox, MP., Pierron, D., Razafindrazaka, H., Adelaar, A., . . . Ricaut, FX. (2016). Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy. Scientific Reports. 6
[Journal article]Authored by: Cox, M.
Kusuma, P., Cox, MP., Brucato, N., Sudoyo, H., Letellier, T., & Ricaut, FX. (2016). Western Eurasian genetic influences in the Indonesian archipelago. Quaternary International. 416, 243-248
[Journal article]Authored by: Cox, M.
Bradshaw, RE., Guo, Y., Sim, AD., Kabir, MS., Chettri, P., Ozturk, IK., . . . Cox, MP. (2016). Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata. Molecular Plant Pathology. 17(2), 210-224
[Journal article]Authored by: Bradshaw, R., Cox, M.
Berry, D., Cox, MP., & Scott, B. (2016). Draft genome sequence of the filamentous fungus Penicillium paxilli (ATCC 26601). Genome Announcements. 3(2)
[Journal article]Authored by: Berry, D., Cox, M., Scott, D.
Cox, MP., & Guillot, EG. (2015). High Frequency Haplotypes are Expected Events, not Historical Figures. F1000Research. 4
[Journal article]Authored by: Cox, M.
de Wit, PJGM., van der Burgt, A., Ökmen, B., Stergiopoulos, I., Abd-Elsalam, KA., Aerts, AL., . . . Bradshaw, RE. (2015). Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry [PLoS Genet, 11(12), (2015)]. PLoS Genetics. 11(12)
[Journal article]Authored by: Bradshaw, R., Cox, M.
Guillot, EG., & Cox, MP. (2015). High Frequency Haplotypes are Expected Events, not Historical Figures.. F1000Res. 4, 666
[Journal article]Authored by: Cox, M.
Burgess, SA., Cox, MP., Flint, SH., Lindsay, D., & Biggs, PJ. (2015). Draft genome sequences of three strains of Geobacillus stearothermophilus isolated from a milk powder manufacturing plant. Genome Announcements. 3(5)
[Journal article]Authored by: Biggs, P., Burgess, S., Cox, M., Flint, S.
Dupont, PY., Eaton, CJ., Wargent, JJ., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, MP. (2015). Fungal endophyte infection of ryegrass reprograms host metabolism and alters development. New Phytologist. 208(4), 1227-1240
[Journal article]Authored by: Cox, M., Dupont, P., Eaton, C., Schmid, J., Scott, D., Wargent, J.
Nicholson, MJ., Eaton, CJ., Stärkel, C., Tapper, BA., Cox, MP., & Scott, B. (2015). Molecular cloning and functional analysis of gene clusters for the biosynthesis of indole-diterpenes in penicillium crustosum and P. Janthinellum. Toxins. 7(8), 2701-2722
[Journal article]Authored by: Cox, M., Eaton, C., Scott, D.
Guillot, EG., Hazelton, ML., Karafet, TM., Stephen Lansing, J., Sudoyo, H., & Cox, MP. (2015). Relaxed observance of traditional marriage rules allows social connectivity without loss of genetic diversity. Molecular Biology and Evolution. 32(9), 2254-2262
[Journal article]Authored by: Cox, M., Hazelton, M.
Sanderson, J., Sudoyo, H., Karafet, TM., Hammer, MF., & Cox, MP. (2015). Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. Genetics. 200(2), 469-481
[Journal article]Authored by: Cox, M.
Kusuma, P., Cox, MP., Pierron, D., Razafindrazaka, H., Brucato, N., Tonasso, L., . . . Ricaut, FX. (2015). Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics. 16(1)
[Journal article]Authored by: Cox, M.
Karmin, M., Saag, L., Vicente, M., Wilson Sayres, MA., Järve, M., Talas, UG., . . . Behar, DM. (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research. 25(4), 459-466
[Journal article]Authored by: Cox, M.
Duchemin, W., Dupont, PY., Campbell, MA., Ganley, ARD., & Cox, MP. (2015). HyLiTE: Accurate and flexible analysis of gene expression in hybrid and allopolyploid species. BMC Bioinformatics. 16(1)
[Journal article]Authored by: Cox, M., Dupont, P.
Amaris, AJR., & Cox, MP. (2015). A flexible theoretical representation for the temporal dynamics of structured populations as paths on polytope complexes. Journal of Mathematical Biology. 71(3), 735-766
[Journal article]Authored by: Cox, M.
Eaton, CJ., Dupont, PY., Solomon, P., Clayton, W., Scott, B., & Cox, MP. (2015). A core gene set describes the molecular basis of Mutualism and Antagonism in Epichloë spp. Molecular Plant-Microbe Interactions. 28(3), 218-231
[Journal article]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.
Tumonggor, MK., Karafet, TM., Downey, S., Lansing, JS., Norquest, P., Sudoyo, H., . . . Cox, MP. (2014). Isolation, contact and social behavior shaped genetic diversity in West Timor. Journal of human genetics. 59(9), 494-503
