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Items: 1 to 50 of 83

1.

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.

2.

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.

PMID:
29370579
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

PMID:
28539369
9.

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.

10.

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.

11.

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.

12.

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.

PMID:
27860510
13.

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.

14.
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

PMID:
25774924
30.

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.

31.

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.

32.

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species.

Duchemin W, Dupont PY, Campbell MA, Ganley AR, Cox MP.

BMC Bioinformatics. 2015 Jan 16;16:8. doi: 10.1186/s12859-014-0433-8.

33.

A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp.

Eaton CJ, Dupont PY, Solomon P, Clayton W, Scott B, Cox MP.

Mol Plant Microbe Interact. 2015 Mar;28(3):218-31. doi: 10.1094/MPMI-09-14-0293-FI.

34.

A flexible theoretical representation for the temporal dynamics of structured populations as paths on polytope complexes.

Amaris AJ, Cox MP.

J Math Biol. 2015 Sep;71(3):735-66. doi: 10.1007/s00285-014-0841-4. Epub 2014 Oct 12.

35.

Isolation, contact and social behavior shaped genetic diversity in West Timor.

Tumonggor MK, Karafet TM, Downey S, Lansing JS, Norquest P, Sudoyo H, Hammer MF, Cox MP.

J Hum Genet. 2014 Sep;59(9):494-503. doi: 10.1038/jhg.2014.62. Epub 2014 Jul 31.

36.

Regime shifts in Balinese subaks.

Lansing JS, Cheong SA, Chew LY, Cox MP, Ho MH, Arthawiguna WA.

Curr Anthropol. 2014 Apr;55(2):232-9. No abstract available.

PMID:
24991686
37.

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.

Guillot EG, Cox MP.

BMC Bioinformatics. 2014 Jun 9;15:175. doi: 10.1186/1471-2105-15-175.

38.

An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns.

Cox MP, Dong T, Shen G, Dalvi Y, Scott DB, Ganley AR.

PLoS Genet. 2014 Mar 6;10(3):e1004180. doi: 10.1371/journal.pgen.1004180. eCollection 2014 Mar.

39.

Semi-automatic selection of summary statistics for ABC model choice.

Prangle D, Fearnhead P, Cox MP, Biggs PJ, French NP.

Stat Appl Genet Mol Biol. 2014 Feb;13(1):67-82. doi: 10.1515/sagmb-2013-0012.

PMID:
24323893
40.

Climate change influenced female population sizes through time across the Indonesian archipelago.

Guillot EG, Tumonggor MK, Lansing JS, Sudoyo H, Cox MP.

Hum Biol. 2013 Feb-Jun;85(1-3):135-52.

PMID:
24297223
41.

Inexpensive photonic crystal spectrometer for colorimetric sensing applications.

Bryan KM, Jia Z, Pervez NK, Cox MP, Gazes MJ, Kymissis I.

Opt Express. 2013 Feb 25;21(4):4411-23. doi: 10.1364/OE.21.004411.

PMID:
23481975
42.

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen.

Bradshaw RE, Slot JC, Moore GG, Chettri P, de Wit PJ, Ehrlich KC, Ganley AR, Olson MA, Rokas A, Carbone I, Cox MP.

New Phytol. 2013 Apr;198(2):525-35. doi: 10.1111/nph.12161. Epub 2013 Mar 1.

43.

Reconstructing past changes in locus-specific recombination rates.

Cox MP, Holland BR, Wilkins MC, Schmid J.

BMC Genet. 2013 Feb 25;14:11. doi: 10.1186/1471-2156-14-11.

44.

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific.

Tumonggor MK, Karafet TM, Hallmark B, Lansing JS, Sudoyo H, Hammer MF, Cox MP.

J Hum Genet. 2013 Mar;58(3):165-73. doi: 10.1038/jhg.2012.154. Epub 2013 Jan 24.

PMID:
23344321
45.

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. 2012;8(11):e1003088. doi: 10.1371/journal.pgen.1003088. Epub 2012 Nov 29. Erratum in: PLoS Genet. 2015 Dec;11(12):e1005775.

46.

Dothistromin genes at multiple separate loci are regulated by AflR.

Chettri P, Ehrlich KC, Cary JW, Collemare J, Cox MP, Griffiths SA, Olson MA, de Wit PJ, Bradshaw RE.

Fungal Genet Biol. 2013 Feb;51:12-20. doi: 10.1016/j.fgb.2012.11.006. Epub 2012 Dec 1.

PMID:
23207690
47.

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

Eaton CJ, Cabrera IE, Servin JA, Wright SJ, Cox MP, Borkovich KA.

PLoS One. 2012;7(10):e48026. doi: 10.1371/journal.pone.0048026. Epub 2012 Oct 31.

48.

A small cohort of Island Southeast Asian women founded Madagascar.

Cox MP, Nelson MG, Tumonggor MK, Ricaut FX, Sudoyo H.

Proc Biol Sci. 2012 Jul 22;279(1739):2761-8. doi: 10.1098/rspb.2012.0012. Epub 2012 Mar 21.

49.

Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia.

Wilder JA, Cox MP, Paquette AM, Alford R, Satyagraha AW, Harahap A, Sudoyo H.

BMC Genet. 2011 Nov 18;12:100. doi: 10.1186/1471-2156-12-100.

50.

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity.

Russell AL, Cox MP, Brown VA, McCracken GF.

BMC Evol Biol. 2011 Apr 1;11:88. doi: 10.1186/1471-2148-11-88.

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