Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Virginia Polytech Institute and State University 1985
  • M.S., Virginia Polytech Institute and State University 1981
  • B.A., State University of New York at Geneseo 1978
• 

  Duke Appointment History

  • Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2003 - 2010
  • Associate Professor in Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2000 - 2003
  • Associate Professor with Tenure, Biology, Trinity College of Arts & Sciences 1993 - 2000
  • Assistant Professor, Biology, Trinity College of Arts & Sciences 1986 - 1993
• Recognition
• 

  In the News

  • AUG 6, 2014

    The News & Observer

    Rainy, cloudy weather triggers a boom of mushrooms
• 

  Awards & Honors

  • Distinguished Mycologist Award. Mycological Society of America. 2014
  • American Academy of Microbiology Fellow. American Society for Microbiology. 2012
  • MSA Fellows. Mycological Society of America. 2002
  • Alexopoulos Prize. Mycological Society of America. 1995
• Expertise
• 

  Global Scholarship

  • Expertise

    • United States of America (Country) 

  • Research

    • Ecuador (Country) 

  • Teaching

    • Australia (Country) 
• Research
• 

  Selected Grants

  • Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
  • Collaborative Research: Evolutionary genomics of plant-fungal symbiosis: coevolution of Pinaceae and their ectomycorrhizal fungi in the genus Suillus awarded by  National Science Foundation 2016 - 2020
  • Molecular Mycology and Pathogenesis Training Program awarded by National Institutes of Health 2015 - 2019
  • Collaborative Research: The Zygomycetes Genealogy of Life (ZyGoLife) - the conundrum of Kingdom Fungi awarded by University of California - Riverside 2015 - 2018
  • DOE Genomics GTL: PlantMicrobe Interfaces awarded by Oak Ridge National Labs 2010 - 2018
  • Dimensions: Collaborative Research: Deconstructing diversity and Ecosystem Function at Multiple Spatial and awarded by  National Science Foundation 2010 - 2016
  • GO! Program- Jessie Uehling awarded by Oak Ridge National Laboratory 2015
  • Pathogen Mediated Diversity and Response to Changing Climate awarded by  National Science Foundation 2010 - 2014
  • Collaborative Research: Ectomycorrhizal fungal diversity of the central Guiana Shield awarded by  National Science Foundation 2009 - 2013
  • Sexual reproduction and virulence of zygomycete fungi awarded by National Institutes of Health 2010 - 2013
  • Collaborative Research: Assembling the Fungal Tree of Life: Resolving the Evolutionary History of the Fungi awarded by  National Science Foundation 2007 - 2012
  • Studies of Cryptococcus neoformans Associated with AIDS awarded by National Institutes of Health 1987 - 2011
  • REVSYS: Phylogenetic and revisionary systematics of North America truffles (Tuber, Ascomycota) awarded by  National Science Foundation 2007 - 2011
  • DISSERTATION RESEARCH: Systematics and Phylogeography of Truffles (Tuber) awarded by  National Science Foundation 2007 - 2010
  • COLLABORATIVE RESEARCH: Effects of Elevated CO2 on Forest N Cycling: Assessment with Large-Scale 15N Tracers and Modelin awarded by  National Science Foundation 2003 - 2007
  • Collaborative Research: Assembling the fungal tree of life awarded by  National Science Foundation 2003 - 2006
  • DISSERTATION RESEARCH: Coevolutionary Diversification in Septobasidium, a Fungal Symbiont of Scale Insects awarded by  National Science Foundation 2004 - 2006
  • A Microbial Observatory in the Duke Forest: Exploring fungal diversity in response to environmental change awarded by  National Science Foundation 2000 - 2004
  • PEET: Monographic Studies of the Cladoniaceae awarded by Smithsonian Institution 1998 - 2004
  • Dissertation Research: The evolution of the A mating genes in the mushroom fungi. awarded by  National Science Foundation 2001 - 2003
  • Phylogenetic systematics and diversity of the Agaricales awarded by  National Science Foundation 2000 - 2003
  • An environmental scanning electron microscope for DU awarded by  National Science Foundation 2001 - 2003
  • Molecular Identification of Pathogenic Fungi awarded by National Institutes of Health 1997 - 2002
  • (97-0463) The Agaricales: Molecular Systematic and Evolution of Mushrooms awarded by  National Science Foundation 1997 - 2000
  • PEET: Monographic Studies in the Cladoniaceae (Lichen-Forming Ascomycetes) awarded by Smithsonian Institution 1997 - 1999
  • (98-0459) PEET: Monographic Studies in the Cladoniaceae (Lichen-Forming Ascomycetes) awarded by Smithsonian Institution 1997 - 1998
  • (94-0421) Biogeography and Speciation in the Oyster Mushroom Pleurotus awarded by  National Science Foundation 1994 - 1997
  • (94-0172) Phylogeny in the Genus Omphalina and the Evolutionary Consequences of Mutualism awarded by  National Science Foundation 1994 - 1996
  • (94-0402) Genetic Analysis of Population Structure in the Oyster Mushroom Pleurotus Ostreatus awarded by  National Science Foundation 1992 - 1995
  • (94-0092) A Molecular Approach to the Phylogeny of Bryophtes Using Chloroplast DNA awarded by  National Science Foundation 1991 - 1995
  • (91-0324) A Molecular Approach to the Phylogeny of Bryophytes Using Chloroplast DNA awarded by  National Science Foundation 1991 - 1994
  • (93-0284) Genetic Analysis of Population Structure in the Oyster Mushroom Pleurotus Ostreatus awarded by  National Science Foundation 1992 - 1994
  • (91-0375) Genetic Variability and Identification of Pathogenic and Non-Pathogenic Rhizoctonia Species awarded by Department of Agriculture 1991 - 1993
  • (91-0197) Systematic Investigations in the Basidiomycete Genus Coprinus Phylogeny, Character Evolution, and Development awarded by  National Science Foundation 1991 - 1993
  • (91-0333) Genetic Analysis of Population Structures in the Oyster Mushroom Pieurotus Ostreatus awarded by  National Science Foundation 1991 - 1992
  • (91-0606) Character Weighting of Nucleotide Sequence Data awarded by  National Science Foundation 1991 - 1992
  • (90-0716) Molecular Systematics of Ribosomal RNA Genes in the Tricholomataceae awarded by  National Science Foundation 1988 - 1991
  • (89-0660) Award for Japanese-Language Study by Researchers in Science and Engineering awarded by  National Science Foundation 1989 - 1991
  • (88-0462) Molecular Systematics of Ribosomal RNA Genes in the Trichometaceal awarded by  National Science Foundation 1988 - 1991
  • (89-0684) Molecular Systematics of Ribosomal RNA Genes in the Tricholomataceae awarded by  National Science Foundation 1988 - 1990
  • (88-0283) Molecular Evolution of Ribosomal RNA Genes in the Rhizoctonia Complex awarded by Department of Agriculture 1988 - 1990
• Publications & Artistic Works
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  Selected Publications