[Journal article]Authored by: Cox, M.
Guillot, EG., & Cox, MP. (2014). SMARTPOP: Inferring the impact of social dynamics on genetic diversity through high speed simulations. BMC Bioinformatics. 15(1)
[Journal article]Authored by: Cox, M.
Schardl, CL., Young, CA., Moore, N., Krom, N., Dupont, PY., Pan, J., . . . Farman, ML. (2014). Genomes of plant-associated clavicipitaceae. Advances in Botanical Research. 70, 291-327
[Journal article]Authored by: Cox, M., Dupont, P.
Lansing, JS., Cheong, SA., Chew, LY., Cox, MP., Ringo, MH., & Arthawiguna, WA. (2014). Regime Shifts in Balinese Subaks. Current Anthropology. 55(2), 232-239
[Journal article]Authored by: Cox, M.
Cox, MP., Dong, T., Shen, GG., Dalvi, Y., Scott, DB., & Ganley, ARD. (2014). An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns. PLoS Genetics. 10(3)
[Journal article]Authored by: Cox, M., Scott, D.
Prangle, D., Fearnhead, P., Cox, MP., Biggs, PJ., & French, NP. (2014). Semi-automatic selection of summary statistics for ABC model choice. Statistical Applications in Genetics and Molecular Biology. 13(1), 67-82
[Journal article]Authored by: Biggs, P., Cox, M., French, N.
Wehi, P., Cox, MP., Roa, T., & Whaanga, H. (2013). Marine resources in Māori oral tradition: He kai moana, he kai mā te hinengaro. Journal of Marine and Island Cultures. 2(2), 59-68
[Journal article]Authored by: Cox, M.
Guillot, EG., Tumonggor, MK., Lansing, JS., Sudoyo, H., & Cox, MP. (2013). Climate change influenced female population sizes through time across the Indonesian archipelago. Human Biology. 85(1-3), 135-152
[Journal article]Authored by: Cox, M.
Schardl, CL., Young, CA., Hesse, U., Amyotte, SG., Andreeva, K., Calie, PJ., . . . Zeng, Z. (2013). Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genetics. 9(2)
[Journal article]Authored by: Cox, M., Schmid, J., Scott, D.
Russell, AL., Cox, MP., Brown, VA., & McCracken, GF. (2011). Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity. BMC Evolutionary Biology. 11(1)
[Journal article]Authored by: Cox, M.
Cox, MP., Peterson, DA., & Biggs, PJ. (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC BIOINFORMATICS. 11,
[Journal article]Authored by: Cox, M.
Cox, MP., & Hammer, MF. (2010). A question of scale: Human migrations writ large and small. BMC BIOLOGY. 8,
[Journal article]Authored by: Cox, M.
Tumonggor, MK., Karafet, TM., Hallmark, B., Lansing, JS., Sudoyo, H., Hammer, MF., . . . Cox, MP. (2013). The Indonesian archipelago: An ancient genetic highway linking Asia and the Pacific. Journal of Human Genetics. 58(3), 165-173
[Journal article]Authored by: Cox, M.
Bradshaw, RE., Slot, JC., Moore, GG., Chettri, P., de Wit, PJGM., Ehrlich, KC., . . . Cox, MP. (2013). Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. New Phytologist. 198(2), 525-535
[Journal article]Authored by: Cox, M.
Cox, MP., Holland, BR., Wilkins, MC., & Schmid, J. (2013). Reconstructing past changes in locus-specific recombination rates. BMC Genetics. 14
[Journal article]Authored by: Cox, M., Schmid, J.
Bradshaw, RE., Slot, JC., Moore, GG., Chettri, P., de Wit, PJGM., Ehrlich, KC., . . . Cox, MP. (2013). Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. New Phytologist.
[Journal article]Authored by: Bradshaw, R., Cox, M.
Chettri, P., Ehrlich, KC., Cary, JW., Collemare, J., Cox, MP., Griffiths, SA., . . . Bradshaw, RE. (2013). Dothistromin genes at multiple separate loci are regulated by AflR. Fungal Genetics and Biology. 51(1), 12-20
[Journal article]Authored by: Cox, M.
Chettri, P., Ehrlich, KC., Cary, JW., Collemare, J., Cox, MP., Griffiths, SA., . . . Bradshaw, RE. (2012). Dothistromin genes at multiple separate loci are regulated by AflR. Fungal Genetics and Biology.
[Journal article]Authored by: Bradshaw, R., Cox, M.
Cox, MP., Ricaut, F-X., Lacan, M., Keyser, C., Duranthon, F., Ludes, B., . . . Crubézy, E. (2012). A time series of prehistoric mitochondrial DNA reveals Western European genetic diversity was largely established by the bronze age. Advances in Anthropology. 2(1), 14-23 Retrieved from http://www.scirp.org/journal/PaperInformation.aspx?paperID=17708
[Journal article]Authored by: Cox, M.
de Wit, PJGM., van der Burgt, A., Ökmen, B., Stergiopoulos, I., Abd-Elsalam, KA., Aerts, AL., . . . Bradshaw, RE. (2012). The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLoS Genetics. 8(11)
