2024 journal article
Eco‐phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont
American Journal of Botany.
2024 journal article
Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome
CURRENT BIOLOGY, 34(5).
2023 journal article
An open-access T-BAS phylogeny for emerging Phytophthora species
PLOS ONE, 18(4).
Ed(s): J. Blair
2023 article
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Hoz, C. J., Magain, N., Piatkowski, B., Cornet, L., Dal Forno, M., Carbone, I., … Lutzoni, F. (2023, February 24). (C. Lemus-Solis, Ed.). SYSTEMATIC BIOLOGY, Vol. 2.
Ed(s): C. Lemus-Solis
2023 journal article
Cassava begomovirus species diversity changes during plant vegetative cycles
Frontiers in Microbiology, 14.
2023 journal article
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.
Towards a nomenclatural clarification of the Peltigera ponojensis/monticola clade including metagenomic sequencing of type material and the introduction of P. globulata Miadl. & Magain sp. nov. LICHENOLOGIST, 55(5), 315–324.
2022 journal article
Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control
PLOS ONE, 17(10).
Ed(s): W. Nierman
2022 article
Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus
Luis, J. M., Carbone, I., Mack, B. M., Lebar, M. D., Cary, J. W., Gilbert, M. K., … Ojiambo, P. S. (2022, June). DATA IN BRIEF, Vol. 42.
2022 journal article
Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus
FUNGAL BIOLOGY, 126(3), 187–200.
2022 article
Gene Flow of Phytophthora infestans Between Refuse Piles, and Organic and Conventional Potato Fields in Southern Flevoland, The Netherlands
Hu, C.-H., Govers, F., Carbone, I., & Ristaino, J. B. (2022, November 5). POTATO RESEARCH, Vol. 11.
2022 article
Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage
Ahmad, J., Zervas, A., Ellegaard-Jensen, L., Hennessy, R. C., Carbone, I., Cornish, V., … Nicolaisen, M. H. (2022, October 6). MICROBIOLOGY RESOURCE ANNOUNCEMENTS, Vol. 10.
2022 journal article
Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana
PHYTOBIOMES JOURNAL, 6(3), 227–235.
2022 journal article
Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination
PLOS COMPUTATIONAL BIOLOGY, 18(8).
2021 journal article
Adaptation of Phytophthora nicotianae to Multiple Sources of Partial Resistance in Tobacco
PLANT DISEASE, 106(3), 906–917.
2021 journal article
An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing
JOURNAL OF VIROLOGICAL METHODS, 300.
2021 journal article
Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale
COMMUNICATIONS BIOLOGY, 4(1).
2021 journal article
Methodological Approaches Frame Insights into Endophyte Richness and Community Composition
MICROBIAL ECOLOGY, 82(1), 21–34.
2021 journal article
Parasites, niche modification and the host microbiome: A field survey of multiple parasites
MOLECULAR ECOLOGY, 30(10), 2404–2416.
2021 journal article
Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation
Journal of General Virology, 102(7).
2020 journal article
Characterization of morphological changes within stromata during sexual reproduction inAspergillus flavus
MYCOLOGIA, 112(5), 908–920.
2020 journal article
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.
2019 journal article
A Response to the Letter to the Editor from Ortega-Beltran and Bandyopadhyay
Agronomy Journal, 111(5), 2629–2631.
2019 journal article
Biocontrol Strains Differentially Shift the Genetic Structure of Indigenous Soil Populations of Aspergillus flavus
Frontiers in Microbiology, 10.
2019 journal article
HPLC quantitation of aflatoxin B1 from fungal mycelium culture
Journal of Microbiological Methods, 158, 14–17.
2019 journal article
Host availability drives distributions of fungal endophytes in the imperilled boreal realm
Nature Ecology & Evolution, 3(10), 1430–1437.
2019 journal article
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.
2019 journal article
Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States
PLOS ONE, 14(3), e0214214.
Ed(s): O. Kniemeyer
2019 journal article
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).
Ed(s): C. Cuomo
2019 journal article
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.
2018 journal article
Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass
Fungal Biology, 122(8), 761–773.
2018 journal article
Cultural and Genetic Approaches to Manage Aflatoxin Contamination: Recent Insights Provide Opportunities for Improved Control
Phytopathology, 108(9), 1024–1037.
2018 report
Management practices for controlling mycotoxins in corn: A three-year summary
(NC State Extension Publications No. AG-852). http://content.ces.ncsu.edu/management-practices-for-controlling-mycotoxins-in-corn
2017 journal article
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.
