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Prof Murray Cox staff profile picture

Contact details +6469517747

Prof Murray Cox DSc, PhD, BSc(Hons), JP, CMInstD

Professor in Computational Biology

Doctoral Supervisor
School of Fundamental Sciences

Deputy Head of School

School of Fundamental Sciences

My research 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.

Professional

Contact details

  • Ph: +64-6-951 7747
    Location: 5.04, Science Tower D
    Campus: Turitea

Qualifications

  • Doctor of Science - University of Otago (2017)
  • Doctor of Philosophy - University of Otago (2003)
  • Bachelor of Science (Honours) - University of Otago (2000)

Fellowships and Memberships

  • Member, Justice of the Peace (Life Member) (2019)
  • Member, Institute of Directors (Other) (2021)

Certifications and Registrations

  • Licence, Supervisor, Massey University

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.

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 16
Team Member 1 0

Current Projects

Project Title: Unravelling the 3D structure of archaic hominin DNA in the human gene

Date Range: 2021 - 2024

Funding Body: Royal Society of New Zealand

Project Team:

Project Title: Getting the balance right: How do allopolyploids successfully integrate interspecific nuclear and cytoplasmic genomes?

Date Range: 2019 - 2023

Funding Body: Royal Society of New Zealand

Project Team:

Project Title: From genotypes to phenotypes: Quantifying the functional load

Date Range: 2018 - 2022

Funding Body: Royal Society of New Zealand

Project Team:

Completed Projects

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

Date Range: 2015 - 2019

Funding Body: Royal Society of New Zealand

Project Team:

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

Olivera, C., Cox, MP., Rowlands, GJ., & Rakonjac, J. (2021). Correlated Transcriptional Responses Provide Insights into the Synergy Mechanisms of the Furazolidone, Vancomycin, and Sodium Deoxycholate Triple Combination in Escherichia coli.. mSphere. , e0062721
[Journal article]Authored by: Cox, M., Rakonjac, J., Rowlands, G.
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Brucato, N., André, M., Tsang, R., Saag, L., Kariwiga, J., Sesuki, K., . . . Ricaut, F-X. (2021). Papua New Guinean genomes reveal the complex settlement of north Sahul.. Mol Biol Evol.
[Journal article]Authored by: Cox, M.
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Sitter, TL., Vaughan, AL., Schoof, M., Jackson, SA., Glare, TR., Cox, MP., . . . Hurst, MRH. (2021). Evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology. 23(9), 5289-5304
[Journal article]Authored by: Cox, M.
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Wu, B., & Cox, MP. (2021). Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi. Environmental Microbiology. 23(6), 3251-3264
[Journal article]Authored by: Cox, M., Wu, B.
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Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, AH., . . . Krone, O. (2021). Author Correction: Dense sampling of bird diversity increases power of comparative genomics (Nature, (2020), 587, 7833, (252-257), 10.1038/s41586-020-2873-9). Nature. 592(7856), E24
[Journal article]Authored by: Battley, P., Cox, M.
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Teixeira, JC., Jacobs, GS., Stringer, C., Tuke, J., Hudjashov, G., Purnomo, GA., . . . Helgen, KM. (2021). Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nature Ecology and Evolution. 5(5), 616-624
[Journal article]Authored by: Cox, M.
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Wu, B., & Cox, MP. (2021). Characterization of bicistronic transcription in budding yeast. mSystems. 6(1)
[Journal article]Authored by: Cox, M., Wu, B.
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Lukito, Y., Lee, K., Noorifar, N., Green, KA., Winter, DJ., Ram, A., . . . Scott, B. (2021). Regulation of host-infection ability in the grass-symbiotic fungus Epichloë festucae by histone H3K9 and H3K36 methyltransferases. Environmental Microbiology. 23(4), 2116-2131
[Journal article]Authored by: Cox, M., Hale, T., Scott, D.
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Lukito, Y., Lee, K., Noorifar, N., Green, KA., Winter, DJ., Ram, A., . . . Scott, B. (2020). Regulation of host-infection ability in the grass-symbiotic fungus Epichloe festucae by histone H3K9 and H3K36 methyltransferases. ENVIRONMENTAL MICROBIOLOGY.
[Journal article]Authored by: Cox, M., Hale, T.
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Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, AH., . . . Krone, O. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature. 587(7833), 252-257
[Journal article]Authored by: Battley, P., Cox, M.
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Glare, T., Campbell, M., Biggs, P., Winter, D., Durrant, A., McKinnon, A., . . . Cox, M. (2020). Mitochondrial evolution in the entomopathogenic fungal genus Beauveria. Archives of Insect Biochemistry and Physiology. 105(4)
[Journal article]Authored by: Biggs, P., Cox, M.
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1
Lukito, Y., Lee, K., Noorifar, N., Green, K., Winter, D., Ram, A., . . . Scott, B. (2020). Host infection by the grass-symbiotic fungus Epichloë festucae requires catalytically active H3K9 and H3K36 methyltransferases.
[Journal article]Authored by: Cox, M.
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Natri, H., Hudjashov, G., Jacobs, G., Kusuma, P., Saag, L., Darusallam, CC., . . . Banovich, N. (2020). Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression.
[Journal article]Authored by: Cox, M.
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Garcia-R, JC., Cox, MP., & Hayman, DTS. (2020). Comparative genetic diversity of Cryptosporidium species causing human infections. Parasitology. 147(13), 1532-1537
[Journal article]Authored by: Cox, M., Garcia Ramirez, J., Hayman, D.
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Vespasiani, D., Jacobs, G., Cook, L., Brucato, N., Leavesley, M., Kinipi, C., . . . Romero, IG. (2020). Denisovan introgression has shaped the immune system of present-day Papuans.
[Journal article]Authored by: Cox, M.
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Teixeira, J., Jacobs, G., Stringer, C., Tuke, J., Hudjashov, G., Purnomo, G., . . . Helgen, K. (2020). Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia.
[Journal article]Authored by: Cox, M.
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Inwood, SN., McLaughlin, GM., Buckley, TR., Cox, MP., Handley, KM., Steeves, TE., . . . Dearden, PK. (2020). Opportunities for modern genetic technologies to maintain and enhance aotearoa New Zealand’s bioheritage. New Zealand Journal of Ecology. 44(2), 1-13
[Journal article]Authored by: Cox, M.
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Pedro, N., Brucato, N., Fernandes, V., André, M., Saag, L., Pomat, W., . . . Ricaut, FX. (2020). Papuan mitochondrial genomes and the settlement of Sahul. Journal of Human Genetics. 65(10), 875-887
[Journal article]Authored by: Cox, M.
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Natri, HM., Bobowik, KS., Kusuma, P., Darusallam, CC., Jacobs, GS., Hudjashov, G., . . . Romero, IG. (2020). Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genetics. 16(5)
[Journal article]Authored by: Cox, M.
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Cagnano, G., Lenk, I., Roulund, N., Jensen, CS., Cox, MP., & Asp, T. (2020). Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis). Mycologia. 112(3), 474-490
[Journal article]Authored by: Cox, M.
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Kondratev, N., Denton-Giles, M., Bradshaw, RE., Cox, MP., & Dijkwel, PP. (2020). Camellia plant resistance and susceptibility to petal blight disease are defined by the timing of defense responses. Molecular Plant-Microbe Interactions. 33(7), 982-995
[Journal article]Authored by: Bradshaw, R., Cox, M., Dijkwel, P.
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Denton-Giles, M., McCarthy, H., Sehrish, T., Dijkwel, Y., Mesarich, CH., Bradshaw, RE., . . . Dijkwel, PP. (2020). Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae. Molecular Plant Pathology. 21(4), 512-526
[Journal article]Authored by: Bradshaw, R., Cox, M., Dijkwel, P., Mesarich, C.
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Bücking, R., Cox, MP., Hudjashov, G., Saag, L., Sudoyo, H., & Stoneking, M. (2020). Erratum: Archaic mitochondrial DNA inserts in modern day nuclear genomes (BMC Genomics (2019) 20 (1017) DOI: 10.1186/s12864-019-6392-8). BMC Genomics. 21(1)