[Journal article]Authored by: Bradshaw, R., Cox, M.
Eaton, CJ., Cabrera, IE., Servin, JA., Wright, SJ., Cox, MP., & Borkovich, KA. (2012). The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in Neurospora crassa. PLoS ONE. 7(10)
[Journal article]Authored by: Cox, M., Eaton, C.
Cox, MP., Nelson, MG., Tumonggor, MK., Ricaut, FX., & Sudoyo, H. (2012). A small cohort of Island Southeast Asian women founded Madagascar. Proceedings of the Royal Society B: Biological Sciences. 279(1739), 2761-2768
[Journal article]Authored by: Cox, M.
Wilder, JA., Cox, MP., Paquette, AM., Alford, R., Satyagraha, AW., Harahap, A., . . . Sudoyo, H. (2011). Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia. BMC GENETICS. 12
[Journal article]Authored by: Cox, M.
Wilder, JA., Cox, MP., Paquette, AM., Alford, R., Satyagraha, AW., Harahap, A., . . . Sudoyo, H. (2011). Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia. BMC Genetics. 12
[Journal article]Authored by: Cox, M.
Lansing, JS., Cox, MP., de Vet, TA., Downey, SS., Hallmark, B., & Sudoyo, H. (2011). An ongoing Austronesian expansion in Island Southeast Asia. Journal of Anthropological Archaeology. 30(3), 262-272
[Journal article]Authored by: Cox, M.
Stephen Lansing, J., Cox, MP., de Vet, TA., Downey, SS., Hallmark, B., & Sudoyo, H. (2011). An ongoing Austronesian expansion in Island Southeast Asia. Journal of Anthropological Archaeology.
[Journal article]Authored by: Cox, M.
Russell, AL., Cox, MP., Brown, VA., & McCracken, GF. (2011). Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity. BMC EVOLUTIONARY BIOLOGY. 11,
[Journal article]Authored by: Cox, M.
Stephen Lansing, J., & Cox, MP. (2011). The domain of the replicators: Selection, neutrality, and cultural evolution. Current Anthropology. 52(1), 105-125
[Journal article]Authored by: Cox, M.
Eaton, CJ., Cox, MP., & Scott, B. (2011). What triggers grass endophytes to switch from mutualism to pathogenism?. Plant Science. 180(2), 190-195
[Journal article]Authored by: Cox, M., Eaton, C., Scott, D.
Ricaut, FX., Thomas, T., Mormina, M., Cox, MP., Bellatti, M., Foley, RA., . . . Mirazon-Lahr, M. (2010). Ancient Solomon Islands mtDNA: Assessing Holocene settlement and the impact of European contact. Journal of Archaeological Science. 37(6), 1161-1170
[Journal article]Authored by: Cox, M.
Razafindrazaka, H., Ricaut, FX., Cox, MP., Mormina, M., Dugoujon, JM., Randriamarolaza, LP., . . . Crubézy, E. (2010). Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar. European Journal of Human Genetics. 18(5), 575-581
[Journal article]Authored by: Cox, M.
Karafet, T., Hallmark, B., Cox, M., Sudoyo, H., Downey, S., Lansing, S., . . . Hammer, M. (2010). Major east-west division underlies Y chromosome stratification across Indonesia. Molecular Biology and Evolution. 27(8), 1833-1844
[Journal article]Authored by: Cox, M.
Hammer, M., Woerner, A., Mendez, F., Watkins, J., Cox, M., & Wall, J. (2010). The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nature Genetics. 42(10), 830-831
[Journal article]Authored by: Cox, M.
Eaton, CJ., Cox, MP., Ambrose, B., Becker, M., Hesse, U., Schardl, CL., . . . Scott, B. (2010). Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis. Plant Physiology. 153(4), 1780-1794
[Journal article]Authored by: Cox, M., Eaton, C., Scott, D.
Cox, MP., Eaton, CJ., & Barry Scott, D. (2010). Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing. Plant Signaling and Behavior. 5(11)
[Journal article]Authored by: Cox, M., Eaton, C., Scott, D.
Cox, MP., Peterson, DA., & Biggs, PJ. (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 11
[Journal article]Authored by: Biggs, P., Cox, M.
Cox, M., & Lansing, S. (2010). Farming and language in island southeast Asia: Reframing Austronesian history. Current Anthropology. 51(2), 241-242
[Journal article]Authored by: Cox, M.
Cox, MP., & Hammer, MF. (2010). A question of scale: Human migrations writ large and small. BMC Biology. 8
[Journal article]Authored by: Cox, M.
Cox, MP., Karafet, TM., Lansing, JS., Sudoyo, H., & Hammer, MF. (2010). Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates. Proceedings of the Royal Society B: Biological Sciences. 277(1687), 1589-1596
[Journal article]Authored by: Cox, M.
Ricaut, FX., Razafindrazaka, H., Cox, MP., Dugoujon, JM., Guitard, E., Sambo, C., . . . Crubézy, E. (2009). A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar. BMC Genomics. 10