  • Journal Articles

    • Cregger, MA, Veach, AM, Yang, ZK, Crouch, MJ, Vilgalys, R, Tuskan, GA, and Schadt, CW. "The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome." Microbiome 6, no. 1 (January 1, 2018).  Full Text
    • Vélez, JM, Tschaplinski, TJ, Vilgalys, R, Schadt, CW, Bonito, G, Hameed, K, Engle, N, and Hamilton, CE. "Erratum to "Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees" [Fungal Ecol. 27 (Part A) (June 2017) 78-86] (Accepted)." Fungal Ecology (January 1, 2018).  Full Text
    • Johansen, RB, Johnston, P, Mieczkowski, P, Perry, GL, Robeson, MS, Vilgalys, R, and Burns, BR. "Scattered far and wide: A broadly distributed temperate dune grass finds familiar fungal root associates in its invasive range." Soil Biology and Biochemistry 112 (September 2017): 177-190.  Full Text
    • Uehling, J, Gryganskyi, A, Hameed, K, Tschaplinski, T, Misztal, PK, Wu, S, Desirò, A, Vande Pol, N, Du, Z, Zienkiewicz, A, Zienkiewicz, K, Morin, E, Tisserant, E, Splivallo, R, Hainaut, M, Henrissat, B, Ohm, R, Kuo, A, Yan, J, Lipzen, A, Nolan, M, LaButti, K, Barry, K, Goldstein, AH, Labbé, J, Schadt, C, Tuskan, G, Grigoriev, I, Martin, F, Vilgalys, R, and Bonito, G. "Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens." Environmental microbiology 19, no. 8 (August 2017): 2964-2983.  Full Text
    • Smith, ME, Henkel, TW, Williams, GC, Aime, MC, Fremier, AK, and Vilgalys, R. "Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa ." New Phytologist 215, no. 1 (July 2017): 443-453.  Full Text
    • Vélez, JM, Tschaplinski, TJ, Vilgalys, R, Schadt, CW, Bonito, G, Hameed, K, Engle, N, and Hamilton, CE. "Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees." Fungal Ecology 27 (June 2017): 78-86.  Full Text
    • Gryganskyi, AP, Mullens, BA, Gajdeczka, MT, Rehner, SA, Vilgalys, R, and Hajek, AE. "Hijacked: Co-option of host behavior by entomophthoralean fungi." PLoS pathogens 13, no. 5 (May 4, 2017): e1006274-.  Full Text
    • Branco, S, Bi, K, Liao, H-L, Gladieux, P, Badouin, H, Ellison, CE, Nguyen, NH, Vilgalys, R, Peay, KG, Taylor, JW, and Bruns, TD. "Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes." Molecular ecology 26, no. 7 (April 2017): 2063-2076.  Full Text
    • Li, Z, Yao, Q, Dearth, SP, Entler, MR, Castro Gonzalez, HF, Uehling, JK, Vilgalys, RJ, Hurst, GB, Campagna, SR, Labbé, JL, and Pan, C. "Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system." Environmental microbiology 19, no. 3 (March 2017): 1041-1053.  Full Text
    • Bonito, G, Hameed, K, Toome-Heller, M, Healy, R, Reid, C, Liao, H-L, Aime, MC, Schadt, C, and Vilgalys, R. "Atractiella rhizophila , sp. nov., an endorrhizal fungus isolated from the Populus root microbiome." Mycologia 109, no. 1 (January 2, 2017): 18-26.  Full Text
    • Rosenthal, LM, Larsson, K-H, Branco, S, Chung, JA, Glassman, SI, Liao, H-L, Peay, KG, Smith, DP, Talbot, JM, Taylor, JW, Vellinga, EC, Vilgalys, R, and Bruns, TD. "Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal." Mycologia 109, no. 1 (January 2, 2017): 115-127.  Full Text
    • Liao, H-L, Chen, Y, and Vilgalys, R. "Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus." PLoS genetics 12, no. 10 (October 13, 2016): e1006348-.  Full Text
    • Johansen, RB, Johnston, P, Mieczkowski, P, Perry, GL, Robeson, MS, Burns, BR, and Vilgalys, R. "A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities." Fungal Ecology 23 (October 2016): 141-155.  Full Text
    • Spatafora, JW, Chang, Y, Benny, GL, Lazarus, K, Smith, ME, Berbee, ML, Bonito, G, Corradi, N, Grigoriev, I, Gryganskyi, A, James, TY, O'Donnell, K, Roberson, RW, Taylor, TN, Uehling, J, Vilgalys, R, White, MM, and Stajich, JE. "A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data." Mycologia 108, no. 5 (September 2016): 1028-1046.  Full Text
    • Bonito, G, Hameed, K, Ventura, R, Krishnan, J, Schadt, CW, and Vilgalys, R. "Isolating a functionally relevant guild of fungi from the root microbiome of Populus." Fungal Ecology 22 (August 2016): 35-42.  Full Text
    • Ekblad, A, Mikusinska, A, Ågren, GI, Menichetti, L, Wallander, H, Vilgalys, R, Bahr, A, and Eriksson, U. "Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization." The New phytologist 211, no. 3 (August 2016): 874-885.  Full Text
    • Gónzalez, D, Rodriguez-Carres, M, Boekhout, T, Stalpers, J, Kuramae, EE, Nakatani, AK, Vilgalys, R, and Cubeta, MA. "Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales." Fungal biology 120, no. 4 (April 2016): 603-619.  Full Text
    • Czaplicki, LM, Cooper, E, Ferguson, PL, Stapleton, HM, Vilgalys, R, and Gunsch, CK. "A New Perspective on Sustainable Soil Remediation-Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants." Remediation (New York, N.Y.) 26, no. 2 (January 2016): 59-72.  Full Text
    • Branco, S, Gladieux, P, Ellison, CE, Kuo, A, LaButti, K, Lipzen, A, Grigoriev, IV, Liao, H-L, Vilgalys, R, Peay, KG, Taylor, JW, and Bruns, TD. "Genetic isolation between two recently diverged populations of a symbiotic fungus." Molecular ecology 24, no. 11 (June 2015): 2747-2758.  Full Text
    • Kuske, CR, Hesse, CN, Challacombe, JF, Cullen, D, Herr, JR, Mueller, RC, Tsang, A, and Vilgalys, R. "Prospects and challenges for fungal metatranscriptomics of complex communities." Fungal Ecology 14 (April 2015): 133-137.  Full Text
    • Glassman, SI, Peay, KG, Talbot, JM, Smith, DP, Chung, JA, Taylor, JW, Vilgalys, R, and Bruns, TD. "A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern." The New phytologist 205, no. 4 (March 2015): 1619-1631.  Full Text
    • Hofstetter, V, Redhead, SA, Kauff, F, Moncalvo, J-M, Matheny, PB, and Vilgalys, R. "Taxonomic Revision and Examination of Ecological Transitions of the Lyophyllaceae (Basidiomycota, Agaricales) Based on a Multigene Phylogeny." Cryptogamie, Mycologie 35, no. 4 (December 2014): 399-425.  Full Text