[Journal article]Authored by: Cox, M.
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Behling, AH., Shepherd, LD., & Cox, MP. (2020). The importance and prevalence of allopolyploidy in Aotearoa New Zealand. Journal of the Royal Society of New Zealand. 50(2), 189-210
[Journal article]Authored by: Cox, M.
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Winter, DJ., Charlton, ND., Krom, N., Shiller, J., Bock, CH., Cox, MP., . . . Young, CA. (2020). Chromosome-level reference genome of venturia effusa, causative agent of pecan scab. Molecular Plant-Microbe Interactions. 33(2), 149-152
[Journal article]Authored by: Cox, M.
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Glare, TR., Durrant, A., Berry, C., Palma, L., Ormskirk, MM., & Cox, MP. (2020). Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus. Genomics. 112(1), 1042-1053
[Journal article]Authored by: Cox, M.
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Bücking, R., Cox, MP., Hudjashov, G., Saag, L., Sudoyo, H., & Stoneking, M. (2019). Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics. 20(1)
[Journal article]Authored by: Cox, M.
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Wall, JD., Stawiski, EW., Ratan, A., Kim, HL., Kim, C., Gupta, R., . . . Peterson, AS. (2019). The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature. 576(7785), 106-111
[Journal article]Authored by: Cox, M.
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Bradshaw, RE., Ormond, S., Dupont, PY., Chettri, P., Ozturk, IK., McDougal, RL., . . . Cox, MP. (2019). Reduced virulence of an introduced forest pathogen over 50 years. Microorganisms. 7(10)
[Journal article]Authored by: Bradshaw, R., Cox, M.
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Wu, B., & Cox, MP. (2019). Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi. Molecular Ecology. 28(23), 5103-5114
[Journal article]Authored by: Cox, M., Wu, B.
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1
Zammit, NW., Siggs, OM., Gray, PE., Horikawa, K., Langley, DB., Walters, SN., . . . Grey, ST. (2019). Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity. Nature Immunology. 20(10), 1299-1310
[Journal article]Authored by: Cox, M.
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Chung, NN., Jacobs, GS., Sudoyo, H., Malik, SG., Chew, LY., Lansing, JS., . . . Cox, MP. (2019). Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales. Royal Society Open Science. 6(8)
[Journal article]Authored by: Cox, M.
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Winter, D., Charlton, N., Krom, N., Shiller, J., Bock, C., Cox, M., . . . Young, C. (2019). Chromosome-level genome reference of Venturia effusa, causative agent of pecan scab.
[Journal article]Authored by: Cox, M.
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Natri, H., Bobowik, K., Kusuma, P., Darusallam, CC., Jacobs, G., Hudjashov, G., . . . Gallego Romero, I. (2019). Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.
[Journal article]Authored by: Cox, M.
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Brzozowska, MM., Havula, E., Allen, RB., & Cox, MP. (2019). Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians. Reviews in Endocrine and Metabolic Disorders. 20(3), 321-332
[Journal article]Authored by: Cox, M.
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Moravec, JC., Marsland, S., & Cox, MP. (2019). Warfare induces post-marital residence change. Journal of Theoretical Biology. 474, 52-62
[Journal article]Authored by: Cox, M.
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Griffiths, AG., Moraga, R., Tausen, M., Gupta, V., Bilton, TP., Campbell, MA., . . . Andersen, SU. (2019). Breaking free: The genomics of allopolyploidy-facilitated niche expansion in white clover. Plant Cell. 31(7), 1466-1487
[Journal article]Authored by: Cox, M.
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Bradshaw, RE., Sim, AD., Chettri, P., Dupont, PY., Guo, Y., Hunziker, L., . . . Barnes, I. (2019). Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains. Molecular Plant Pathology. 20(6), 784-799
[Journal article]Authored by: Bradshaw, R., Cox, M.
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Brucato, N., Fernandes, V., Kusuma, P., Cerny, V., Mulligan, CJ., Soares, P., . . . Saitou, N. (2019). Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia. Genome Biology and Evolution. 11(3), 748-758
[Journal article]Authored by: Cox, M.
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Chujo, T., Lukito, Y., Eaton, CJ., Dupont, PY., Johnson, LJ., Winter, D., . . . Scott, B. (2019). Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genetics and Biology. 125, 71-83
[Journal article]Authored by: Cox, M., Scott, D.
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Whaanga, H., Wehi, P., Cox, M., Roa, T., & Kusabs, I. (2018). Māori oral traditions record and convey indigenous knowledge of marine and freshwater resources. New Zealand Journal of Marine and Freshwater Research. 52(4), 487-496
[Journal article]Authored by: Cox, M.
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Winter, D., Ganley, ARD., Young, C., Liachko, I., Schardl, C., Dupont, P-Y., . . . Cox, M. (2018). Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae.
[Journal article]Authored by: Cox, M.
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Winter, DJ., Ganley, ARD., Young, CA., Liachko, I., Schardl, CL., Dupont, PY., . . . Cox, MP. (2018). Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genetics. 14(10)
[Journal article]Authored by: Cox, M., Scott, D.
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Wehi, PM., Cox, MP., Roa, T., & Whaanga, H. (2018). Correction to: Human Perceptions of Megafaunal Extinction Events Revealed by Linguistic Analysis of Indigenous Oral Traditions (Human Ecology, (2018), 46, 4, (461-470), 10.1007/s10745-018-0004-0). Human Ecology. 46(4), 471
[Journal article]Authored by: Cox, M.
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Robertson, SP., Hindmarsh, JH., Berry, S., Cameron, VA., Cox, MP., Dewes, O., . . . Wilcox, P. (2018). Genomic medicine must reduce, not compound, health inequities: The case for hauora-enhancing genomic resources for New Zealand. New Zealand Medical Journal. 131(1480), 81-89
[Journal article]Authored by: Cox, M.
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Wehi, PM., Cox, MP., Roa, T., & Whaanga, H. (2018). Human Perceptions of Megafaunal Extinction Events Revealed by Linguistic Analysis of Indigenous Oral Traditions. Human Ecology. 46(4), 461-470
[Journal article]Authored by: Cox, M.
