Rytas J. Vilgalys | Scholars@Duke

Rytas J. Vilgalys
Professor of Biology

Current Appointments & Affiliations

Professor of Biology, Biology, Trinity College of Arts & Sciences 2000
Assistant Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2010

Contact Information

Box 90338, Durham, NC 27708-0338
Room 137, Biological Sciences Building, 130 Science Drive, Durham, NC 27708
fungi@duke.edu (919) 660-7361
http://www.biology.duke.edu/fungi/mycolab/

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
Expertise
Global Scholarship
- Expertise
  - United States of America (Country)
- Research
  - Ecuador (Country)
- Teaching
  - Australia (Country)
Research
Selected Grants
- Molecular Mycology and Pathogenesis Training Program awarded by National Institutes of Health 2019 - 2024
- Convergence RAISE: Harnessing Extracellular Vesicle Mediated Interkingdom Communication awarded by National Science Foundation 2019 - 2022
- Development of a Full-Field X-ray Fluorescence Imaging System for Near Real-Time Trace Element Microanalysis in Complex Biological Systems 2019 - 2021
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- DOE Genomics GTL: PlantMicrobe Interfaces 2010 - 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
- DOE Genomics GTL: PlantMicrobe Interfaces 2010 - 2019
- Collaborative Research: The Zygomycetes Genealogy of Life (ZyGoLife) - the conundrum of Kingdom Fungi awarded by University of California, Riverside 2015 - 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 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) 1997 - 1999
- (98-0459) PEET: Monographic Studies in the Cladoniaceae (Lichen-Forming Ascomycetes) 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 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 1988 - 1990
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Liao, Hui-Ling, Gregory Bonito, J Alejandro Rojas, Khalid Hameed, Steven Wu, Christopher W. Schadt, Jessy Labbé, et al. “Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition..” Molecular Plant Microbe Interactions : Mpmi 32, no. 7 (July 2019): 853–64. https://doi.org/10.1094/mpmi-05-18-0133-r.
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  - Veličkovic, Dušan, Hui-Ling Liao, Rytas Vilgalys, Rosalie K. Chu, and Christopher R. Anderton. “Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization..” Journal of Natural Products 82, no. 5 (May 2019): 1382–86. https://doi.org/10.1021/acs.jnatprod.8b01050.
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  - Policelli, Nahuel, Thomas D. Bruns, Rytas Vilgalys, and Martin A. Nuñez. “Suilloid fungi as global drivers of pine invasions..” The New Phytologist 222, no. 2 (April 2019): 714–25. https://doi.org/10.1111/nph.15660.
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  - Bier, R. L., J. J. Wernegreen, R. J. Vilgalys, J. C. Ellis, and E. S. Bernhardt. “Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage.” Limnology and Oceanography, January 1, 2019. https://doi.org/10.1002/lno.11301.
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  - Bonito, Gregory, Gian Maria Niccolò Benucci, Khalid Hameed, Deborah Weighill, Piet Jones, Ko-Hsuan Chen, Daniel Jacobson, Christopher Schadt, and Rytas Vilgalys. “Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype..” Frontiers in Microbiology 10 (January 2019). https://doi.org/10.3389/fmicb.2019.00481.
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  - Hibbett, D. S., M. Blackwell, T. Y. James, J. W. Spatafora, J. W. Taylor, and R. Vilgalys. “Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota.” Ima Fungus 9, no. 2 (December 1, 2018): 291–98. https://doi.org/10.5598/imafungus.2018.09.02.05.
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  - Liao, Hui-Ling, Yuan Chen, and Rytas Vilgalys. “Correction: Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus..” Plos Genetics 14, no. 10 (October 19, 2018). https://doi.org/10.1371/journal.pgen.1007742.
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  - Misztal, Pawel K., Despoina S. Lymperopoulou, Rachel I. Adams, Russell A. Scott, Steven E. Lindow, Thomas Bruns, John W. Taylor, et al. “Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi..” Environmental Science & Technology 52, no. 15 (August 2018): 8272–82. https://doi.org/10.1021/acs.est.8b00806.
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  - Vélez, J. M., T. J. Tschaplinski, R. Vilgalys, C. W. Schadt, G. Bonito, K. Hameed, N. Engle, and C. E. Hamilton. “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](S1754504817300326)(10.1016/j.funeco.2017.03.001).” Fungal Ecology 33 (June 1, 2018). https://doi.org/10.1016/j.funeco.2017.12.004.
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  - Gryganskyi, Andrii P., Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, et al. “Phylogenetic and Phylogenomic Definition of Rhizopus Species..” G3 (Bethesda) 8, no. 6 (May 31, 2018): 2007–18. https://doi.org/10.1534/g3.118.200235.
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  - Cregger, M. A., A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan, and C. W. Schadt. “The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome..” Microbiome 6, no. 1 (February 12, 2018). https://doi.org/10.1186/s40168-018-0413-8.