    • Liao, H-L, Chen, Y, Bruns, TD, Peay, KG, Taylor, JW, Branco, S, Talbot, JM, and Vilgalys, R. "Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ." Environmental microbiology 16, no. 12 (December 2014): 3730-3742.  Full Text
    • Bonito, G, Reynolds, H, Robeson, MS, Nelson, J, Hodkinson, BP, Tuskan, G, Schadt, CW, and Vilgalys, R. "Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants." Molecular ecology 23, no. 13 (July 2014): 3356-3370.  Full Text
    • Talbot, JM, Bruns, TD, Taylor, JW, Smith, DP, Branco, S, Glassman, SI, Erlandson, S, Vilgalys, R, Liao, H-L, Smith, ME, and Peay, KG. "Endemism and functional convergence across the North American soil mycobiome." Proceedings of the National Academy of Sciences of the United States of America 111, no. 17 (April 14, 2014): 6341-6346.  Full Text
    • Losada, L, Pakala, SB, Fedorova, ND, Joardar, V, Shabalina, SA, Hostetler, J, Pakala, SM, Zafar, N, Thomas, E, Rodriguez-Carres, M, Dean, R, Vilgalys, R, Nierman, WC, and Cubeta, MA. "Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3." FEMS microbiology letters 352, no. 2 (March 2014): 165-173. (Letter)  Full Text
    • Cubeta, MA, Thomas, E, Dean, RA, Jabaji, S, Neate, SM, Tavantzis, S, Toda, T, Vilgalys, R, Bharathan, N, Fedorova-Abrams, N, Pakala, SB, Pakala, SM, Zafar, N, Joardar, V, Losada, L, and Nierman, WC. "Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP." Genome announcements 2, no. 5 (January 2014).  Full Text
    • Lodge, DJ, Padamsee, M, Matheny, PB, Aime, MC, Cantrell, SA, Boertmann, D, Kovalenko, A, Vizzini, A, Dentinger, BTM, Kirk, PM, Ainsworth, AM, Moncalvo, J-M, Vilgalys, R, Larsson, E, Lücking, R, Griffith, GW, Smith, ME, Norvell, LL, Desjardin, DE, Redhead, SA, Ovrebo, CL, Lickey, EB, Ercole, E, Hughes, KW, Courtecuisse, R, Young, A, Binder, M, Minnis, AM, Lindner, DL, Ortiz-Santana, B, Haight, J, Læssøe, T, Baroni, TJ, Geml, J, and Hattori, T. "Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)." Fungal Diversity 64, no. 1 (January 2014): 1-99.  Full Text
    • Losada, L, Pakala, SB, Fedorova, ND, Joardar, V, Shabalina, SA, Hostetler, J, Pakala, SM, Zafar, N, Thomas, E, Rodriguez-Carres, M, Dean, R, Vilgalys, R, Nierman, WC, and Cubeta, MA. "Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3." FEMS Microbiology Letters 352, no. 2 (2014): 165-173.  Full Text
    • Benítez, M-S, Hersh, MH, Vilgalys, R, and Clark, JS. "Pathogen regulation of plant diversity via effective specialization." Trends Ecol Evol 28, no. 12 (December 2013): 705-711.  Full Text  Link to Item
    • Benítez, MS, Hersh, MH, Vilgalys, R, and Clark, JS. "Pathogen regulation of plant diversity via effective specialization." Trends in Ecology and Evolution 28, no. 12 (December 1, 2013): 705-711. (Review)  Full Text
    • Bonito, G, Smith, ME, Nowak, M, Healy, RA, Guevara, G, Cázares, E, Kinoshita, A, Nouhra, ER, Domínguez, LS, Tedersoo, L, Murat, C, Wang, Y, Moreno, BA, Pfister, DH, Nara, K, Zambonelli, A, Trappe, JM, and Vilgalys, R. "Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage." PLoS One 8, no. 1 (2013): e52765-.  Full Text  Link to Item
    • Golonka, AM, and Vilgalys, R. "Nectar inhabiting yeasts in Virginian populations of Silene latifolia (Caryophyllaceae) and coflowering species." American Midland Naturalist 169, no. 2 (2013): 235-258.  Full Text
    • Gryganskyi, AP, Humber, RA, Smith, ME, Miadlikovska, J, Wu, S, Voigt, K, Walther, G, Anishchenko, IM, and Vilgalys, R. "Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694]." Molecular Phylogenetics and Evolution 66, no. 3 (2013): 1099--.  Full Text
    • Gryganskyi, AP, Humber, RA, Stajich, JE, Mullens, B, Anishchenko, IM, and Vilgalys, R. "Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex." PLoS ONE 8, no. 8 (2013).  Full Text
    • Healy, RA, Smith, ME, Bonito, GM, Pfister, DH, Ge, Z-W, Guevara, GG, Williams, G, Stafford, K, Kumar, L, Lee, T, Hobart, C, Trappe, J, Vilgalys, R, and McLaughlin, DJ. "High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales." Molecular Ecology 22, no. 6 (2013): 1717-1732.  Full Text
    • Shakya, M, Gottel, N, Castro, H, Yang, ZK, Gunter, L, Labbé, J, Muchero, W, Bonito, G, Vilgalys, R, Tuskan, G, and al, E. "A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees." PLoS ONE 8, no. 10 (2013).  Full Text
    • Talbot, JM, Bruns, TD, Smith, DP, Branco, S, Glassman, SI, Erlandson, S, Vilgalys, R, and Peay, KG. "Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition." Soil Biology and Biochemistry 57 (2013): 282-291.  Full Text
    • Weber, CF, Vilgalys, R, and Kuske, CR. "Changes in fungal community composition in response to elevated atmospheric CO₂ and nitrogen fertilization varies with soil horizon." Frontiers in Microbiology 4, no. APR (2013).  Full Text
    • Gryganskyi, AP, Humber, RA, Smith, ME, Miadlikowska, J, Wu, S, Voigt, K, Walther, G, Anishchenko, IM, and Vilgalys, R. "Molecular phylogeny of the Entomophthoromycota." Mol Phylogenet Evol 65, no. 2 (November 2012): 682-694.  Full Text  Link to Item
    • Hersh, MH, Vilgalys, R, and Clark, JS. "Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival." Ecology 93, no. 3 (March 2012): 511-520.  Link to Item
    • Bonito, G, Smith, ME, Brenneman, T, and Vilgalys, R. "Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants." Plant and Soil 356, no. 1-2 (2012): 357-366.  Full Text
    • Dunbar, J, Eichorst, SA, Gallegos-Graves, LV, Silva, S, Xie, G, Hengartner, NW, Evans, RD, Hungate, BA, Jackson, RB, Megonigal, JP, Schadt, CW, Vilgalys, R, Zak, DR, and Kuske, CR. "Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide." Environmental Microbiology 14, no. 5 (2012): 1145-1158.  Full Text
    • Gryganskyi, AP, Humber, RA, Smith, ME, Hodge, K, Huang, B, Voigt, K, and Vilgalys, R. "Phylogenetic lineages in Entomophthoromycota." Persoonia. (2012). (Academic Article)