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Moravec, JC., Atkinson, Q., Bowern, C., Greenhill, SJ., Jordan, FM., Ross, RM., . . . Cox, MP. (2018). Post-marital residence patterns show lineage-specific evolution. Evolution and Human Behavior. 39(6), 594-601
[Journal article]Authored by: Cox, M.
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Hudjashov, G., Endicott, P., Post, H., Nagle, N., Ho, SYW., Lawson, DJ., . . . Herrera, RJ. (2018). Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Scientific Reports. 8(1)
[Journal article]Authored by: Cox, M.
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Brucato, N., Fernandes, V., Mazières, S., Kusuma, P., Cox, MP., Ng'ang'a, JW., . . . Ricaut, FX. (2018). The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor. American Journal of Human Genetics. 102(1), 58-68
[Journal article]Authored by: Cox, M.
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Campbell, MA., Tapper, BA., Simpson, WR., Johnson, RD., Mace, W., Ram, A., . . . Cox, MP. (2017). Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy. Mycologia. 109(5), 715-729
[Journal article]Authored by: Cox, M., Scott, D.
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Lansing, JS., Abundo, C., Jacobs, GS., Guillot, EG., Thurner, S., Downey, SS., . . . Cox, MP. (2017). Kinship structures create persistent channels for language transmission. Proceedings of the National Academy of Sciences of the United States of America. 114(49), 12910-12915
[Journal article]Authored by: Cox, M.
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Hudjashov, G., Karafet, TM., Lawson, DJ., Downey, S., Savina, O., Sudoyo, H., . . . Cox, MP. (2017). Complex Patterns of Admixture across the Indonesian Archipelago. Molecular Biology and Evolution. 34(10), 2439-2452
[Journal article]Authored by: Cox, M.
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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.
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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.
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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.
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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.
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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., Zhang, N.
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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.
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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.
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Pagani, L., Lawson, DJ., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, M., . . . Metspalu, M. (2016). Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 538(7624), 238-242
[Journal article]Authored by: Cox, M.
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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.
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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.
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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.
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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.
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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.
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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.
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2
2
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.
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15
12
Cox, MP., & Guillot, EG. (2016). High Frequency Haplotypes are Expected Events, not Historical Figures. F1000Research. 4
[Journal article]Authored by: Cox, M.
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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.
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4
3
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., Guo, Y.
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26
23
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: Cox, M., Scott, D.
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1
Eaton, CJ., Dupont, P-Y., 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 : MPMI. 28, 218-231
[Journal article]Authored by: Cox, M., Scott, D.
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Cox, MP., & Guillot, EG. (2015). High Frequency Haplotypes are Expected Events, not Historical Figures. F1000Research. 4
[Journal article]Authored by: Cox, M.
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3
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., Guo, Y.
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5
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.
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4
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., Scott, D., Wargent, J.
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93
73
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., Scott, D.
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17
16
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.
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13
13
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.
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13
12
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.
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23
21
Karmin, M., Saag, L., Vicente, M., Wilson Sayres, MA., Järve, M., Talas, UG., . . . Kivisild, T. (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.
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188
174
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.
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10
12
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.
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2
1
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., Scott, D.
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39
36
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.
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12
12
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.
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5
5
Schardl, CL., Young, CA., Moore, N., Krom, N., Dupont, PY., Pan, J., . . . Farman, ML. (2014). Genomes of plant-associated clavicipitaceae. 70, 291-327
[Journal article]Authored by: Cox, M.
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26
23
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.
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9
11
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.
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32
32
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.
