Ignazio Carbone

Coomber, A., Saville, A., Carbone, I., & Ristaino, J. B. (2023). An open-access T-BAS phylogeny for emerging Phytophthora species. PLOS ONE, 18(4). https://doi.org/10.1371/journal.pone.0283540

Hoz, C. J., Magain, N., Piatkowski, B., Cornet, L., Dal Forno, M., Carbone, I., … Lutzoni, F. (2023, February 24). Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria (C. Lemus-Solis, Ed.). SYSTEMATIC BIOLOGY, Vol. 2. https://doi.org/10.1093/sysbio/syad008

Dye, A. E., Muga, B., Mwangi, J., Hoyer, J. S., Ly, V., Rosado, Y., … Ascencio-Ibáñez, J. T. (2023). Cassava begomovirus species diversity changes during plant vegetative cycles. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1163566

Miadlikowska, J., Magain, N., Medeiros, I. D., Hoz, C. J., Carbone, I., LaGreca, S., … Lutzoni, F. (2023). Towards a nomenclatural clarification of the <i>Peltigera ponojensis/monticola</i> clade including metagenomic sequencing of type material and the introduction of <i>P. globulata</i> Miadl. & Magain sp. nov. LICHENOLOGIST, 55(5), 315–324. https://doi.org/10.1017/S0024282923000373

Jin, J., McCorkle, K. L., Cornish, V., Carbone, I., Lewis, R. S., & Shew, H. D. (2022). Adaptation of Phytophthora nicotianae to Multiple Sources of Partial Resistance in Tobacco. PLANT DISEASE, 106(3), 906–917. https://doi.org/10.1094/PDIS-06-21-1241-RE

Aimone, C. D., Hoyer, J. S., Dye, A. E., Deppong, D. O., Duffy, S., Carbone, I., & Hanley-Bowdoin, L. (2022). An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing. JOURNAL OF VIROLOGICAL METHODS, 300. https://doi.org/10.1016/j.jviromet.2021.114405

Molo, M. S., White, J. B., Cornish, V., Gell, R. M., Baars, O., Singh, R., … Carbone, I. (2022). Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control. PLOS ONE, 17(10). https://doi.org/10.1371/journal.pone.0276556

Luis, J. M., Carbone, I., Mack, B. M., Lebar, M. D., Cary, J. W., Gilbert, M. K., … Ojiambo, P. S. (2022, June). Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus. DATA IN BRIEF, Vol. 42. https://doi.org/10.1016/j.dib.2022.108033

Luis, J. M., Carbone, I., Mack, B. M., Lebar, M. D., Cary, J. W., Gilbert, M. K., … Ojiambo, P. S. (2022). Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus. FUNGAL BIOLOGY, 126(3), 187–200. https://doi.org/10.1016/j.funbio.2022.01.001

Hu, C.-H., Govers, F., Carbone, I., & Ristaino, J. B. (2022, November 5). Gene Flow of Phytophthora infestans Between Refuse Piles, and Organic and Conventional Potato Fields in Southern Flevoland, The Netherlands. POTATO RESEARCH, Vol. 11. https://doi.org/10.1007/s11540-022-09597-2

Ahmad, J., Zervas, A., Ellegaard-Jensen, L., Hennessy, R. C., Carbone, I., Cornish, V., … Nicolaisen, M. H. (2022, October 6). Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, Vol. 10. https://doi.org/10.1128/mra.00663-22

Hoyer, J. S., Wilkins, O. W., Munshi, A., Wiese, E., Dubey, D., Renard, S., … Ascencio-Ibanez, J. T. (2022). Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana. PHYTOBIOMES JOURNAL, 6(3), 227–235. https://doi.org/10.1094/PBIOMES-12-21-0077-R

Guo, F., Carbone, I., & Rasmussen, D. A. (2022). Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination. PLOS COMPUTATIONAL BIOLOGY, 18(8). https://doi.org/10.1371/journal.pcbi.1010422