    • Gryganskyi, AP, Humber, RA, Smith, ME, Miadlikovska, J, Wu, S, Voigt, K, Walther, G, Anishchenko, IM, and Vilgalys, R. "Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694] (DOI:10.1016/j.ympev.2012.07.026)." Molecular Phylogenetics and Evolution (2012).  Full Text
    • Guevara, , Gonzalo, , Bonito, G, Trappe, JM, Cázares, E, Williams, G, Healy, RA, Schadt, CW, and Vilgalys, R. "New North American truffles (Tuber spp.) and their ectomycorrhizal associations." Mycologia 2012 (2012). (Academic Article)
    • Healy, RA, Smith, ME, Bonito, GM, Pfister, DH, Ge, Z-W, Guevara, GG, Williams, G, Stafford, K, Kumar, L, Lee, T, and al, E. "High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales." Molecular Ecology (2012).  Full Text
    • Henkel, TW, Aime, MC, Chin, MML, Miller, SL, Vilgalys, R, and Smith, ME. "Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield." Biodiversity and Conservation 21, no. 9 (2012): 2195-2220.  Full Text
    • Henkel, TW, Husbands, D, Bonito, GM, Vilgalys, R, and Smith, ME. "New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence." Mycologia in press (2012). (Academic Article)
    • Smith, ME, Henkel, TW, Uehling, JK, Fremier, AK, Clarke, HD, and Vilgalys, R. "Ectomycorrhizal fungal community in a tropical forest dominated by the Neotropical Dipterocarp, Pakaraimea dipterocarpaceae." PLOS ONE (in press) (2012). (Academic Article)
    • Thaler, AD, Dover, CLV, and Vilgalys, R. "Ascomycete phylotypes recovered from a Gulf of Mexico methane seep are identical to an uncultured deep-sea fungal clade from the Pacific." Fungal Ecology 5, no. 2 (2012): 270-273.  Full Text
    • Uehling, JK, Henkel, TW, Aime, MC, Vilgalys, R, and Smith, ME. "New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield." Mycologia 103 (2012): 883-894. (Academic Article)
    • Uehling, JK, Henkel, TW, Aime, MC, Vilgalys, R, and Smith, ME. "Four new species of Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, and a key to the lowland neotropical species." Fungal Biology. In Press (2012). (Academic Article)
    • Uehling, JK, Henkel, TW, Aime, MC, Vilgalys, R, and Smith, ME. "New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa." Fungal Biology 116, no. 12 (2012): 1263-1274.  Full Text
    • Uehling, JK, Henkel, TW, Aime, MC, Vilgalys, R, and Smith, ME. "New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield." Mycologia 104, no. 2 (2012): 547-556.  Full Text
    • Uehling, JK, Henkel, TW, Vilgalys, R, and Smith, ME. "Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests." Mycorrhiza 22, no. 7 (2012): 577-581.  Full Text
    • Baroni, TJ, Hofstetter, V, Largent, DL, and Vilgalys, R. "Entocybe is proposed as a new genus in the Entolomataceae (Agaricomycetes, Basidiomycota) based on morphological and molecular evidence." North American Fungi 6, no. 12 (2011): 1-19.  Full Text
    • Bonito, G, Brenneman, T, and Vilgalys, R. "Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae)." Mycorrhiza 21, no. 7 (2011): 601-612.  Full Text
    • Bonito, G, Trappe, JM, Donovan, S, and Vilgalys, R. "The Asian black truffle Tuber indicum can form ectomycorrhizas with North American host plants and complete its life cycle in non-native soils." Fungal Ecology 4, no. 1 (2011): 83-93.  Full Text
    • Gottel, NR, Castro, HF, Kerley, M, Yang, Z, Pelletier, DA, Podar, M, Karpinets, T, Uberbacher, E, Tuskan, GA, Vilgalys, R, Doktycz, MJ, and Schadt, CW. "Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types." Applied and Environmental Microbiology 77, no. 17 (2011): 5934-5944.  Full Text
    • Porter, TM, Martin, W, James, TY, Longcore, JE, Gleason, FH, Adler, PH, Letcher, PM, and Vilgalys, R. "Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA." Fungal Biology 115, no. 4-5 (2011): 381-392.  Full Text
    • Smith, ME, Henkel, TW, Aime, MC, Fremier, AK, and Vilgalys, R. "Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest." New Phytologist 192, no. 3 (2011): 699-712.  Full Text
    • Weber, CF, Zak, DR, Hungate, BA, Jackson, RB, Vilgalys, R, Evans, RD, Schadt, CW, Megonigal, JP, and Kuske, CR. "Responses of soil cellulolytic fungal communities to elevated atmospheric CO ₂ are complex and variable across five ecosystems." Environmental Microbiology 13, no. 10 (2011): 2778-2793.  Full Text
    • Gryganskyi, AP, Lee, SC, Litvintseva, AP, Smith, ME, Bonito, G, Porter, TM, Anishchenko, IM, Heitman, J, and Vilgalys, R. "Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex." PloS one 5, no. 12 (December 9, 2010): e15273-.  Full Text  Open Access Copy
    • Bonito, G, Isikhuemhen, OS, and Vilgalys, R. "Identification of fungi associated with municipal compost using DNA-based techniques." Bioresource Technology 101, no. 3 (2010): 1021-1027.  Full Text
    • Bonito, G, Trappe, JM, Rawlinson, P, and Vilgalys, R. "Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex." Mycologia 102, no. 5 (2010): 1042-1057.  Full Text
    • Bonito, GM, Gryganskyi, AP, Trappe, JM, and Vilgalys, R. "A global meta-analysis of Tuber ITS rDNA sequences: Species diversity, host associations and long-distance dispersal." Molecular Ecology 19, no. 22 (2010): 4994-5008.  Full Text
    • Findley, K, Rodriguez-Carres, M, Metin, B, Kroiss, J, Fonseca, Á, Vilgalys, R, and Heitman, J. "Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the tremellales." Eukaryotic Cell 8, no. 3 (2009): 353-361.  Full Text
    • James, TY, Litvintseva, AP, Vilgalys, R, Morgan, JAT, Taylor, JW, Fisher, MC, Berger, L, Weldon, C, Preez, LD, and Longcore, JE. "Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations." PLoS Pathogens 5, no. 5 (2009).  Full Text
    • McLaughlin, DJ, Hibbett, DS, Lutzoni, F, Spatafora, JW, and Vilgalys, R. "The search for the fungal tree of life." Trends in Microbiology 17, no. 11 (2009): 488-497.  Full Text
    • Parrent, JL, and Vilgalys, R. "Expression of genes involved in symbiotic carbon and nitrogen transport in Pinus taeda mycorrhizal roots exposed to CO2 enrichment and nitrogen fertilization." Mycorrhiza 19, no. 7 (2009): 469-479.  Full Text