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26
27
Eaton, CJ., Cabrera, IE., Servin, JA., Wright, SJ., Cox, MP., & Borkovich, KA. (2013). Correction: The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in.. PloS one. 8(3)
[Journal article]Authored by: Cox, M.
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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.
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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.
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10
12
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., Scott, D.
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249
232
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.
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19
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.
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786
Cox, MP., & Hammer, MF. (2010). A question of scale: Human migrations writ large and small. BMC BIOLOGY. 8,
[Journal article]Authored by: Cox, M.
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11
Cox, MP. (2009). Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations Under a Range of Demographic Models. HUMAN BIOLOGY. 81(5-6), 911-933
[Journal article]Authored by: Cox, M.
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4
Cox, MP. (2005). Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in island southeast Asia. HUMAN BIOLOGY. 77(2), 179-188
[Journal article]Authored by: Cox, M.
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25
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.
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71
60
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: Bradshaw, R., Cox, M.
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38
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.
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3
3
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.
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34
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: Bradshaw, R., Cox, M.
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24
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.
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23
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.
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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.
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171
139
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.
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19
17
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.
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41
40
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.
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5
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.
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4
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.
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33
31
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.
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16
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.
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9
8
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., Scott, D.
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102
90
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.
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6
6
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.
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41
40
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.
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96
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.
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65
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., Scott, D.
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95
85
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., Scott, D.
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7
4
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.
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874
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.
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Cox, MP., & Hammer, MF. (2010). A question of scale: Human migrations writ large and small. BMC Biology. 8
[Journal article]Authored by: Cox, M.
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12
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.
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40
39
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.
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19
16
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.
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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.
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40
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.
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64
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.
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27
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.
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40
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.
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30
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.
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98
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.
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15
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.
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15
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.
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26
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.
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53
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.
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162
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.
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60
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.
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56
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.
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19
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.
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28
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.
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5
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.
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13