[Journal article]Authored by: Cox, M.
Lansing, S., Cox, M., Downey, S., Janssen, M., & Schoenfelder, J. (2009). A robust budding model of Balinese water temple networks. World Archaeology. 41(1), 112-133
[Journal article]Authored by: Cox, M.
Cox, M., Morales, D., Woerner, A., Sozanski, J., Wall, J., & Hammer, M. (2009). Autosomal resequence data reveal late stone age signals of population expansion in sub-Saharan African foraging and farming populations. PLoS ONE. 4(7), E6366-E6373
[Journal article]Authored by: Cox, M.
Wall, J., Cox, M., Mendez, F., Woerner, A., Severson, T., & Hammer, M. (2008). A novel DNA sequence database for analyzing human demographic history. Genome Research. 18, 1354-1361
[Journal article]Authored by: Cox, M.
Russell, A., Goodman, S., & Cox, M. (2008). Coalescent analyses support multiple mainland-to-island dispersals in the evolution of Malagasy Triaenops bats (Chiroptera: Hipposideridae). Journal of Biogeography. 35(6), 995-1003
[Journal article]Authored by: Cox, M.
Pilkington, M., Wilder, J., Mendez, F., Cox, M., Woerner, A., Angui, T., . . . Hammer, M. (2008). Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa. Molecular Biology and Evolution. 25(3), 517-525
[Journal article]Authored by: Cox, M.
Lansing, S., Watkins, J., Hallmark, B., Cox, M., Karafet, T., Sudoyo, H., . . . Hammer, M. (2008). Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations. Proceedings of the National Academy of Sciences of the United States of America. 105(33), 11645-11650
[Journal article]Authored by: Cox, M.
Hammer, M., Mendez, F., Cox, M., Woerner, A., & Wall, J. (2008). Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genetics. 4(9), 1-8
[Journal article]Authored by: Cox, M.
Downey, S., Hallmark, B., Cox, M., Norquest, P., & Lansing, S. (2008). Computational feature-sensitive reconstruction of language relationships: Developing the ALINE distance for comparative historical linguistic reconstruction. Journal of Quantitative Linguistics. 15(4), 340-369
[Journal article]Authored by: Cox, M.
Cox, M., Woerner, A., Wall, J., & Hammer, M. (2008). Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow. BMC Genetics. 9(1), 76-87
[Journal article]Authored by: Cox, M.
Cox, M., Mendez, F., Karafet, T., Pilkington, M., Kingan, S., Destro Bisol, G., . . . Hammer, M. (2008). Testing for archaic hominin admixture on the X chromosome: Model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent. Genetics. 178(1), 427-437
[Journal article]Authored by: Cox, M.
Cox, M. (2008). Accuracy of molecular dating with the rho statistic: Deviations from coalescent expectations under a range of demographic models. Human Biology. 80(4), 335-357
[Journal article]Authored by: Cox, M.
Woerner, A., Cox, M., & Hammer, M. (2007). Recombination-filtered genomic datasets by information maximization. Bioinformatics. 23(14), 1851-1853
[Journal article]Authored by: Cox, M.
Lansing, S., Cox, M., Downey, S., Gabler, B., Hallmark, B., Karafet, T., . . . Hammer, M. (2007). Coevolution of languages and genes on the island of Sumba, eastern Indonesia. Proceedings of the National Academy of Sciences of the United States of America. 104(41), 16022-16026
[Journal article]Authored by: Cox, M.
Garrigan, D., Kingan, S., Pilkington, M., Wilder, J., Cox, M., Soodyall, H., . . . Hammer, M. (2007). Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data. Genetics. 177(4), 2195-2207
[Journal article]Authored by: Cox, M.
Cox, M., Redd, A., Karafet, T., Ponder, C., Lansing, S., Sudoyo, H., . . . Hammer, M. (2007). A Polynesian motif on the Y chromosome: Population structure in remote Oceania. Human Biology. 79(5), 525-535
[Journal article]Authored by: Cox, M.
Cox, M., & Mirazon Lahr, M. (2006). Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands. American Journal of Human Biology. 18(1), 35-50
[Journal article]Authored by: Cox, M.
Cox, M. (2006). Extreme patterns of variance in small populations: Placing limits on human Y-chromosome diversity through time in the Vanuatu Archipelago. Annals of Human Genetics. 71(3), 390-406
[Journal article]Authored by: Cox, M.
Cox, M. (2006). Minimal hierarchical analysis of global human Y-chromosome SNP diversity by PCR-RFLP. Anthropological Science. 114(1), 69-74
[Journal article]Authored by: Cox, M.

