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Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae.

Denton-Giles M, McCarthy H, Sehrish T, Dijkwel Y, Mesarich CH, Bradshaw RE, Cox MP, Dijkwel PP.

Mol Plant Pathol. 2020 Feb 15. doi: 10.1111/mpp.12913. [Epub ahead of print]


Correction to: Archaic mitochondrial DNA inserts in modern day nuclear genomes.

Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M.

BMC Genomics. 2020 Jan 17;21(1):55. doi: 10.1186/s12864-020-6449-8.


Archaic mitochondrial DNA inserts in modern day nuclear genomes.

Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M.

BMC Genomics. 2019 Dec 26;20(1):1017. doi: 10.1186/s12864-019-6392-8. Erratum in: BMC Genomics. 2020 Jan 17;21(1):55.


Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab.

Winter DJ, Charlton ND, Krom N, Shiller J, Bock CH, Cox MP, Young CA.

Mol Plant Microbe Interact. 2020 Feb;33(2):149-152. doi: 10.1094/MPMI-08-19-0236-A. Epub 2019 Dec 2.


Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi.

Wu B, Cox MP.

Mol Ecol. 2019 Dec;28(23):5103-5114. doi: 10.1111/mec.15275. Epub 2019 Nov 6.


Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales.

Chung NN, Jacobs GS, Sudoyo H, Malik SG, Chew LY, Lansing JS, Cox MP.

R Soc Open Sci. 2019 Aug 28;6(8):190733. doi: 10.1098/rsos.190733. eCollection 2019 Aug.


Reduced Virulence of an Introduced Forest Pathogen over 50 Years.

Bradshaw RE, Ormond S, Dupont PY, Chettri P, Ozturk IK, McDougal RL, Bulman LS, Cox MP.

Microorganisms. 2019 Oct 5;7(10). pii: E420. doi: 10.3390/microorganisms7100420.


Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity.

Zammit NW, Siggs OM, Gray PE, Horikawa K, Langley DB, Walters SN, Daley SR, Loetsch C, Warren J, Yap JY, Cultrone D, Russell A, Malle EK, Villanueva JE, Cowley MJ, Gayevskiy V, Dinger ME, Brink R, Zahra D, Chaudhri G, Karupiah G, Whittle B, Roots C, Bertram E, Yamada M, Jeelall Y, Enders A, Clifton BE, Mabbitt PD, Jackson CJ, Watson SR, Jenne CN, Lanier LL, Wiltshire T, Spitzer MH, Nolan GP, Schmitz F, Aderem A, Porebski BT, Buckle AM, Abbott DW, Ziegler JB, Craig ME, Benitez-Aguirre P, Teo J, Tangye SG, King C, Wong M, Cox MP, Phung W, Tang J, Sandoval W, Wertz IE, Christ D, Goodnow CC, Grey ST.

Nat Immunol. 2019 Oct;20(10):1299-1310. doi: 10.1038/s41590-019-0492-0. Epub 2019 Sep 18.


Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.

Brzozowska MM, Havula E, Allen RB, Cox MP.

Rev Endocr Metab Disord. 2019 Sep;20(3):321-332. doi: 10.1007/s11154-019-09505-z. Review.


Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus.

Glare TR, Durrant A, Berry C, Palma L, Ormskirk MM, Cox MP.

Genomics. 2020 Jan;112(1):1042-1053. doi: 10.1016/j.ygeno.2019.06.020. Epub 2019 Jun 19.


Warfare induces post-marital residence change.

Moravec JC, Marsland S, Cox MP.

J Theor Biol. 2019 Aug 7;474:52-62. doi: 10.1016/j.jtbi.2019.05.002. Epub 2019 May 3.


Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover.

Griffiths AG, Moraga R, Tausen M, Gupta V, Bilton TP, Campbell MA, Ashby R, Nagy I, Khan A, Larking A, Anderson C, Franzmayr B, Hancock K, Scott A, Ellison NW, Cox MP, Asp T, Mailund T, Schierup MH, Andersen SU.

Plant Cell. 2019 Jul;31(7):1466-1487. doi: 10.1105/tpc.18.00606. Epub 2019 Apr 25.


Multiple Deeply Divergent Denisovan Ancestries in Papuans.

Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson DJ, Mondal M, Pagani L, Ricaut FX, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP.

Cell. 2019 May 2;177(4):1010-1021.e32. doi: 10.1016/j.cell.2019.02.035. Epub 2019 Apr 11.


Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains.

Bradshaw RE, Sim AD, Chettri P, Dupont PY, Guo Y, Hunziker L, McDougal RL, Van der Nest A, Fourie A, Wheeler D, Cox MP, Barnes I.

Mol Plant Pathol. 2019 Jun;20(6):784-799. doi: 10.1111/mpp.12791. Epub 2019 Apr 1.


Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis.

Chujo T, Lukito Y, Eaton CJ, Dupont PY, Johnson LJ, Winter D, Cox MP, Scott B.

Fungal Genet Biol. 2019 Apr;125:71-83. doi: 10.1016/j.fgb.2019.02.001. Epub 2019 Feb 4.


Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia.

Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze JF, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut FX.

Genome Biol Evol. 2019 Mar 1;11(3):748-758. doi: 10.1093/gbe/evz028.


Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae.

Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont PY, Berry D, Ram A, Scott B, Cox MP.

PLoS Genet. 2018 Oct 24;14(10):e1007467. doi: 10.1371/journal.pgen.1007467. eCollection 2018 Oct.


Human Perceptions of Megafaunal Extinction Events Revealed by Linguistic Analysis of Indigenous Oral Traditions.

Wehi PM, Cox MP, Roa T, Whaanga H.

Hum Ecol Interdiscip J. 2018;46(4):461-470. doi: 10.1007/s10745-018-0004-0. Epub 2018 Jun 4.


Genomic medicine must reduce, not compound, health inequities: the case for hauora-enhancing genomic resources for New Zealand.

Robertson SP, Hindmarsh JH, Berry S, Cameron VA, Cox MP, Dewes O, Doughty RN, Gray G, Jacobsen JC, Laurence A, Matisoo-Smith E, Morton S, Shelling AN, Sika-Paotonu D, Rolleston A, Skinner JR, Snell RG, Sporle A, Print C, Merriman TR, Hudson M, Wilcox P.

N Z Med J. 2018 Aug 17;131(1480):81-89.


Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles.

Hudjashov G, Endicott P, Post H, Nagle N, Ho SYW, Lawson DJ, Reidla M, Karmin M, Rootsi S, Metspalu E, Saag L, Villems R, Cox MP, Mitchell RJ, Garcia-Bertrand RL, Metspalu M, Herrera RJ.

Sci Rep. 2018 Jan 29;8(1):1823. doi: 10.1038/s41598-018-20026-8.


Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy.

Campbell MA, Tapper BA, Simpson WR, Johnson RD, Mace W, Ram A, Lukito Y, Dupont PY, Johnson LJ, Scott DB, Ganley ARD, Cox MP.

Mycologia. 2017;109(5):715-729. doi: 10.1080/00275514.2017.1406174. Epub 2018 Jan 25.


The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor.

Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng'ang'a JW, Omar M, Simeone-Senelle MC, Frassati C, Alshamali F, Fin B, Boland A, Deleuze JF, Stoneking M, Adelaar A, Crowther A, Boivin N, Pereira L, Bailly P, Chiaroni J, Ricaut FX.

Am J Hum Genet. 2018 Jan 4;102(1):58-68. doi: 10.1016/j.ajhg.2017.11.011.


Kinship structures create persistent channels for language transmission.

Lansing JS, Abundo C, Jacobs GS, Guillot EG, Thurner S, Downey SS, Chew LY, Bhattacharya T, Chung NN, Sudoyo H, Cox MP.

Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):12910-12915. doi: 10.1073/pnas.1706416114. Epub 2017 Nov 20.


Complex Patterns of Admixture across the Indonesian Archipelago.

Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP.

Mol Biol Evol. 2017 Oct 1;34(10):2439-2452. doi: 10.1093/molbev/msx196.


Insights into the Geobacillus stearothermophilus species based on phylogenomic principles.

Burgess SA, Flint SH, Lindsay D, Cox MP, Biggs PJ.

BMC Microbiol. 2017 Jun 26;17(1):140. doi: 10.1186/s12866-017-1047-x.


Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network.

Brucato N, Kusuma P, Beaujard P, Sudoyo H, Cox MP, Ricaut FX.

Sci Rep. 2017 Jun 7;7(1):2919. doi: 10.1038/s41598-017-03204-y.


Diagnosing a painful abdominal hernia.

Nagra NS, Cox MP, Nana GR, Isherwood J.

Emerg Med J. 2017 Jun;34(6):356. doi: 10.1136/emermed-2016-205820. No abstract available.


The last sea nomads of the Indonesian archipelago: genomic origins and dispersal.

Kusuma P, Brucato N, Cox MP, Letellier T, Manan A, Nuraini C, Grangé P, Sudoyo H, Ricaut FX.

Eur J Hum Genet. 2017 Aug;25(8):1004-1010. doi: 10.1038/ejhg.2017.88. Epub 2017 May 17.


Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.

Dupont PY, Cox MP.

G3 (Bethesda). 2017 Apr 3;7(4):1301-1314. doi: 10.1534/g3.116.038448.


Host Tissue Environment Directs Activities of an Epichloë Endophyte, While It Induces Systemic Hormone and Defense Responses in Its Native Perennial Ryegrass Host.

Schmid J, Day R, Zhang N, Dupont PY, Cox MP, Schardl CL, Minards N, Truglio M, Moore N, Harris DR, Zhou Y.

Mol Plant Microbe Interact. 2017 Feb;30(2):138-149. doi: 10.1094/MPMI-10-16-0215-R. Epub 2017 Mar 3.


The Case of the Missing Ancient Fungal Polyploids.

Campbell MA, Ganley AR, Gabaldón T, Cox MP.