    • Hartman, WH, Richardson, CJ, Vilgalys, R, and Bruland, GL. "Environmental and anthropogenic controls over bacterial communities in wetland soils." Proc Natl Acad Sci U S A 105, no. 46 (November 18, 2008): 17842-17847.  Full Text  Link to Item
    • Porter, TM, Schadt, CW, Rizvi, L, Martin, AP, Schmidt, SK, Scott-Denton, L, Vilgalys, R, and Moncalvo, JM. "Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life." Molecular Phylogenetics and Evolution 46, no. 2 (2008): 635-644.  Full Text
    • Ceresini, PC, Shew, HD, James, TY, Vilgalys, RJ, and Cubeta, MA. "Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci. (Published online)" BMC Evol Biol 7 (September 13, 2007): 163-.  Full Text  Link to Item
    • Arnold, AE, Henk, DA, Eells, RL, Lutzoni, F, and Vilgalys, R. "Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR." Mycologia 99, no. 2 (March 2007): 185-206.  Link to Item
    • Henk, DA, and Vilgalys, R. "Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium." American Journal of Botany 94, no. 9 (2007): 1515-1526.  Full Text
    • Hibbett, DS, Binder, M, Bischoff, JF, Blackwell, M, Cannon, PF, Eriksson, OE, Huhndorf, S, James, T, Kirk, PM, Lücking, R, Lumbsch, HT, Lutzoni, F, Matheny, PB, McLaughlin, DJ, Powell, MJ, Redhead, S, Schoch, CL, Spatafora, JW, Stalpers, JA, Vilgalys, R, Aime, MC, Aptroot, A, Bauer, R, Begerow, D, Benny, GL, Castlebury, LA, Crous, PW, Dai, Y-C, Gams, W, Geiser, DM, Griffith, GW, Gueidan, C, Hawksworth, DL, Hestmark, G, Hosaka, K, Humber, RA, Hyde, KD, Ironside, JE, Kõljalg, U, and Kurtzman, CP et al. "A higher-level phylogenetic classification of the Fungi." Mycological Research 111, no. 5 (2007): 509-547.  Full Text
    • Parrent, JL, and Vilgalys, R. "Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO₂ and nitrogen fertilization." New Phytologist 176, no. 1 (2007): 164-174.  Full Text
    • James, TY, Kauff, F, Schoch, CL, Matheny, PB, Hofstetter, V, Cox, CJ, Celio, G, Gueidan, C, Fraker, E, Miadlikowska, J, Lumbsch, HT, Rauhut, A, Reeb, V, Arnold, AE, Amtoft, A, Stajich, JE, Hosaka, K, Sung, G-H, Johnson, D, O'Rourke, B, Crockett, M, Binder, M, Curtis, JM, Slot, JC, Wang, Z, Wilson, AW, Schüssler, A, Longcore, JE, O'Donnell, K, Mozley-Standridge, S, Porter, D, Letcher, PM, Powell, MJ, Taylor, JW, White, MM, Griffith, GW, Davies, DR, Humber, RA, Morton, JB, and Sugiyama, J et al. "Reconstructing the early evolution of Fungi using a six-gene phylogeny." Nature 443, no. 7113 (October 19, 2006): 818-822.  Full Text  Link to Item
    • Parrent, JL, Morris, WF, and Vilgalys, R. "CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities." Ecology 87, no. 9 (September 2006): 2278-2287.  Link to Item
    • Litvintseva, AP, Thakur, R, Vilgalys, R, and Mitchell, TG. "Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana." Genetics 172, no. 4 (April 2006): 2223-2238.  Full Text  Link to Item
    • González, D, Cubeta, MA, and Vilgalys, R. "Phylogenetic utility of indels within ribosomal DNA and β-tubulin sequences from fungi in the Rhizoctonia solani species complex." Molecular Phylogenetics and Evolution 40, no. 2 (2006): 459-470.  Full Text
    • James, TY, Letcher, PM, Longcore, JE, Mozley-Standridge, SE, Porter, D, Powell, MJ, Griffith, GW, and Vilgalys, R. "A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)." Mycologia 98, no. 6 (2006): 860-871.  Full Text
    • James, TY, Srivilai, P, Kües, U, and Vilgalys, R. "Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function." Genetics 172, no. 3 (2006): 1877-1891.  Full Text
    • Matheny, PB, Curtis, JM, Hofstetter, V, Aime, MC, Moncalvo, J-M, Ge, Z-W, Yang, Z-L, Slot, JC, Ammirati, JF, Baroni, TJ, Bougher, NL, Hughes, KW, Lodge, DJ, Kerrigan, RW, Seidl, MT, Aanen, DK, DeNitis, M, Daniele, GM, Desjardin, DE, Kropp, BR, Norvell, LL, Parker, A, Vellinga, EC, Vilgalys, R, and Hibbett, DS. "Major clades of Agaricales: A multilocus phylogenetic overview." Mycologia 98, no. 6 (2006): 982-995.  Full Text
    • Moncalvo, J-M, Nilsson, RH, Koster, B, Dunham, SM, Bernauer, T, Matheny, PB, Porter, TM, Margaritescu, S, Weiß, M, Garnica, S, Danell, E, Langer, G, Langer, E, Larsson, E, Larsson, K-H, and Vilgalys, R. "The cantharelloid clade: Dealing with incongruent gene trees and phylogenetic reconstruction methods." Mycologia 98, no. 6 (2006): 937-948.  Full Text
    • Parrent, JL, Morris, WF, and Vilgalys, R. "CO₂-enrichment and nutrient availability alter ectomycorrhizal fungal communities." Ecology 87, no. 9 (2006): 2278-2287.  Full Text
    • Yahr, R, Vilgalys, R, and DePriest, PT. "Erratum: Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis (New Phytologist (2006) 171 (847-860))." New Phytologist 172, no. 2 (2006): 377--.  Full Text
    • Yahr, R, Vilgalys, R, and Depriest, PT. "Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis." New Phytologist 171, no. 4 (2006): 847-860.  Full Text
    • O'Brien, HE, Parrent, JL, Jackson, JA, Moncalvo, J-M, and Vilgalys, R. "Fungal community analysis by large-scale sequencing of environmental samples." Appl Environ Microbiol 71, no. 9 (September 2005): 5544-5550.  Full Text  Link to Item
    • Fierer, N, Jackson, JA, Vilgalys, R, and Jackson, RB. "Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays." Appl Environ Microbiol 71, no. 7 (July 2005): 4117-4120.  Full Text  Link to Item
    • Didukh, M, Vilgalys, R, Wasser, SP, Isikhuemhen, OS, and Nevo, E. "Notes on Agaricus section Duploannulati using molecular and morphological data." Mycological research 109, no. Pt 6 (June 2005): 729-740. (Academic Article)
    • Litvintseva, AP, Kestenbaum, L, Vilgalys, R, and Mitchell, TG. "Comparative analysis of environmental and clinical populations of Cryptococcus neoformans." J Clin Microbiol 43, no. 2 (February 2005): 556-564.  Full Text  Link to Item