Book

Cox, MP. (2017). The genetic history of human populations in Island Southeast Asia during the Late Pleistocene and Holocene. In P. Bellwood (Ed.) First Islanders: Prehistory and Human Migration in Island Southeast Asia. (pp. 107 - 116). : John Wiley & Sons
[Chapter]Authored by: Cox, M.
Cox, MP. (2013). Southeast Asia Islands and Oceania: Human Genetics. In I. Ness, & P. Bellwood (Eds.) Encyclopedia of Global Human Migration. (pp. 293 - 301). Malden, MA: Wiley-Blackwell
[Chapter]Authored by: Cox, M.
Cox, M. (2008). The genetic environment of Melanesia: Clines, clusters and contact. In VT. Koven (Ed.) Population Genetics Research Progress. (pp. 45 - 83). Hauppauge, NY, United States: Nova Science Publishers Inc
[Chapter]Authored by: Cox, M.
Hagelberg, E., Cox, M., Schiefenhovel, W., & Frame, I. (2008). A genetic perspective on the origins and dispersal of the Austronesians: Mitochondrial DNA variation from Madagascar to Easter Island. In A. Sanchez Mazas, R. Blench, MD. Ross, I. Peiros, & M. Lin (Eds.) Past Human Migrations in East Asia: Matching Archaeology, Linguistcs and Genetics. (pp. 356 - 377). Oxon, United Kingdom: Routledge
[Chapter]Authored by: Cox, M.