Am Nat. 2016 Dec;188(6):602-614. Epub 2016 Sep 26. Review.


Genomic insights into the peopling of the Southwest Pacific.

Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F, Bedford S, Clark GR, Reepmeyer C, Petchey F, Fernandes D, Fu Q, Harney E, Lipson M, Mallick S, Novak M, Rohland N, Stewardson K, Abdullah S, Cox MP, Friedlaender FR, Friedlaender JS, Kivisild T, Koki G, Kusuma P, Merriwether DA, Ricaut FX, Wee JT, Patterson N, Krause J, Pinhasi R, Reich D.

Nature. 2016 Oct 27;538(7626):510-513. doi: 10.1038/nature19844. Epub 2016 Oct 3.


Genomic analyses inform on migration events during the peopling of Eurasia.

Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M.

Nature. 2016 Oct 13;538(7624):238-242. doi: 10.1038/nature19792. Epub 2016 Sep 21.


Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo.

Brucato N, Kusuma P, Cox MP, Pierron D, Purnomo GA, Adelaar A, Kivisild T, Letellier T, Sudoyo H, Ricaut FX.

Mol Biol Evol. 2016 Sep;33(9):2396-400. doi: 10.1093/molbev/msw117. Epub 2016 Jul 5.


Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation.

Cox MP, Hudjashov G, Sim A, Savina O, Karafet TM, Sudoyo H, Lansing JS.

Mol Biol Evol. 2016 Sep;33(9):2273-84. doi: 10.1093/molbev/msw099. Epub 2016 Jun 7.


Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains.

Lange C, Weld RJ, Cox MP, Bradshaw RE, McLean KL, Stewart A, Steyaert JM.

PeerJ. 2016 May 12;4:e2023. doi: 10.7717/peerj.2023. eCollection 2016.


Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy.

Kusuma P, Brucato N, Cox MP, Pierron D, Razafindrazaka H, Adelaar A, Sudoyo H, Letellier T, Ricaut FX.

Sci Rep. 2016 May 18;6:26066. doi: 10.1038/srep26066.


High Frequency Haplotypes are Expected Events, not Historical Figures.

Guillot EG, Cox MP.

Version 2. F1000Res. 2015 Sep 4 [revised 2016 Jan 1];4:666. doi: 10.12688/f1000research.7023.2. eCollection 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.

de Wit PJ, van der Burgt A, Ökmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE.

PLoS Genet. 2015 Dec 22;11(12):e1005775. doi: 10.1371/journal.pgen.1005775. eCollection 2015 Dec. No abstract available.


Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.

Burgess SA, Cox MP, Flint SH, Lindsay D, Biggs PJ.

Genome Announc. 2015 Oct 15;3(5). pii: e00939-15. doi: 10.1128/genomeA.00939-15.


Fungal endophyte infection of ryegrass reprograms host metabolism and alters development.

Dupont PY, Eaton CJ, Wargent JJ, Fechtner S, Solomon P, Schmid J, Day RC, Scott B, Cox MP.

New Phytol. 2015 Dec;208(4):1227-40. doi: 10.1111/nph.13614. Epub 2015 Aug 25.


Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum.

Nicholson MJ, Eaton CJ, Stärkel C, Tapper BA, Cox MP, Scott B.

Toxins (Basel). 2015 Jul 23;7(8):2701-22. doi: 10.3390/toxins7082701.


Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.

Guillot EG, Hazelton ML, Karafet TM, Lansing JS, Sudoyo H, Cox MP.

Mol Biol Evol. 2015 Sep;32(9):2254-62. doi: 10.1093/molbev/msv102. Epub 2015 May 12.


Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata.

Bradshaw RE, Guo Y, Sim AD, Kabir MS, Chettri P, Ozturk IK, Hunziker L, Ganley RJ, Cox MP.

Mol Plant Pathol. 2016 Feb;17(2):210-24. doi: 10.1111/mpp.12273. Epub 2015 Jun 2.


Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.

Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut FX.

BMC Genomics. 2015 Mar 17;16:191. doi: 10.1186/s12864-015-1394-7.


Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.

Sanderson J, Sudoyo H, Karafet TM, Hammer MF, Cox MP.

Genetics. 2015 Jun;200(2):469-81. doi: 10.1534/genetics.115.176842. Epub 2015 Apr 7.


Clean graphene electrodes on organic thin-film devices via orthogonal fluorinated chemistry.

Beck JH, Barton RA, Cox MP, Alexandrou K, Petrone N, Olivieri G, Yang S, Hone J, Kymissis I.

Nano Lett. 2015 Apr 8;15(4):2555-61. doi: 10.1021/acs.nanolett.5b00110. Epub 2015 Mar 23.


A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T.

Genome Res. 2015 Apr;25(4):459-66. doi: 10.1101/gr.186684.114. Epub 2015 Mar 13.


Draft Genome Sequence of the Filamentous Fungus Penicillium paxilli (ATCC 26601).

Berry D, Cox MP, Scott B.

Genome Announc. 2015 Mar 12;3(2). pii: e00071-15. doi: 10.1128/genomeA.00071-15.

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