2017 journal article
Global population structure and adaptive evolution of aflatoxin-producing fungi
Ecology and Evolution, 7(21), 9179–9191.
2017 journal article
Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants
Current Opinion in Plant Biology, 38, 78–83.
2017 journal article
Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe
Molecular Ecology, 27(3), 737–751.
2017 journal article
Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis
Ecology and Evolution, 7(16), 6231–6246.
2017 journal article
Virulence Structure Within Populations of Pseudoperonospora cubensis in the United States
PHYTOPATHOLOGY, 107(6), 777–785.
2016 journal article
Occurrence and Distribution of Mating Types of Pseudoperonospora cubensis in the United States
Phytopathology, 107(3), 313–321.
2016 journal article
Sexual Reproduction in Aspergillus flavus Sclerotia: Acquisition of Novel Alleles from Soil Populations and Uniparental Mitochondrial Inheritance
PLOS ONE, 11(1).
2016 journal article
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.
2015 journal article
Characterization and distribution of mating-type genes of the turfgrass pathogen Sclerotinia homoeocarpa on a global scale
FUNGAL GENETICS AND BIOLOGY, 81, 25–40.
2015 journal article
Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus
Molecular Ecology, 24(8), 1889–1909.
2015 journal article
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.
2015 journal article
Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species
Current Genetics, 61(4), 567–577.
Contributors: E. Lassiter n, C. Russ *, C. Nusbaum *, Q. Zeng *, A. Saville n, R. Olarte n, n , C. Hu n
2015 journal article
Nuclear heterogeneity in conidial populations of Aspergillus flavus
FUNGAL GENETICS AND BIOLOGY, 84, 62–72.
2015 journal article
Sexual recombination in Aspergillus tubingensis
MYCOLOGIA, 107(2), 307–312.
2015 report
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.
2014 review
Challenges in analysis and interpretation of microsatellite data for population genetic studies
[Review of ]. ECOLOGY AND EVOLUTION, 4(22), 4399–4428.
2014 journal article
GENETIC VARIATION IN HORIZONTALLY TRANSMITTED FUNGAL ENDOPHYTES OF PINE NEEDLES REVEALS POPULATION STRUCTURE IN CRYPTIC SPECIES
AMERICAN JOURNAL OF BOTANY, 101(8), 1362–1374.
2014 journal article
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
Bioinformatics, 30(10), 1488–1490.
2014 journal article
Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity
ECOLOGY AND EVOLUTION, 4(18), 3642–3661.
2014 journal article
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.
2013 journal article
Development and characterization of 14 microsatellite loci for the plant pathogenic fungus Sclerotinia homoeocarpa
Molecular Ecology Resources, 13(5), 966–968.
2013 journal article
Fragmentation of an aflatoxin-like gene cluster in a forest pathogen
NEW PHYTOLOGIST, 198(2), 525–535.
2013 review
Mycotoxins that affect the North American agri-food sector: state of the art and directions for the future
[Review of ]. WORLD MYCOTOXIN JOURNAL, 7(1), 63–82.
2013 journal article
Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013
Molecular Ecology Resources, 13(5), 966–968.
2013 journal article
Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn
PHYTOPATHOLOGY, 104(1), 75–85.
2013 journal article
Sexual reproduction in Aspergillus tubingensis from section Nigri
Mycologia, 105(5), 1153–1163.
2013 journal article
Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale
PLoS Pathogens, 9(8), e1003574.
Ed(s): B. McDonald
2012 journal article
A calibrated human Y-chromosomal phylogeny based on resequencing
GENOME RESEARCH, 23(2), 388–395.
2012 report
Renaming the dollar spot fungus
Golf Course Management Current Research.
2011 journal article
A multidimensional study of endophytic fungal diversity
IMA Fungus, 2(1), 2–4.
2011 journal article
Climate change impacts on mycotoxin risks in US maize
World Mycotoxin Journal, 4(1), 79–93.
2011 journal article
Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis
MOLECULAR ECOLOGY, 21(6), 1453–1476.
2011 journal article
Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa
PLoS ONE, 6(5), e19688.
Ed(s): K. Nielsen
2011 journal article
Phylogenetic history of Phytophthora cryptogea and P. drechsleri Isolates from floriculture crops in North Carolina greenhouses
Phytopathology, 101(11), 1373–1384.
2011 journal article
Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn
TOXIN REVIEWS, 30(2-3), 59–70.
2011 journal article
Sexual reproduction in aflatoxin-producing Aspergillus nomius
Mycologia, 103(1), 174–183.