Conference

Chujo, T., Lukito, Y., Eaton, C., Dupont, P-Y., Johnson, L., Cox, M., . . . Scott, DB. (2016). Heterochromatin protein I regulates alkaloid biosynthesis and the mutualistic symbiotic interaction between Epichloë festucae and its host Lolium perenne. Poster session presented at the meeting of 13th European Conference on Fungal Genetics (ECFG13), Paris-La Villette
[Conference Poster]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.
Sammarro, M., Schrefheere, A., Biggs, P., marshall, J., Tate, J., Cox, M., . . . Vignes, MCL. (2016). Challenges and leads for modelling complex molecular biological systems. Poster session presented at the meeting of Complex Networks and Applications 2016 workshop. Marseilles, France
[Conference Poster]Authored by: Biggs, P., Cox, M., French, N., Marshall, J., Marsland, S., Vignes, M.
Dupont, P., Eaton, CJ., Wargent, J., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, MP. (2015, March). Insights into the molecular mechanisms underlying grass-endophyte symbiosis. Presented at Plant-fungal interaction symposium
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Eaton, C., Schmid, J., Scott, D., Wargent, J.
Dupont, P., Eaton, CJ., Wargent, J., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, MP.(2015, March). Insights into the molecular mechanisms underlying grass-endophyte symbiosis. .
[Conference]Authored by: Cox, M., Eaton, C., Schmid, J., Scott, D., Wargent, J.
Ozturk, IK., Dupont, PY., McDougal, RL., Cox, MP., Eaton, CJ., & Bradshaw, RE. (2015, September). Secondary metabolome of the forest pathogen Dothistroma septosporum. Presented at Dothistroma septosporum. Australasian Plant Pathology Society Conference 2015
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M., Dupont, P., Eaton, C.Contributed to by: Dupont, P.
Scott, DB., Chujo, T., Lukito, Y., Dupont, PY., Eaton, CJ., & Cox, MP. (2015, September). Heterochromatic marks play an important role in regulating the symbiotic interaction between Epichloë festucae and Lolium perenne and symbiosis-specific secondary metabolite gene expression. Presented at 9th International Symposium on Fungal Endophytes of Grasses and 1st International Symposium on Plant Microbiomes. Melbourne.
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.Contributed to by: Dupont, P.
Dupont, PY., Eaton, C., Wargent, J., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, M. (2015). Endophyte infection of ryegrass alters metabolism development and response to stress. Poster session presented at the meeting of 28th Fungal Genetics Conference. California, United States of America
[Conference Poster]Authored by: Cox, M., Dupont, P., Eaton, C., Schmid, J., Scott, D., Wargent, J.
Cox, ., campbell, ., Dong, T., shen, ., Dalvi, Y., scott, ., . . . Ganley, ARD. (2015). Epichloe endophytes: a powerful model system for determining genomic responses to genome merger. Poster session presented at the meeting of 28th Fungal Genetics Conference, Asilomar, California, USA
[Conference Poster]Authored by: Cox, M.
Ozturk, IK., McDougal, R., Dupont, PY., Cox, MP., Eaton, CJ., & Bradshaw, RE. (2014). Secondary metabolome of the forest pathogen Dothistroma septosporum. Poster session presented at the meeting of NZMS/NZSBMB 2014 conference
[Conference Poster]Authored by: Bradshaw, R., Cox, M., Dupont, P., Eaton, C.Contributed to by: Dupont, P.
Eaton, CJ., Dupont, PY., Solomon, P., Clayton, W., Scott, B., & Cox, MP. (2014). A core gene set underpins the shift from mutualistm to antagonism in multiple Epichloë symbiotic mutants.. Poster session presented at the meeting of QMB Plant Molecular Biology, Queenstown
[Conference Poster]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.
Tate, JA., Sehrish, T., Soltis, DE., Soltis, PS., & Cox, MP. (2014, November). Exploring the floral transcriptome of reciprocally formed Tragopogon miscellus (Asteraceae) allopolyploids. Presented at Australasian Systematic Botany Society conference. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Cox, M., Tate, J.
Spagnuolo, J., Cox, M., & Rakonjac, J. (2014, November). The stress of novel drug targets. Presented at “Molecules and Microbes more –omic than ever?” NZMS/NZSBMB Joint Conference. Wellington.
[Conference Oral Presentation]Authored by: Cox, M., Rakonjac, J.
Dupont, P., Eaton, CJ., Wargent, JJ., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, MP. (2014, August). Endophyte infection of ryegrass alters metabolism, development and response to stress. Presented at Queenstown Molecular Biology Meeting (Plant and Main meetings)
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Eaton, C., Schmid, J., Scott, D., Wargent, J.
Schmid, J., Day, R., Zhang, N., Cox, M., Dupont, P-Y., & Truglio, M. (2014, August). Tissue-specific interactions between the transcriptomes of the fungal endophyte Neotyphodium lolii and its perennial ryegrass host. Presented at The 10th International Mycological Congress (IMC10). Bangkok, Thailand.
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Schmid, J.
Ganley, ARD., Cox, M., Dong, T., Shen, G., Dalvi, Y., & Scott, DB. (2014). Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns. Poster session presented at the meeting of 35th Lorne Genome Conference, Lorne Australia. Lorne, Victoria, Australia