Oita, S., Ibanez, A., Lutzoni, F., Miadlikowska, J., Geml, J., Lewis, L. A., … Arnold, A. E. (2021). Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. COMMUNICATIONS BIOLOGY, 4(1). https://doi.org/10.1038/s42003-021-01826-7

Crouch, J. A., Beirn, L. A., Boehm, M. J., Carbone, I., Clarke, B. B., Kerns, J. P., … Tredway, L. P. (2021). Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana. PLANT DISEASE, 105(3), 691–694. https://doi.org/10.1094/PDIS-06-20-1296-A

Oita, S., Carey, J., Kline, I., Ibanez, A., Yang, N., Hom, E. F. Y., … Arnold, A. E. (2021). Methodological Approaches Frame Insights into Endophyte Richness and Community Composition. MICROBIAL ECOLOGY, 82(1), 21–34. https://doi.org/10.1007/s00248-020-01654-y

Kayleigh R. O'Keeffe, Halliday, F. W., Jones, C. D., Carbone, I., & Mitchell, C. E. (2021). Parasites, niche modification and the host microbiome: A field survey of multiple parasites. MOLECULAR ECOLOGY, 30(10), 2404–2416. https://doi.org/10.1111/mec.15892

Aimone, C. D., Lavington, E., Hoyer, J. S., Deppong, D. O., Mickelson-Young, L., Jacobson, A., … Duffy, S. (2021). Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. Journal of General Virology, 102(7). https://doi.org/10.1099/jgv.0.001622

Luis, J. M., Carbone, I., Payne, G. A., Bhatnagar, D., Cary, J. W., Moore, G. G., … Ojiambo, P. S. (2020). Characterization of morphological changes within stromata during sexual reproduction inAspergillus flavus. MYCOLOGIA, 112(5), 908–920. https://doi.org/10.1080/00275514.2020.1800361

Molo, M., Heiniger, R., Boerema, L., & Carbone, I. (2019). A Response to the Letter to the Editor from Ortega-Beltran and Bandyopadhyay. Agronomy Journal, 111(5), 2629–2631.

Lewis, M. H., Carbone, I., Luis, J. M., Payne, G. A., Bowen, K. L., Hagan, A. K., … Ojiambo, P. S. (2019). Biocontrol Strains Differentially Shift the Genetic Structure of Indigenous Soil Populations of Aspergillus flavus. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.01738

Gell, R. M., & Carbone, I. (2019). HPLC quantitation of aflatoxin B1 from fungal mycelium culture. Journal of Microbiological Methods, 158, 14–17. https://doi.org/10.1016/j.mimet.2019.01.008

U’Ren, J. M., Lutzoni, F., Miadlikowska, J., Zimmerman, N. B., Carbone, I., May, G., & Arnold, A. E. (2019). Host availability drives distributions of fungal endophytes in the imperilled boreal realm. Nature Ecology & Evolution, 3(10), 1430–1437. https://doi.org/10.1038/s41559-019-0975-2

Koehler, A. M., Larkin, M. T., Rogers, L. W., Carbone, I., Cubeta, M. A., & Shew, H. D. (2019). Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina. Mycologia, 111(3), 456–465. https://doi.org/10.1080/00275514.2019.1584503

Cullen, M., Jacob, M. E., Cornish, V., VanderSchel, I. Q., Cotter, H. V. T., Cubeta, M. A., … Gilger, B. C. (2019). Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States. PLOS ONE, 14(3), e0214214. https://doi.org/10.1371/journal.pone.0214214

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Magain, N., … Lutzoni, F. (2019). T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees. Microbiology Resource Announcements, 8(29). https://doi.org/10.1128/MRA.00328-19

Molo, M. S., Heiniger, R. W., Boerema, L., & Carbone, I. (2019). Trial Summary on the Comparison of Various Non-Aflatoxigenic Strains of Aspergillus flavus on Mycotoxin Levels and Yield in Maize. AGRONOMY JOURNAL, 111(2), 942–946. https://doi.org/10.2134/agronj2018.07.0473