    • Aime, MC, Vilgalys, R, and Jr, OKM. "The crepidotaceae (Basidiomycota, Agaricales): Phylogeny and taxonomy of the genera and revision of the family based on molecular evidence." American Journal of Botany 92, no. 1 (2005): 74-82.  Full Text
    • Didukh, M, Vilgalys, R, Wasser, SP, Isikhuemhen, OS, and Nevo, E. "Notes on Agaricus section Duploannulati using molecular and morphological data." Mycological Research 109, no. 6 (2005): 729-740.  Full Text
    • Wallenstein, MD, and Vilgalys, RJ. "Quantitative analyses of nitrogen cycling genes in soils." Pedobiologia 49, no. 6 (2005): 665-672.  Full Text
    • Diezmann, S, Cox, CJ, Schönian, G, Vilgalys, RJ, and Mitchell, TG. "Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis." J Clin Microbiol 42, no. 12 (December 2004): 5624-5635.  Full Text  Link to Item
    • Lutzoni, F, Kauff, F, Cox, CJ, McLaughlin, D, Celio, G, Dentinger, B, Padamsee, M, Hibbett, D, James, TY, Baloch, E, Grube, M, Reeb, V, Hofstetter, V, Schoch, C, Arnold, AE, Miadlikowska, J, Spatafora, J, Johnson, D, Hambleton, S, Crockett, M, Shoemaker, R, Sung, G-H, Lücking, R, Lumbsch, T, O'Donnell, K, Binder, M, Diederich, P, Ertz, D, Gueidan, C, Hansen, K, Harris, RC, Hosaka, K, Lim, Y-W, Matheny, B, Nishida, H, Pfister, D, Rogers, J, Rossman, A, Schmitt, I, Sipman, H, and Stone, J et al. "Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits." Am J Bot 91, no. 10 (October 2004): 1446-1480.  Full Text  Link to Item
    • Marra, RE, Huang, JC, Fung, E, Nielsen, K, Heitman, J, Vilgalys, R, and Mitchell, TG. "A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)." Genetics 167, no. 2 (June 2004): 619-631.  Full Text  Link to Item
    • Zervakis, GI, Moncalvo, JM, and Vilgalys, R. "Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa." Microbiology 150, no. Pt 3 (March 2004): 715-726. (Academic Article)
    • James, TY, Kües, U, Rehner, SA, and Vilgalys, R. "Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi." Fungal Genetics and Biology 41, no. 3 (2004): 381-390.  Full Text
    • James, TY, Liou, S-R, and Vilgalys, R. "The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor." Fungal Genetics and Biology 41, no. 8 (2004): 813-825.  Full Text
    • Peintner, U, Moncalvo, J-M, and Vilgalys, R. "Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota)." Mycologia 96, no. 5 (2004): 1042-1058.
    • Yahr, R, Vilgalys, R, and Depriest, PT. "Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens." Molecular Ecology 13, no. 11 (2004): 3367-3378.  Full Text
    • Zervakis, GI, Moncalvo, J-M, and Vilgalys, R. "Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa." Microbiology 150, no. 3 (2004): 715-726.
    • Litvintseva, AP, Marra, RE, Nielsen, K, Heitman, J, Vilgalys, R, and Mitchell, TG. "Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa." Eukaryot Cell 2, no. 6 (December 2003): 1162-1168.  Link to Item
    • Davis, EC, Franklin, JB, Shaw, AJ, and Vilgalys, R. "Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis." Am J Bot 90, no. 11 (November 2003): 1661-1667.  Full Text  Link to Item
    • Ceresini, PC, Shew, HD, Vilgalys, RJ, Gale, LR, and Cubeta, MA. "Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities." Phytopathology 93, no. 5 (May 2003): 610-615.  Full Text  Link to Item
    • Morehouse, EA, James, TY, Ganley, ARD, Vilgalys, R, Berger, L, Murphy, PJ, and Longcore, JE. "Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone." Mol Ecol 12, no. 2 (February 2003): 395-403.  Link to Item
    • Pringle, A, Moncalvo, J-M, and Vilgalys, R. "Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica." Mycorrhiza 13, no. 4 (2003): 227-231.  Full Text
    • Vilgalys, R. "Taxonomic misidentification in public DNA databases." New Phytologist 160, no. 1 (2003): 4-5.  Full Text
    • Ceresini, PC, Shew, HD, Vilgalys, RJ, Rosewich, UL, and Cubeta, MA. "Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina." Mycologia 94, no. 3 (May 2002): 450-460.  Link to Item
    • Ceresini, PC, Shew, HD, Vilgalys, RJ, and Cubeta, MA. "Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina." Mycologia 94, no. 3 (May 2002): 437-449.  Link to Item
    • Henkel, TW, Terborgh, J, and Vilgalys, RJ. "Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana." Mycological Research 106, no. 5 (2002): 515-531.  Full Text
    • Hofstetter, V, Clémençon, H, Vilgalys, R, and Moncalvo, J-M. "Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences." Mycological Research 106, no. 9 (2002): 1043-1059.  Full Text
    • Moncalvo, J-M, Vilgalys, R, Redhead, SA, Johnson, JE, James, TY, Aime, MC, Hofstetter, V, Verduin, SJW, Larsson, E, Baroni, TJ, Thorn, RG, Jacobsson, S, Clémençon, H, and Jr, OKM. "One hundred and seventeen clades of euagarics." Molecular Phylogenetics and Evolution 23, no. 3 (2002): 357-400.  Full Text
    • Peintner, U, Horak, E, Moser, M, and Vilgalys, R. "Rozites, Cuphocybe and Rapacea are taxonomic synonyms of Cortinarius: New combinations and new names." Mycotaxon 83 (2002): 447-451.
    • Peintner, U, Horak, E, Moser, MM, and Vilgalys, R. "Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences." Mycologia 94, no. 4 (2002): 620-629.
    • Peintner, U, Moser, M, and Vilgalys, R. "Thaxterogaster is a taxonomic synonym of Cortinarius: New combinations and new names." Mycotaxon 81 (2002): 177-184.
    • Redhead, SA, Lutzoni, F, Moncalvo, J-M, and Vilgalys, R. "Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics)." Mycotaxon 83 (2002): 19-57.
    • Xu, J, Luo, G, Vilgalys, RJ, Brandt, ME, and Mitchell, TG. "Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD." Microbiology 148, no. Pt 1 (January 2002): 203-212.  Full Text  Link to Item
    • Xu, J, Luo, G, Vilgalys, RJ, Brandt, ME, and Mitchell, TG. "Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD." Microbiology 148, no. 1 (2002): 203-212.
