Journal
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.
[Journal article]Authored by: Cox, M.Read Online:
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Brucato, N., Fernandes, V., Kusuma, P., Černý, V., Mulligan, CJ., Soares, P., . . . Ricaut, FX. (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.Read Online:
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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., Lukito, Y., Scott, D., Winter, D.Read Online:
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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.Read Online:
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Winter, DJ., Ganley, A., Young, C., Liachko, I., Schardl, C., Dupont, P-Y., . . . Cox, M. (2018). Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae.
[Journal article]Authored by: Cox, M.Read Online:
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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: Berry, D., Cox, M., Scott, D., Winter, D.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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., Hudjasov, G.Read article at Massey Research Online:
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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.Read Online:
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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., Lukito, Y., Scott, D.Read Online:
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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.Read Online:
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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., Hudjasov, G.Read article at Massey Research Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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., Hudjasov, G.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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., Hazelton, M.Read Online:
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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., Hudjasov, G.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
Cox, MP., & Guillot, EG. (2015). High Frequency Haplotypes are Expected Events, not Historical Figures.
F1000Research. 4
[Journal article]Authored by: Cox, M.Read Online:
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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.Read Online:
Guillot, EG., & Cox, MP. (2015). High Frequency Haplotypes are Expected Events, not Historical Figures..
F1000Res. 4, 666
[Journal article]Authored by: Cox, M.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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., Hudjasov, G.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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.Read Online:
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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.Read Online:
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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 Neurospora crassa..
PloS one. 8(3)
[Journal article]Authored by: Cox, M.Read Online:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
Cox, MP., & Hammer, MF. (2010). A question of scale: Human migrations writ large and small.
BMC BIOLOGY. 8,
[Journal article]Authored by: Cox, M.Read Online:
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.Read Online:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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., Wilkins, M.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Online:
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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.Read Abstract:
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.Read Online:
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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.Read Online:
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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.Read Abstract:
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Conference
Jacobs, GS., Hudjashov, G., Lauri, S., Pradiptajati, K., Darusallam, CC., Lawson, DJ., . . . Cox, MP.Multiple deeply divergent Denisovan ancestries in Papuans.
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. (pp. 112 - 112). 0002-9483.
[Conference]Authored by: Cox, M.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., Vignes, M.Read Abstract:
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.Read Abstract:
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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.
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[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.Read Abstract:
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.Read Abstract:
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.Read Abstract:
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.Read Abstract:
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., Wilkins, M., Zhang, N.Read Online:
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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., Wilkins, M., Zhang, N.Read Abstract:
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.view less...