Salgado-Salazar, C., Beirn, L. A., Ismaiel, A., Boehm, M. J., Carbone, I., Putman, A. I., … Crouch, J. A. (2018). Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass. Fungal Biology, 122(8), 761–773. https://doi.org/10.1016/J.FUNBIO.2018.04.004

Ojiambo, P. S., Battilani, P., Cary, J. W., Blum, B. H., & Carbone, I. (2018). Cultural and Genetic Approaches to Manage Aflatoxin Contamination: Recent Insights Provide Opportunities for Improved Control. Phytopathology, 108(9), 1024–1037. https://doi.org/10.1094/PHYTO-04-18-0134-RVW

Molo, M., Heiniger, R., Boerema, L., & Carbone, I. (2018). Management practices for controlling mycotoxins in corn: A three-year summary (NC State Extension Publications No. AG-852). Retrieved from North Carolina State University website: http://content.ces.ncsu.edu/management-practices-for-controlling-mycotoxins-in-corn

Blanco-Meneses, M., Carbone, I., & Ristaino, J. B. (2018). Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe. Molecular Ecology, 27(3), 737–751. https://doi.org/10.1111/mec.14453

Drott, M. T., Lazzaro, B. P., Brown, D. L., Carbone, I., & Milgroom, M. G. (2017). Balancing selection for aflatoxin in
            Aspergillus flavus
            is maintained through interference competition with, and fungivory by insects. Proceedings of the Royal Society B: Biological Sciences, 284(1869), 20172408. https://doi.org/10.1098/rspb.2017.2408

Moore, G. G., Olarte, R. A., Horn, B. W., Elliott, J. L., Singh, R., O'Neal, C. J., & Carbone, I. (2017). Global population structure and adaptive evolution of aflatoxin-producing fungi. Ecology and Evolution, 7(21), 9179–9191. https://doi.org/10.1002/ece3.3464

Thomas, A., Carbone, I., Cohen, Y., & Ojiambo, P. S. (2017). Occurrence and Distribution of Mating Types of Pseudoperonospora cubensis in the United States. Phytopathology, 107(3), 313–321. https://doi.org/10.1094/phyto-06-16-0236-r

O’Keeffe, K. R., Carbone, I., Jones, C. D., & Mitchell, C. E. (2017). Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants. Current Opinion in Plant Biology, 38, 78–83. https://doi.org/10.1016/j.pbi.2017.04.014

Thomas, A., Carbone, I., Choe, K., Quesada-Ocampo, L. M., & Ojiambo, P. S. (2017). Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis. Ecology and Evolution, 7(16), 6231–6246. https://doi.org/10.1002/ece3.3194

Thomas, A., Carbone, I., Lebeda, A., & Ojiambo, P. S. (2017). Virulence Structure Within Populations of Pseudoperonospora cubensis in the United States. PHYTOPATHOLOGY, 107(6), 777–785. https://doi.org/10.1094/phyto-07-16-0277-r

Horn, B. W., Gell, R. M., Singh, R., Sorensen, R. B., & Carbone, I. (2016). Sexual Reproduction in Aspergillus flavus Sclerotia: Acquisition of Novel Alleles from Soil Populations and Uniparental Mitochondrial Inheritance. PLOS ONE, 11(1). https://doi.org/10.1371/journal.pone.0146169

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Kauff, F., … Lutzoni, F. (2016). T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics, 33(8), btw808. https://doi.org/10.1093/bioinformatics/btw808

Putman, A. I., Tredway, L. P., & Carbone, I. (2015). Characterization and distribution of mating-type genes of the turfgrass pathogen Sclerotinia homoeocarpa on a global scale. FUNGAL GENETICS AND BIOLOGY, 81, 25–40. https://doi.org/10.1016/j.fgb.2015.05.012

Olarte, R. A., Worthington, C. J., Horn, B. W., Moore, G. G., Singh, R., Monacell, J. T., … Carbone, I. (2015). Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus. Molecular Ecology, 24(8), 1889–1909. https://doi.org/10.1111/mec.13153