2011 chapter
The Population Dynamics of Aflatoxigenic Aspergilli
In R. G. Guevara-González (Ed.), Aflatoxins - Biochemistry and Molecular Biology.
Ed(s): R. Guevara-González
2010 journal article
Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia
PHYTOPATHOLOGY, 101(1), 147–153.
2010 conference paper
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).
Ed(s): S. Frankel, J. Kliejunas & K. Palmieri
2009 journal article
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.
2009 journal article
Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches
PHYTOPATHOLOGY, 99(6), 765–774.
2009 journal article
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.
2009 journal article
Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus
MOLECULAR ECOLOGY, 18(23), 4870–4887.
2009 journal article
Sexual reproduction in Aspergillus flavus
MYCOLOGIA, 101(3), 423–429.
2009 journal article
The sexual state of Aspergillus parasiticus
MYCOLOGIA, 101(2), 275–280.
2008 journal article
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
BMC GENOMICS, 9.
Contributors: A. Powell*, G. Conant* , D. Brown n, n & R. Dean n
2008 journal article
Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus
FUNGAL GENETICS AND BIOLOGY, 45(9), 1292–1299.
2008 journal article
Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer
CANADIAN JOURNAL OF FOREST RESEARCH, 38(6), 1576–1589.
2008 journal article
GT-Miner: a graph-theoretic data miner, viewer, and model processor
Bioinformation, 3(5), 235–237.
2008 journal article
Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi
MYCOLOGIA, 100(4), 555–564.
2008 journal article
Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus
FUNGAL GENETICS AND BIOLOGY, 46(2), 169–175.
2008 journal article
Virulence structure of the Eastern US wheat powdery mildew population
PLANT DISEASE, 92(7), 1074–1082.
2007 journal article
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.
Contributors: L. Gómez-Alpizar n, n & J. Ristaino*
2007 journal article
Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster
BMC EVOLUTIONARY BIOLOGY, 7.
2007 journal article
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.
2007 journal article
New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington
PHYTOPATHOLOGY, 97(4), 470–483.
2007 journal article
Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus
MOLECULAR ECOLOGY, 16(20), 4401–4417.
2007 journal article
The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes
BMC EVOLUTIONARY BIOLOGY, 7.
2006 journal article
SNAP: Combine and Map modules for multilocus population genetic analysis
Bioinformatics, 22(11), 1399–1401.
2005 journal article
Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci
JOURNAL OF BACTERIOLOGY, 187(16), 5700–5708.
Contributors: L. Charles n, n , K. Davies *, D. Bird n , M. Burke n, B. Kerry*, C. Opperman n
2005 journal article
The genome sequence of the rice blast fungus Magnaporthe grisea
NATURE, 434(7036), 980–986.
2004 chapter
Inferring Process from Pattern in Fungal Population Genetics
In Fungal Genomics (pp. 29–58).
2004 journal article
Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent
GENETICS, 166(4), 1611–1629.
2004 journal article
SNAP: workbench management tool for evolutionary population genetic analysis
BIOINFORMATICS, 21(3), 402–404.
2002 journal article
Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum
Phytopathology, 92(7), 785–793.
2001 journal article
A microbial population-species interface: nested cladistic and coalescent inference with multilocus data
Molecular Ecology, 10(4), 947–964.
2001 journal article
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.
1999 journal article
A Method for Designing Primer Sets for Speciation Studies in Filamentous Ascomycetes
Mycologia, 91(3), 553.
1999 journal article
Patterns of Descent in Clonal Lineages and Their Multilocus Fingerprints Are Resolved with Combined Gene Genealogies
Evolution, 53(1), 11.
1995 journal article
A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum
Current Genetics, 27(2), 166–176.
1993 journal article
Ribosomal DNA Sequence Divergence within Internal Transcribed Spacer 1 of the Sclerotiniaceae
Mycologia, 85(3), 415.
1991 journal article
Mycelial Incompatibility and Molecular Markers Identify Genetic Variability in Field Populations of Sclerotinia sclerotiorum
Phytopathology, 81(4), 480–485.
1990 journal article
Mycelial interactions in Sclerotinia sclerotiorum
Experimental Mycology, 14(3), 255–267.
journal article
A transcriptional network associated with natural variation in Drosophila aggressive behavior
Edwards, A. C., Ayroles, J. F., Stone, E. A., Carbone, M. A., Lyman, R. F., & Mackay, T. F. C. Genome Biology, 10(7).
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