[Conference Poster]Authored by: Cox, M., Scott, D.
Ganley, ARD., & Cox, MP. (2013). Universal rules for the transcriptional response to polyploidy. Poster session presented at the meeting of Queenstown Molecular Biology Meetings 2013. Queenstown, New Zealand
[Conference Poster]Authored by: Cox, M.
Eaton, C., Dupont, P-Y., Cox, M., Tanaka, A., & Scott, B. (2013, November). Friends don't eat friends: loss of endophyte mutualism triggers activation of host degradation. Presented at 9th Australasian Plant Pathology Conference (APPS 2013). University of Auckland, Auckland.
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.
Eaton, C., Dupont, P-Y., Cox, M., Child, P., & Scott, B. (2013, November). Exploring the molecular basis of symbiosis through next generation RNA sequencing. Presented at 19th Australasian Plant Pathology Conference Workshop on “Illuminating genomics of plant pathogens – what to do with your genome sequence”. University of Auckland, Auckland.
[Conference Oral Presentation]Authored by: Cox, M., Dupont, P., Eaton, C., Scott, D.
Vaughan, T., Cox, M., Biggs, P., Drummond, A., & French, N. (2012). Demographic histories of host-associated campylobacter populations in New Zealand. In First Infectious Disease Research Centre [IDReC] Science Symposium: Delegate Handbook(pp. 72 - 72). , First Infectious Disease Research Centre [IDReC] Science Symposium New Zealand: Infectious Disease Research Centre, Massey University
[Conference Abstract]Authored by: Biggs, P., Cox, M., French, N.
Bradshaw, RE., Guo, Y., Kabir, S., Chettri, P., Cox, MP., Okmen, B., . . . de Witt, PJGM. (2012, July). Protecting forest crops from disease: can comparative genomics provide management solutions?. Presented at 15th International Molecular Plant-Microbe Interactions Congress.. Kyoto, Japan.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M.
Bradshaw, RE., Chettri, P., Aerts, A., Sun, H., Grigoriev, IV., Cox, MP., . . . de Witt, PJGM. (2012). Forest pathogen genes in surprising places: Tales from a beautifully-assembled genome. Poster session presented at the meeting of 33rd Lorne Genome Conference, Lorne Australia. Lorne Australia
[Conference Poster]Authored by: Bradshaw, R., Cox, M.
Schmid, J., Wilkins, M., Zhang, N., Bradshaw, R., Cox, M., Cannon, R., . . . Schardl, C. (2012, June). Why do so many fungal open reading frames contain repeats?. Presented at The 18th Congress of the International Society for Human and Animal Mycology. Berlin, Germany.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M., Schmid, J., Zhang, N.
Vaughan, T., Cox, M., Biggs, P., Drummond, A., & French, N. (2012, October). Non-parametric inference of the demographic history of host-associated Campylobacter in New Zealand. Presented at Allan Wilson Centre for Molecular Ecology and Evolution Annual Meeting 2012. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Biggs, P., Cox, M., French, N.
Schmid, J., Wilkins, M., Zhang, N., Bradshaw, R., Cox, M., Cannon, R., . . . Schardl, C. (2012). Why do so many fungal open reading frames contain repeats?. In Mycoses: diagnosis, therapy and prophylaxis of fungal diseases Vol. 55 (pp. 67 - 68). , 18th Congress of the International Society for Human and Animal Mycology [ISHAM 2012]: From Laboratory to Clinic: Blackwell Verlag GmbH
[Conference Abstract]Authored by: Bradshaw, R., Cox, M., Schmid, J., Wilkins, M., Zhang, N.
Schmid, J., Wilkins, M., Zhang, N., Bradshaw, R., Cox, M., Cannon, R., . . . Schardl, C. (2012). Why do so many fungal open reading frames contain repeats?.
[Conference Poster]Authored by: Cox, M., Schmid, J., Wilkins, M., Zhang, N.
Eaton, CJ., Cox, MP., Schardl, C., & Scott, B. (2011, August). Symbiotic stress: unraveling a plants response to pathogen infection. Presented at Queenstown Research Week Plant Stress Response Satellite meeting. Queenstown, New Zealand.
[Conference Oral Presentation]Authored by: Cox, M., Eaton, C.
Bradshaw, RE., Chettri, P., Guo, Y., Kabir, S., Cox, MP., Okmen, B., . . . De Wit, P. (2011, August). Progress towards understanding plant-pathogen interactions in Dothistroma needle blight.. Presented at 5th international Dothistroma alliance research meeting. Suonenjoki, Finland.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M.
Bradshaw, R., Aerts, A., Sun, H., Cox, M., Chettri, P., Goodwin, S., . . . Grigoriev, I. (2011). The genome of the Dothideomycete forest pathogen Dothistroma septosporum. Poster session presented at the meeting of 26th Fungal Genetics Conference. Asilomar, California, United States
[Conference Poster]Authored by: Bradshaw, R., Cox, M.
Eaton, C. (2011, March). Decoding symbiosis - molecular insights into the basis of grass-fungal interactions. Presented at 26th Fungal Genetics Conference at Asilomar. Asilomar, United States.
[Conference Oral Presentation]Authored by: Cox, M., Eaton, C.
Eaton, C., Cox, M., Hesse, U., Schardl, C., & Scott, D. (2010, August). Transcriptome analysis of Epichloe festucae - perennial ryegrass symbiotic associations. Presented at IMC9 - The biology of fungi. Edinburgh, United Kingdom.
[Conference Oral Presentation]Authored by: Cox, M., Eaton, C., Scott, D.