Call, A., Sun, Y.-X., Yu, Y., Pearman, P. B., Thomas, D. T., Trigiano, R. N., … Xiang, Q.-Y. J. (2015). Genetic structure and post-glacial expansion ofCornus floridaL. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling. Journal of Systematics and Evolution, 54(2), 136–151. https://doi.org/10.1111/jse.12171

Lassiter, E. S., Russ, C., Nusbaum, C., Zeng, Q., Saville, A. C., Olarte, R. A., … Ristaino, J. B. (2015). Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species. Current Genetics, 61(4), 567–577. https://doi.org/10.1007/s00294-015-0480-3

Runa, F., Carbone, I., Bhatnagar, D., & Payne, G. A. (2015). Nuclear heterogeneity in conidial populations of Aspergillus flavus. FUNGAL GENETICS AND BIOLOGY, 84, 62–72. https://doi.org/10.1016/j.fgb.2015.09.003

Olarte, R. A., Horn, B. W., Singh, R., & Carbone, I. (2015). Sexual recombination in Aspergillus tubingensis. MYCOLOGIA, 107(2), 307–312. https://doi.org/10.3852/14-233

Meyers, M., Heiniger, R., Boerema, L., & Carbone, I. (2015). The Use of Management Practices to Reduce Mycotoxin Contamination in Corn (NC State Extension Publication No. AG-807). Raleigh, NC: North Carolina Cooperative Extension Service.

Putman, A. I., & Carbone, I. (2014). [Review of Challenges in analysis and interpretation of microsatellite data for population genetic studies]. ECOLOGY AND EVOLUTION, 4(22), 4399–4428. https://doi.org/10.1002/ece3.1305

Oono, R., Lutzoni, F., Arnold, A. E., Kaye, L., Jana M. U'Ren, May, G., & Carbone, I. (2014). GENETIC VARIATION IN HORIZONTALLY TRANSMITTED FUNGAL ENDOPHYTES OF PINE NEEDLES REVEALS POPULATION STRUCTURE IN CRYPTIC SPECIES. AMERICAN JOURNAL OF BOTANY, 101(8), 1362–1374. https://doi.org/10.3732/ajb.1400141

Monacell, J. T., & Carbone, I. (2014). Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics. Bioinformatics, 30(10), 1488–1490. https://doi.org/10.1093/bioinformatics/btu055

Miller, J. D., Schaafsma, A. W., Bhatnagar, D., Bondy, G., Carbone, I., Harris, L. J., … Zhou, T. (2014). [Review of Mycotoxins that affect the North American agri-food sector: state of the art and directions for the future]. WORLD MYCOTOXIN JOURNAL, 7(1), 63–82. https://doi.org/10.3920/wmj2013.1624

Barnes, I., Wingfield, M. J., Carbone, I., Kirisits, T., & Wingfield, B. D. (2014). Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity. ECOLOGY AND EVOLUTION, 4(18), 3642–3661. https://doi.org/10.1002/ece3.1200

Horn, B. W., Sorensen, R. B., Lamb, M. C., Sobolev, V. S., Olarte, R. A., Worthington, C. J., & Carbone, I. (2014). Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn. PHYTOPATHOLOGY, 104(1), 75–85. https://doi.org/10.1094/phyto-05-13-0129-r

Jana M. U'Ren, Riddle, J. M., Monacell, J. T., Carbone, I., Miadlikowska, J., & Arnold, A. E. (2014). Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. MOLECULAR ECOLOGY RESOURCES, 14(5), 1032–1048. https://doi.org/10.1111/1755-0998.12252

Wei, W., Ayub, Q., Chen, Y., McCarthy, S., Hou, Y., Carbone, I., … Tyler-Smith, C. (2013). A calibrated human Y-chromosomal phylogeny based on resequencing. GENOME RESEARCH, 23(2), 388–395. https://doi.org/10.1101/gr.143198.112

Putman, A. I., Carbone, I., & Tredway, L. P. (2013). Development and characterization of 14 microsatellite loci for the plant pathogenic fungus Sclerotinia homoeocarpa. Molecular Ecology Resources, 13(5), 966–968.