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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. (2015). The genetic history of human populations in Island Southeast Asia during the Late Pleistocene and Holocene. In P. Bellwood (Ed.) Prehistory of the Indo-Malaysian Archipelago. Canberra, Australia: Australian National University Press
[Chapter]Authored by: Cox, M.
Cox, MP. (2015). The genetic history of human populations in Island Southeast Asia during the Late Pleistocene and Holocene. In P. Bellwood (Ed.) Prehistory of the Indo-Malaysian Archipelago. Canberra, Australia: Australian National University Press
[Chapter]Authored by: Cox, M.
Cox, MP. (2015). The genetic history of human populations in Island Southeast Asia during the Late Pleistocene and Holocene. In P. Bellwood (Ed.) Prehistory of the Indo-Malaysian Archipelago. Canberra, Australia: Australian National University Press
[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.
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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.

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Conference

Jacobs, GS., Hudjashov, G., Saag, L., Kusuma, P., Darusallam, CC., Lawson, DJ., . . . Cox, MP.Multiple Deeply Divergent Denisovan Ancestries in Papuans. Cell. 177 (4)(pp. 1010 - 1021.e32). 0092-8674.
[Conference]Authored by: Cox, M.
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Schrefheere, A., Campbell, M., Tate, J., Cox, M., & Vignes, MCL.Statistical modelling of expression patterns in hybrid species. Paper presented at the meeting of JOURNÉES OUVERTES DE BIOLOGIE INFORMATIQUE & MATHÉMATIQUES. Lyon, France
[Conference Paper]Authored by: Cox, M., Tate, J., Vignes, M.
Chujo, T., Lukito, Y., Eaton, C., Dupont, P-Y., Johnson, L., Cox, M., . . . Scott, B. (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., 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., Tate, J., Vignes, M.
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Bradshaw, RE., Guo, Y., Sim, AD., Kabir, MS., Chettri, P., Ozturk, IK., . . . Cox, MP. (2015, August). Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata. Presented at New Zealand Next Generation Sequencing Conference. Palmerston North, New Zealand.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M., Guo, Y.
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Bradshaw, RE., Guo, Y., Sim, A., Kabir, MS., Chettri, P., Ozturk, IK., . . . Cox, MP. (2015, October). A gene expression study provides insights into how Dothistroma septosporum causes disease. Presented at Determining Invasiveness And Risk Of Dothistroma Management Committee Meeting. Krakow, Poland.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M., Guo, Y.
Bradshaw, RE., Guo, Y., Sim, A., Kabir, MS., Chettri, P., Ozturk, IK., . . . Cox, MP. (2015, September). Transcriptome of the foliar gymnosperm pathogen Dothistroma septosporum. Presented at Australasian Plant Pathology Conference. Fremantle, WA, Australia.
[Conference Oral Presentation]Authored by: Bradshaw, R., Cox, M., Guo, Y.
Cox, MP., Campbell, M., Dong, T., Shen, G-G., Dalvi, Y., Scott, B., . . . Ganley, ARD. (2015). Epichloë endophytes: a powerful model system for determining genomic responses to genome merger. Poster session presented at the meeting of 28th Fungal Genetics Conference, Pacific Grove, California
[Conference Poster]Authored by: Cox, M., Scott, D.
Dupont, P-Y., Eaton, C., Wargent, J., Fechtner, S., Solomon, P., Schmid, J., . . . Cox, M. (2015). Epichloë endophytes: a powerful model system for determining genomic responses to genome merger. Poster session presented at the meeting of 28th Fungal Genetics Conference, Pacific Grove, California
[Conference Poster]Authored by: Cox, M., 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. Presented at Plant-fungal interaction symposium
[Conference Oral Presentation]Authored by: Cox, M., 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., 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.
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., Scott, D.
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., 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.
Eaton, CJ., Dupont, PY., Solomon, P., Clayton, W., Scott, B., & Cox, MP. (2014). A core gene set underpins the shift from mutualism to antagonism in multiple Epichloë symbiotic mutants.. Poster session presented at the meeting of 24th Queenstown Molecular Biology Meeting. Queenstown, New Zealand
[Conference Poster]Authored by: Cox, M., 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.
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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., 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.
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.
Eaton, CJ., Dupont, PY., Cox, M., Tanaka, A., & Scott, DB. (2013, November). Friends don't eat friends: loss of endophyte mutualism triggers activation of host degradation. Presented at 19th Australasian Plant Pathology Conference (APPS 2013). University of Auckland, New Zealand.
[Conference Oral Presentation]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 19th Australasian Plant Pathology Conference (APPS 2013). Auckland, New Zealand.
[Conference Oral Presentation]Authored by: Cox, M., 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”. Auckland, New Zealand.
[Conference Oral Presentation]Authored by: Cox, M., Scott, D.
Bradshaw, RE., Guo, Y., Kabir, MS., Chettri, P., Cox, MP., Okmen, B., . . . de Wit, 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., Guo, Y.
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.
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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., Zhang, N.
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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.
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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., Zhang, N.
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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., Zhang, N.
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4
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.
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., 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., Scott, D.

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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.
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Teaching and Supervision

Contact Supervisor

Summary of Doctoral Supervision

Position Current Completed
Main Supervisor 0 2
Co-supervisor 2 8

Current Doctoral Supervision

Co-supervisor of:

  • Usama Mukhtar - Doctor of Philosophy
    Physiological changes and cytonuclear interactions after allopolyploidy in Tragopogon
  • Sidra Hussain - Doctor of Philosophy
    Evolution of Cytonuclear Coordination in Tragopogon (Asteraceae) Allopolyploids

Completed Doctoral Supervision

Main Supervisor of:

  • 2019 - Jiri Moravec - Doctor of Philosophy
    Computational approaches to the study of post-marital residence
  • 2015 - Elsa Guillot - Doctor of Philosophy
    Modelling the role of social structures in population genetics

Co-supervisor of:

  • 2021 - Catrina Olivera - Doctor of Philosophy
    Synergistic triple combination antibiotic therapy for Gram-negative bacterial infections
  • 2019 - Lokugama Hewage Panchamee Dharmadasa - Doctor of Philosophy
    Investigations into the Uptake and Effects of Long-term Cadmium and Arsenic Exposure on the Earthworm Eisenia fetida
  • 2019 - Nikolai Kondratev - Doctor of Philosophy
    Identification of mechanisms defining resistance and susceptibility of Camellia plants to necrotrophic petal blight disease
  • 2019 - Paul Richard Yulo - Doctor of Philosophy
    Evolution of the Spherical Cell Shape in Bacteria
  • 2018 - Simren Brar - Doctor of Philosophy
    Genetic diversity and gene expression analysis of Phytophthora pluvialis, a foliar pathogen of conifers
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  • 2015 - Julian Spagnuolo - Doctor of Philosophy
    Extracytoplasmic Stress Responses Induced by a Model Secretin
  • 2015 - Matthew Denton-Giles - Doctor of Philosophy
    Characterization of incompatible and compatible Camellia-Ciborinia camelliae plant-pathogen interactions
  • 2014 - Saumya Agrawal - Doctor of Philosophy
    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

Other Links