IP

Glare, TR., Hampton, JG., Cox, MP., & Bienkowski, DA.(2015). . 13/837,735: USA: Biocontrol Composition
[Patent]Authored by: Cox, M.
Glare, TR., Hampton, JG., Cox, MP., & Ormskirk, MM.(2015). . 61/745,701: USA: Polynucleotides, Polypeptides, and Methods of Use
[Patent]Authored by: Cox, M.

Other

Schmid, J., Zhou, Y., Truglio, M., Cox, M., Dupont, PY., Zhang, N., . . . Day, R. (2015, November). Interplay of Epichloë fectucae var. lolii and its host Lolium perenne as assessed by tissue-specific transcriptome analysis.
[Oral Presentation]Authored by: Cox, M., Dupont, P., Schmid, J.

Supervision and Teaching

Summary of Doctoral Supervision

Position Current Completed
Supervisor 1 1
CoSupervisor 5 3

Courses Coordinated

Current Doctoral Supervision

Supervisor of:

  • Jiri Moravec - PhD
    The dynamics of postmarital residence change.

CoSupervisor of:

  • Valentijn Jansen - PhD
    Investigating the cyto-nuclear limitations in hybridization in plants
  • Panchamee Dharmadasa - PhD
    Genetic, epigenetic and reproductive impacts of low-level exposure to environmentally ubiquitous contaminants
  • Nikolai Kondratev - PhD
    Carmellia petal blight resistance: Uncovering the veil
  • Jessie Owen - PhD
    Biophysical approaches to elucidating structure-function relationships in polysaccharide co-polymer systems
  • Paul Richard Yulo - PhD
    Genetics and Evolution of Cell Shape in Bacteria

Completed Doctoral Supervision

Supervisor of:

CoSupervisor of:

  • 2015 - Julian Robert Spagnuolo - PhD
    Extracytoplasmic Stress Responses Induced by a Model Secretin
  • 2015 - Matthew Denton-Giles - PhD
    Characterization of incompatible and compatible Camellia-Ciborinia camelliae plant-pathogen interactions
  • 2014 - Saumya Agrawal - PhD
    Characterisation of the human nucleolar organiser regions

Media and Links

Media

  • 01 Jan 2015 - Newspaper, Magazine, Radio, Online
    Extensive International Media Interest
    2012-2015 International Media Interest Radio interviews on BBC World, the Canadian Broadcasting Corporation and Radio New Zealand. Articles in New Scientist, The Economist, The New York Times and othe

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