Bradshaw, R. E., Slot, J. C., Moore, G. G., Chettri, P., Wit, P. J. G. M., Ehrlich, K. C., … Cox, M. P. (2013). Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. NEW PHYTOLOGIST, 198(2), 525–535. https://doi.org/10.1111/nph.12161

Agostini, C., Albaladejo, R. G., Aparicio, A., Arthofer, W., Berrebi, P., Boag, P. T., … Gettova, L. (2013). Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013. Molecular Ecology Resources, 13(5), 966–968.

Horn, B. W., Olarte, R. A., Peterson, S. W., & Carbone, I. (2013). Sexual reproduction in Aspergillus tubingensis from section Nigri. Mycologia, 105(5), 1153–1163. https://doi.org/10.3852/13-101

Moore, G. G., Elliott, J. L., Singh, R., Horn, B. W., Dorner, J. W., Stone, E. A., … Carbone, I. (2013). Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale. PLoS Pathogens, 9(8), e1003574. https://doi.org/10.1371/journal.ppat.1003574

Olarte, R. A., Horn, B. W., Dorner, J. W., Monacell, J. T., Singh, R., Stone, E. A., & Carbone, I. (2012). Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis. MOLECULAR ECOLOGY, 21(6), 1453–1476. https://doi.org/10.1111/j.1365-294x.2011.05398.x

Beirn, L., Clarke, B. B., Tredway, L., Carbone, I., Boehm, M. J., Orshinsky, A. M., & Crouch, J. (2012). Renaming the dollar spot fungus. Golf Course Management Current Research.

Arnold, A. E., Carbone, I., Lutzoni, F., & May, G. (2011). A multidimensional study of endophytic fungal diversity. IMA Fungus, 2(1), 2–4.

Wu, F., Bhatnagar, D., Bui-Klimke, T., Carbone, I., Hellmich, R., Munkvold, G., … Takle, E. (2011). Climate change impacts on mycotoxin risks in US maize. World Mycotoxin Journal, 4(1), 79–93. https://doi.org/10.3920/wmj2010.1246

Litvintseva, A. P., Carbone, I., Rossouw, J., Thakur, R., Govender, N. P., & Mitchell, T. G. (2011). Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa. PLoS ONE, 6(5), e19688. https://doi.org/10.1371/journal.pone.0019688

Olson, H. A., Carbone, I., & Benson, D. M. (2011). Phylogenetic history of Phytophthora cryptogea and P. drechsleri Isolates from floriculture crops in North Carolina greenhouses. Phytopathology, 101(11), 1373–1384.

Kaye, A. C., Moyer, J. W., Parks, E. J., Carbone, I., & Cubeta, M. A. (2011). Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia. PHYTOPATHOLOGY, 101(1), 147–153. https://doi.org/10.1094/phyto-01-10-0035

Abbas, H. K., Weaver, M. A., Horn, B. W., Carbone, I., Monacell, J. T., & Shier, W. T. (2011). Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn. TOXIN REVIEWS, 30(2-3), 59–70. https://doi.org/10.3109/15569543.2011.591539

Horn, B. W., Moore, G. G., & Carbone, I. (2011). Sexual reproduction in aflatoxin-producing Aspergillus nomius. Mycologia, 103(1), 174–183. https://doi.org/10.3852/10-115

Moore, G. G., Beltz, S. B., Carbone, I., Ehrlich, K. C., & Horn, B. W. (2011). The Population Dynamics of Aflatoxigenic Aspergilli. In R. G. Guevara-González (Ed.), Aflatoxins - Biochemistry and Molecular Biology. https://doi.org/10.5772/23698

Goss, E. M., Larsen, M., Carbone, I. G., Givens, D. R., Chastagner, G. A., Grünwald, N. J., … Palmieri, K. M. (2010). Population genetic analysis reveals ancient evolution and recent migration of P. ramorum [Tech. Rep. PSW-GTR-229.]. In S. J. Frankel, J. T. Kliejunas, & K. M. Palmieri (Eds.), Proceedings of the Sudden Oak Death Fourth Science Symposium (pp. 116–118). https://doi.org/10.2737/psw-gtr-229