    • Xu, J, Onyewu, C, Yoell, HJ, Ali, RY, Vilgalys, RJ, and Mitchell, TG. "Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans." Antimicrob Agents Chemother 45, no. 2 (February 2001): 420-427.  Full Text  Link to Item
    • Gonzalez, D, Carling, DE, Kuninaga, S, Vilgalys, R, and Cubetae, MA. "Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs." Mycologia 93, no. 6 (2001): 1138-1150.
    • Hughes, KW, Petersen, RH, Johnson, JE, Moncalvo, J-M, Vilgalys, R, Redhead, SA, Thomas, T, and McGhee, LL. "Infragenic phylogeny of Collybia s. str. based on sequences of ribosomal ITS and LSU regions." Mycological Research 105, no. 2 (2001): 164-172.  Full Text
    • James, TY, Moncalvo, J-M, Li, S, and Vilgalys, R. "The other fly room: J. T. Patterson and Texas genetics." Genetics 157, no. 1 (2001): 1-5.
    • James, TY, Moncalvo, JM, Li, S, and Vilgalys, R. "Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune." Genetics 157, no. 1 (January 2001): 149-161. (Academic Article)
    • James, TY, and Vilgalys, R. "Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling." Molecular Ecology 10, no. 2 (2001): 471-479.  Full Text
    • Kües, U, James, TY, Vilgalys, R, and Challen, MP. "The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic homobasidiomycete Coprinus bilanatus." Current Genetics 39, no. 1 (2001): 16-24.  Full Text
    • Mueller, GM, Wu, Q-X, Huang, Y-Q, Guo, S-Y, Aldana-Gomez, R, and Vilgalys, R. "Assessing biogeographic relationships between North American and Chinese macrofungi." Journal of Biogeography 28, no. 2 (2001): 271-281.  Full Text
    • Peintner, U, Bougher, NL, Castellano, MA, Moncalvo, J-M, Moser, MM, Trappe, JM, and Vilgalys, R. "Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae)." American Journal of Botany 88, no. 12 (2001): 2168-2179.
    • Redhead, SA, Vilgalys, R, Moncalvo, J-M, Johnson, J, and Jr, HJS. "Coprinus Pers. and the disposition of Coprinus species sensu lato." Taxon 50, no. 1 (2001): 203-241.
    • Forche, A, Xu, J, Vilgalys, R, and Mitchell, TG. "Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers." Fungal Genet Biol 31, no. 3 (December 2000): 189-203.  Full Text  Link to Item
    • Xu, J, Vilgalys, R, and Mitchell, TG. "Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans." Mol Ecol 9, no. 10 (October 2000): 1471-1481.  Link to Item
    • Moncalvo, JM, Lutzoni, FM, Rehner, SA, Johnson, J, and Vilgalys, R. "Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences." Syst Biol 49, no. 2 (June 2000): 278-305.  Link to Item
    • Xu, J, Ali, RY, Gregory, DA, Amick, D, Lambert, SE, Yoell, HJ, Vilgalys, RJ, and Mitchell, TG. "Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans." Curr Microbiol 40, no. 4 (April 2000): 269-273.  Link to Item
    • Xu, J, Ramos, AR, Vilgalys, R, and Mitchell, TG. "Clonal and spontaneous origins of fluconazole resistance in Candida albicans." J Clin Microbiol 38, no. 3 (March 2000): 1214-1220.  Link to Item
    • Isikhuemhen, OS, Moncalvo, J-M, Nerud, F, and Vilgalys, R. "Mating compatibility and phylogeography in Pleurotus tuberregium." Mycological Research 104, no. 6 (2000): 732-737.  Full Text
    • Isikhuemhen, OS, Nerud, F, and Vilgalys, R. "Cultivation studies on wild and hybrid strains of Pleurotus tuberregium (Fr.) Sing. on wheat straw substrate." World Journal of Microbiology and Biotechnology 16, no. 5 (2000): 431-435.  Full Text
    • James, TY, Porter, D, Leander, CA, Vilgalys, R, and Longcore, JE. "Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics." Canadian Journal of Botany 78, no. 3 (2000): 336-350.
    • McEwen, JG, Taylor, JW, Carter, D, Xu, J, Felipe, MS, Vilgalys, R, Mitchell, TG, Kasuga, T, White, T, Bui, T, and Soares, CM. "Molecular typing of pathogenic fungi." Med Mycol 38 Suppl 1 (2000): 189-197. (Review)  Link to Item
    • Moncalvo, J-M, Drehmel, D, and Vilgalys, R. "Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): Phylogenetic implications." Molecular Phylogenetics and Evolution 16, no. 1 (2000): 48-63.  Full Text
    • Pringle, A, Moncalvo, J-M, and Vilgalys, R. "High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica." Mycologia 92, no. 2 (2000): 259-268.
    • Redhead, SA, Seifert, KA, Vilgalys, R, and Moncalvo, J-M. "Rhacophyllus and Zerovaemyces - Teleomorphs or anamorphs?." Taxon 49, no. 4 (2000): 789-798.
    • Schönian, G, Forche, A, Tietz, HJ, Müller, M, Gräser, Y, Vilgalys, R, Mitchell, TG, and Presber, W. "[Genetic structure of geographically different populations of candida albicans]." Mycoses 43 Suppl 2 (2000): 51-56.  Link to Item
    • Thorn, RG, Moncalvo, J-M, Reddy, CA, and Vilgalys, R. "Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi." Mycologia 92, no. 2 (2000): 241-252.
    • Forche, A, Schönian, G, Gräser, Y, Vilgalys, R, and Mitchell, TG. "Genetic structure of typical and atypical populations of Candida albicans from Africa." Fungal Genet Biol 28, no. 2 (November 1999): 107-125.  Full Text  Link to Item
    • Xu, J, Vilgalys, R, and Mitchell, TG. "Lack of genetic differentiation between two geographically diverse samples of Candida albicans isolated from patients infected with human immunodeficiency virus." J Bacteriol 181, no. 4 (February 1999): 1369-1373.  Link to Item
    • Baroni, TJ, Legon, NW, Vilgalys, R, and Lodge, DJ. "Calocybe cyanea - A rare and beautiful agaric is discovered in Puerto Rico." Mycologist 13, no. 1 (1999): 7-10.
    • Drehmel, D, Moncalvo, J-M, and Vilgalys, R. "Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: Implications for taxonomy and character evolution." Mycologia 91, no. 4 (1999): 610-618.
    • Gräser, Y, Fari, ME, Vilgalys, R, Kuijpers, AFA, Hoog, GSD, Presber, W, and Tietz, H-J. "Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region." Medical Mycology 37, no. 2 (1999): 105-114.  Full Text
    • James, TY, Porter, D, Hamrick, JL, and Vilgalys, R. "Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune." Evolution 53, no. 6 (1999): 1665-1677.
