Peer-Reviewed Publications

1. Moore, G. G., Singh, R., Horn, B. W., and I. Carbone. 2009. Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus. Molecular Ecology, In Press.

2. Parks, R., Carbone, I., Murphy, P and C. Cowger. 2009. Population genetic analysis of an eastern U.S. wheat powdery mildew population reveals geographic subdivision and recent common ancestry with U.K. and Israeli populations. Phytopathology 99:840-849.

3. Lourenço Jr., V., Moya, A., González-Candelas, F., Carbone, I., Maffia, L. A. and E. S. G. Mizubuti. 2009. Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches. Phytopathology 99: 765-774.

4. Horn, B. W., Moore, G. G. and I. Carbone. 2009. Sexual reproduction in Aspergillus flavus. Mycologia 101:423-429.

5. Goss, E. M., Carbone, I., and N. J. Grünwald. 2009. Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum. Molecular Ecology 18, 1161-1174.

6. Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. The sexual state of Aspergillus parasiticus. Mycologia 101: 275-280.

7. Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus. Fungal Genetics and Biology 46:169-175.

8. Ramirez-Prado, J. H., Moore, G. G., Horn, B. W. and I Carbone. 2008. Characterization and population analysis of the mating-type genes in Aspergillus flavus and A. parasiticus. Fungal Genetics and Biology 45:1292-1299.

9. Brown DE, Powell A. J., Carbone I. and R. A Dean. 2008. GT-Miner: a graph-theoretic data miner, viewer and model processor. Bioinformation 3(5): 235-237.

10. Powell, A. J. Conant, G. C., Brown, D. E. Carbone, I. and R. A. Dean. 2008. Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens.  BMC Genomics 9:147.

11. Parks, R., Carbone, I. Murphy, J. P., Marshall, D. S. and C. Cowger. 2008. Virulence structure of the Eastern U.S. wheat powdery mildew population.  Plant Disease 92:1074-1082.

12. Charlton, N.D., Carbone, I., Tavantzis, S.M., and M.A. Cubeta. 2008. Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi. Mycologia 100:555-564.

13. Clark, C. M. and I. Carbone. 2007. Chloroplast DNA phylogeography in long lived Huon Pine (Lagarostrobos franklinii), a Tasmanian rainforest conifer. Canadian Journal of Forest Research 38: 1576-1589.

14. Carbone, I., Jakobek, J. L., Ramirez-Prado, J. H. and B. W. Horn. 2007.  Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus.  Molecular Ecology 16: 4401-4417.

15. Carbone, I., Ramirez-Prado, J. H., Jakobek, J. L., and B. W. Horn. 2007. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC Evolutionary Biology 7:111.

16. Moser, J. M., Carbone, I., Arasu, P. and G. Gibson. 2007. Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancyclostoma caninum). Journal of Parasitology 93: 796-805.

17. Deng, J., Carbone, I. and R. A Dean.  2007.  The evolutionary history of Cytochrome P450 genes in four filamentous ascomycetes.  BMC Evolutionary Biology 7: 30.

18. Gómez-Alpizar, L, I. Carbone, and J. B. Ristaino. 2007. An Andean origin of Phytophthora infestans inferred from nuclear and mitochondrial gene genealogies. Proc Nat. Acad. Sci. 104: 3306-3311.

19. Malvárez, G, Carbone, I., Grünwald N. J., Subbarao, K. V., Schafer, M. and L. M. Kohn.  2007.  New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington.  Phytopathology 97: 512-525

20. Aylor, D. L., Price, E.W. and I. Carbone. 2006. SNAP: Combine and Map modules for multilocus population genetic analysis.  Bioinformatics 22: 1399-1401. |   Abstract  |  PDF  |

21. Charles, L., Carbone, I., Davies, K.G., Bird, D., Burke, M., Kerry, B.R., and Opperman, C.H. 2005. Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci. Journal of Bacteriology 187: 5700-5708.

22. Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T., Orbach, M.J., Thon, M., Kulkarni, R., Xu, J-R.,Pan, H., Read, N.D., Lee, Y-H., Carbone, I., Brown, D., Oh, Y.Y., Donofrio, N., Jeong, J.S., Soanes, D.M., Djonovic, S., Kolomiets, E., Rehmeyer, C., Li, W., Harding, M., Kim S., Lebrun M-H., Bohnert, H., Coughlan, S., Butler, J., Calvo, S., Ma, L-J., Nicol, R., Purcell, S., Nusbaum, C., Galagan, J.E., Birren, B.W. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986.

23. Price, E.W., and I. Carbone. 2005. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21: 402-404. |   PDF reprint  |

24. Carbone, I., Y. Liu, B. I. Hillman and M. G. Milgroom. 2004. Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics 166: 1611-1629. |   PDF reprint  |  SNAP Workbench  |

25. Phillips, D.V., I. Carbone, S. E. Gold, and L. M. Kohn. 2002. Phylogeography and genotype - symptom associations in early and late season infections of canola by Sclerotinia sclerotiorum. Phytopathology 92: 785-793. |   PDF reprint  |

26. Carbone, I. and L. M. Kohn. 2001. Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation. Molecular Ecology 10: 2409-2422.  |   PDF reprint  |  Fingerprints  | 

27. Carbone, I. and L. M. Kohn. 2001. A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Molecular Ecology 10: 947-964.  |  PDF reprint |  Samples  |  Loci  |  Sequences  |  Haplotypes  |   Tables 1, 2, 3 |

28. Carbone, I., J. B. Anderson, and L. M. Kohn. 1999. Patterns of descent in clonal lineages and their multilocus fingerprints are resolved with combined gene genealogies. Evolution 53: 11-21. |   PDF reprint  |

29. Carbone, I., and L. M. Kohn. 1999. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553-556. |   PDF reprint  |

30. Carbone, I., J. B. Anderson, and L. M. Kohn. 1995. A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum. Current Genetics 27: 166-176.

31. Carbone, I., and L. M. Kohn. 1993. Ribosomal DNA sequence divergence within internal transcribed spacer 1 of the Sclerotiniaceae. Mycologia 85: 415-427.

32. Kohn, L. M., E. Stasovski, I. Carbone, J. Royer, and J. B. Anderson. 1991. Mycelial incompatibility and molecular markers identify genetic variability in field populations of Sclerotinia sclerotiorum. Phytopathology 81: 480-485.

33. Kohn, L. M., I. Carbone, and J. B. Anderson. 1990. Mycelial interactions in Sclerotinia sclerotiorum. Experimental Mycology 14: 255-267.

Book Chapter

1. Carbone, I. and L. M. Kohn. 2004. Inferring process from pattern in fungal population genetics, pp. 29-58. In Fungal Genomics, Applied Mycology and Biotechnology Series (D. K. Arora and G. G. Khachatourians, editors), Vol. 4. Elsevier Science. |   PDF reprint  |