Goss, E. M., Carbone, I., & Grunwald, N. J. (2009). Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum. MOLECULAR ECOLOGY, 18(6), 1161–1174. https://doi.org/10.1111/j.1365-294X.2009.04089.x

Lourenco, V., Jr., Moya, A., Gonzalez-Candelas, F., Carbone, I., Maffia, L. A., & Mizubuti, E. S. G. (2009). Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches. PHYTOPATHOLOGY, 99(6), 765–774. https://doi.org/10.1094/PHYTO-99-6-0765

Parks, R., Carbone, I., Murphy, J. P., & Cowger, C. (2009). Population Genetic Analysis of an Eastern US Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with UK and Israeli Populations. PHYTOPATHOLOGY, 99(7), 840–849. https://doi.org/10.1094/PHYTO-99-7-0840

Moore, G. G., Singh, R., Horn, B. W., & Carbone, I. (2009). Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus. MOLECULAR ECOLOGY, 18(23), 4870–4887. https://doi.org/10.1111/j.1365-294X.2009.04414.x

Horn, B. W., Ramirez-Prado, J. H., & Carbone, I. (2009). Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus. FUNGAL GENETICS AND BIOLOGY, 46(2), 169–175. https://doi.org/10.1016/j.fgb.2008.11.004

Horn, B. W., Moore, G. G., & Carbone, I. (2009). Sexual reproduction in Aspergillus flavus. MYCOLOGIA, 101(3), 423–429. https://doi.org/10.3852/09-011

Horn, B. W., Ramirez-Prado, J. H., & Carbone, I. (2009). The sexual state of Aspergillus parasiticus. MYCOLOGIA, 101(2), 275–280. https://doi.org/10.3852/08-205

Powell, A. J., Conant, G. C., Brown, D. E., Carbone, I., & Dean, R. A. (2008). Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. BMC GENOMICS, 9. https://doi.org/10.1186/1471-2164-9-147

Ramirez-Prado, J. H., Moore, G. G., Horn, B. W., & Carbone, I. (2008). Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus. FUNGAL GENETICS AND BIOLOGY, 45(9), 1292–1299. https://doi.org/10.1016/j.fgb.2008.06.007

Clark, C. M., & Carbone, I. (2008). Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer. CANADIAN JOURNAL OF FOREST RESEARCH, 38(6), 1576–1589. https://doi.org/10.1139/X07-209

Brown, D. E., Powell, A. J., Carbone, I., & Dean, R. A. (2008). GT-Miner: a graph-theoretic data miner, viewer, and model processor. Bioinformation, 3(5), 235–237. https://doi.org/10.6026/97320630003235

Charlton, N. D., Carbone, I., Tavantzis, S. M., & Cubeta, M. A. (2008). Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi. MYCOLOGIA, 100(4), 555–564. https://doi.org/10.3852/07-108R

Parks, R., Carbone, I., Murphy, J. P., Marshall, D., & Cowger, C. (2008). Virulence structure of the Eastern US wheat powdery mildew population. PLANT DISEASE, 92(7), 1074–1082. https://doi.org/10.1094/PDIS-92-7-1074

Gomez-Alpizar, L., Carbone, I., & Ristaino, J. B. (2007). An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(9), 3306–3311. https://doi.org/10.1073/pnas.0611479104

Carbone, I., Ramirez-Prado, J. H., Jakobek, J. L., & Horn, B. W. (2007). Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC EVOLUTIONARY BIOLOGY, 7. https://doi.org/10.1186/1471-2148-7-111

Moser, J. M., Carbone, I., Arasu, P., & Gibson, G. (2007). Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancylostoma caninum). JOURNAL OF PARASITOLOGY, 93(4), 796–805. https://doi.org/10.1645/GE-1096R.1

Malvarez, G., Carbone, I., Grunwald, N. J., Subbarao, K. V., Schafer, M., & Kohn, L. M. (2007). New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington. PHYTOPATHOLOGY, 97(4), 470–483. https://doi.org/10.1094/PHYTO-97-4-0470