    • Jr, JSH, and Vilgalys, R. "Phylogenetic Relationships in the Mushroom Genus Coprinus and Dark-Spored Allies Based on Sequence Data from the Nuclear Gene Coding for the Large Ribosomal Subunit RNA: Divergent Domains, Outgroups, and Monophyly." Molecular Phylogenetics and Evolution 13, no. 1 (1999): 1-19.  Full Text
    • Xu, J, Mitchell, TG, and Vilgalys, R. "PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans." Mol Ecol 8, no. 1 (January 1999): 59-73.  Link to Item
    • Xu, J, Vilgalys, R, and Mitchell, TG. "Colony size can be used to determine the MIC of fluconazole for pathogenic yeasts." J Clin Microbiol 36, no. 8 (August 1998): 2383-2385.  Link to Item
    • Johnson, J, and Vilgalys, R. "Phylogenetic systematics of Lepiota sensu lato based on nuclear large subunit rDNA evidence." Mycologia 90, no. 6 (1998): 971-979.
    • McPartland, JM, Vilgalys, RJ, and Cubeta, MA. "Mushroom poisoning." Am Fam Physician 55, no. 5 (April 1997): 1797-1812. (Review)  Link to Item
    • Cubeta, MA, and Vilgalys, R. "Population biology of the Rhizoctonia solani complex." Phytopathology 87, no. 4 (1997): 480-483.
    • Lewis, LA, Mishler, BD, and Vilgalys, R. "Phylogenetic Relationships of the Liverworts (Hepaticae), a Basal Embryophyte Lineage, Inferred from Nucleotide Sequence Data of the Chloroplast GenerbcL." Molecular Phylogenetics and Evolution 7, no. 3 (1997): 377-393.  Full Text
    • Gräser, Y, Volovsek, M, Arrington, J, Schönian, G, Presber, W, Mitchell, TG, and Vilgalys, R. "Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination." Proc Natl Acad Sci U S A 93, no. 22 (October 29, 1996): 12473-12477.  Link to Item
    • Haase, G, Spatafora, JW, Mitchell, TG, and Vilgalys, R. "Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens [2]." Journal of Clinical Microbiology 34, no. 8 (1996): 2049-2050.
    • Yoder, AD, Cartmill, M, Ruvolo, M, Smith, K, and Vilgalys, R. "Ancient single origin for Malagasy primates." Proceedings of the National Academy of Sciences of the United States of America 93, no. 10 (1996): 5122-5126.  Full Text
    • Yoder, AD, Vilgalys, R, and Ruvolo, M. "Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: The phylogenetic significance of third-position transversions." Molecular Biology and Evolution 13, no. 10 (1996): 1339-1350.
    • Spatafora, JW, Mitchell, TG, and Vilgalys, R. "Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens." J Clin Microbiol 33, no. 5 (May 1995): 1322-1326.  Link to Item
    • Vilgalys, R, and Cubeta, MA. "Molecular systematics and population biology of Rhizoctonia." Annual Review of Phytopathology 32 (1994): 135-155.
    • Vilgalys, R, and Lin, SB. "Assessment of species distributions in Pleurotus based on trapping of airborne basidiospores." Mycologia 86, no. 2 (1994): 270-274.
    • Vilgalys, R, and Sun, BL. "Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences." Proceedings of the National Academy of Sciences of the United States of America 91, no. 10 (1994): 4599-4603.
    • Vilgalys, R, and Sun, BL. "Erratum: Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences (Proceedings of the National Academy of Sciences of the United States of America (May 10, 1994) 91 (4599-4603))." Proceedings of the National Academy of Sciences of the United States of America 91, no. 16 (1994): 7832--.  Full Text
    • Meyer, W, Mitchell, TG, Freedman, EZ, and Vilgalys, R. "Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans." J Clin Microbiol 31, no. 9 (September 1993): 2274-2280.  Link to Item
    • Moncalvo, JM, Rehner, SA, and Vilgalys, R. "Systematics of Lyophyllum section difformia based on evidence from culture studies and ribosomal DNA sequences." Mycologia 85, no. 5 (1993): 788-794.
    • Vilgalys, R, Smith, A, Sun, BL, and Jr, OKM. "Intersterility groups in the Pleurotus ostreatus complex from the continental United States and adjacent Canada." Canadian Journal of Botany 71, no. 1 (1993): 113-128.
    • Barns, TD, Vilgalys, R, Barns, SM, Gonzalez, D, Hibbett, DS, Lane, DJ, Simon, L, Stickel, S, Szaro, TM, Weisburg, WG, and Sogin, ML. "Evolutionary relationships within the fungi: Analyses of nuclear small subunit rRNA sequences." Molecular Phylogenetics and Evolution 1, no. 3 (1992): 231-241.
    • Kay, E, and Vilgalys, R. "Spatial distribution and genetic relationships among individuals in a natural population of the oyster mushroom Pleurotus ostreatus." Mycologia 84, no. 2 (1992): 173-182.
    • Hibbett, DS, and Vilgalys, R. "Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA." Mycologia 83, no. 4 (1991): 425-439.
    • Vilgalys, R. "Speciation and species concepts in the Collybia dryophila complex." Mycologia 83, no. 6 (1991): 758-773.
    • Vilgalys, R, and Gonzalez, D. "Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola." Current Genetics 18, no. 3 (1990): 277-280.
    • Vilgalys, R, and Hester, M. "Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species." Journal of Bacteriology 172, no. 8 (1990): 4238-4246.
• Teaching & Mentoring
• 

  Recent Courses

  • BIOLOGY 293: Research Independent Study 2018
  • BIOLOGY 493: Research Independent Study 2018
  • BIOLOGY 540L: Mycology 2018
  • BIOLOGY 557L: Microbial Ecology and Evolution 2017
  • BIOLOGY 792: Research 2017
  • BIOLOGY 791T: Tutorial 2016
• Scholarly, Clinical, & Service Activities
• 

  Presentations & Appearances

  • Mycological Society of American Annual Meeting. August 13, 2013  2013
  • Seminar: Mountain Lake Biological Station weekly seminar. July 25, 2013  2013
  • Seminar presentation in Goteborg, Sweden. May 23, 2013  2013
  • Middle Atlantic States Mycology Conf.. April 27, 2013  2013
  • Oak Ridge National Labs. July 8, 2011  2011
• 

  Outreach & Engaged Scholarship

  • Unknown. Mushroom Identification. December 22, 2013  2013
  • Unknown. Mushroom classes and workshops. December 22, 2013  2013

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