Carbone, I., Jakobek, J. L., Ramirez-Prado, J. H., & Horn, B. W. (2007). Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. MOLECULAR ECOLOGY, 16(20), 4401–4417. https://doi.org/10.1111/j.1365-294X.2007.03464.x

Deng, J., Carbone, I., & Dean, R. A. (2007). The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes. BMC EVOLUTIONARY BIOLOGY, 7. https://doi.org/10.1186/1471-2148-7-30

Aylor, D. L., Price, E. W., & Carbone, I. (2006). SNAP: Combine and Map modules for multilocus population genetic analysis. Bioinformatics, 22(11), 1399–1401. https://doi.org/10.1093/bioinformatics/bt/136

Charles, L., Carbone, I., Davies, K. G., Bird, D., Burke, M., Kerry, B. R., & Opperman, C. H. (2005). Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci. JOURNAL OF BACTERIOLOGY, 187(16), 5700–5708. https://doi.org/10.1128/JB.187.16.5700-5708.2005

Price, E. W., & Carbone, I. (2005). SNAP: workbench management tool for evolutionary population genetic analysis. BIOINFORMATICS, 21(3), 402–404. https://doi.org/10.1093/bioinformatics/bti003

Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K., Orbach, M. J., … Birren, B. W. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. NATURE, 434(7036), 980–986. https://doi.org/10.1038/nature03449

Carbone, I., & Kohn, L. (2004). Inferring Process from Pattern in Fungal Population Genetics. In Fungal Genomics (pp. 29–58). https://doi.org/10.1016/s1874-5334(04)80005-4

Carbone, I., Liu, Y. C., Hillman, B. I., & Milgroom, M. G. (2004). Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. GENETICS, 166(4), 1611–1629. https://doi.org/10.1534/genetics.166.4.1611

Phillips, D. V., Carbone, I., Gold, S. E., & Kohn, L. M. (2002). Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum. Phytopathology, 92(7), 785–793. https://doi.org/10.1094/phyto.2002.92.7.785

Carbone, I., & Kohn, L. M. (2001). A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Molecular Ecology, 10(4), 947–964. https://doi.org/10.1046/j.1365-294x.2001.01244.x

Carbone, I., & Kohn, L. M. (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(10), 2409–2422. https://doi.org/10.1046/j.0962-1083.2001.01380.x

Carbone, I., & Kohn, L. M. (1999). A Method for Designing Primer Sets for Speciation Studies in Filamentous Ascomycetes. Mycologia, 91(3), 553. https://doi.org/10.2307/3761358

Carbone, I., Anderson, J. B., & Kohn, L. M. (1999). Patterns of Descent in Clonal Lineages and Their Multilocus Fingerprints Are Resolved with Combined Gene Genealogies. Evolution, 53(1), 11. https://doi.org/10.2307/2640916

Carbone, I., Anderson, J. B., & Kohn, L. M. (1995). A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum. Current Genetics, 27(2), 166–176. https://doi.org/10.1007/bf00313431

Carbone, I., & Kohn, L. M. (1993). Ribosomal DNA Sequence Divergence within Internal Transcribed Spacer 1 of the Sclerotiniaceae. Mycologia, 85(3), 415. https://doi.org/10.2307/3760703

Kohn, L. M., Stasovski, E., Carbone, I., Royer, J., & Anderson, J. B. (1991). Mycelial Incompatibility and Molecular Markers Identify Genetic Variability in Field Populations of Sclerotinia sclerotiorum. Phytopathology, 81(4), 480–485. https://doi.org/10.1094/phyto-81-480

Kohn, L. M., Carbone, I., & Anderson, J. B. (1990). Mycelial interactions in Sclerotinia sclerotiorum. Experimental Mycology, 14(3), 255–267. https://doi.org/10.1016/0147-5975(90)90023-m

Edwards, A. C., Ayroles, J. F., Stone, E. A., Carbone, M. A., Lyman, R. F., & Mackay, T. F. C. A transcriptional network associated with natural variation in Drosophila aggressive behavior. Genome Biology, 10(7).