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  - Johansen, R. B., P. Johnston, P. Mieczkowski, G. L. W. Perry, M. S. Robeson, R. Vilgalys, and B. R. Burns. “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 1, 2017): 177–90. https://doi.org/10.1016/j.soilbio.2017.05.007.
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  - Uehling, J., A. Gryganskyi, K. Hameed, T. Tschaplinski, P. K. Misztal, S. Wu, A. Desirò, et al. “Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens..” Environmental Microbiology 19, no. 8 (August 2017): 2964–83. https://doi.org/10.1111/1462-2920.13669.
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  - Smith, Matthew E., Terry W. Henkel, Gwendolyn C. Williams, M Catherine Aime, Alexander K. Fremier, and Rytas Vilgalys. “Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa..” The New Phytologist 215, no. 1 (July 2017): 443–53. https://doi.org/10.1111/nph.14570.
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  - Vélez, J. M., T. J. Tschaplinski, R. Vilgalys, C. W. Schadt, G. Bonito, K. Hameed, N. Engle, and C. E. Hamilton. “Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees.” Fungal Ecology 27 (June 1, 2017): 78–86. https://doi.org/10.1016/j.funeco.2017.03.001.
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  - Gryganskyi, Andrii P., Bradley A. Mullens, Michael T. Gajdeczka, Stephen A. Rehner, Rytas Vilgalys, and Ann E. Hajek. “Hijacked: Co-option of host behavior by entomophthoralean fungi..” Plos Pathogens 13, no. 5 (May 4, 2017). https://doi.org/10.1371/journal.ppat.1006274.
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  - Branco, Sara, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Hélène Badouin, Christopher E. Ellison, Nhu H. Nguyen, et al. “Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes..” Molecular Ecology 26, no. 7 (April 2017): 2063–76. https://doi.org/10.1111/mec.13892.
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  - Li, Zhou, Qiuming Yao, Stephen P. Dearth, Matthew R. Entler, Hector F. Castro Gonzalez, Jessie K. Uehling, Rytas J. Vilgalys, et al. “Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system..” Environmental Microbiology 19, no. 3 (March 2017): 1041–53. https://doi.org/10.1111/1462-2920.13605.
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  - Rosenthal, Lisa M., Karl-Henrik Larsson, Sara Branco, Judy A. Chung, Sydney I. Glassman, Hui-Ling Liao, Kabir G. Peay, et al. “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 19, 2017): 115–27. https://doi.org/10.1080/00275514.2017.1281677.
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  - Bonito, Gregory, Khalid Hameed, Merje Toome-Heller, Rosanne Healy, Chantal Reid, Hui-Ling Liao, M Catherine Aime, Christopher Schadt, and Rytas Vilgalys. “Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome..” Mycologia 109, no. 1 (January 9, 2017): 18–26. https://doi.org/10.1080/00275514.2016.1271689.
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  - Liao, Hui-Ling, Yuan Chen, and Rytas Vilgalys. “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). https://doi.org/10.1371/journal.pgen.1006348.
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  - Johansen, R. B., P. Johnston, P. Mieczkowski, G. L. W. Perry, M. S. Robeson, B. R. Burns, and R. Vilgalys. “A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities.” Fungal Ecology 23 (October 1, 2016): 141–55. https://doi.org/10.1016/j.funeco.2016.08.003.
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  - Spatafora, Joseph W., Ying Chang, Gerald L. Benny, Katy Lazarus, Matthew E. Smith, Mary L. Berbee, Gregory Bonito, et al. “A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data..” Mycologia 108, no. 5 (September 2016): 1028–46. https://doi.org/10.3852/16-042.
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  - Bonito, G., K. Hameed, R. Ventura, J. Krishnan, C. W. Schadt, and R. Vilgalys. “Isolating a functionally relevant guild of fungi from the root microbiome of Populus.” Fungal Ecology 22 (August 1, 2016): 35–42. https://doi.org/10.1016/j.funeco.2016.04.007.
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  - Ekblad, Alf, Anna Mikusinska, Göran I. Ågren, Lorenzo Menichetti, Håkan Wallander, Rytas Vilgalys, Adam Bahr, and Ulrika Eriksson. “Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization..” The New Phytologist 211, no. 3 (August 2016): 874–85. https://doi.org/10.1111/nph.13961.
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  - Gónzalez, Dolores, Marianela Rodriguez-Carres, Teun Boekhout, Joost Stalpers, Eiko E. Kuramae, Andreia K. Nakatani, Rytas Vilgalys, and Marc A. Cubeta. “Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales..” Fungal Biology 120, no. 4 (April 2016): 603–19. https://doi.org/10.1016/j.funbio.2016.01.012.
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  - Czaplicki, L. M., E. Cooper, P. L. Ferguson, H. M. Stapleton, R. Vilgalys, and C. K. Gunsch. “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. https://doi.org/10.1002/rem.21458.
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  - Branco, Sara, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButti, Anna Lipzen, Igor V. Grigoriev, et al. “Genetic isolation between two recently diverged populations of a symbiotic fungus..” Molecular Ecology 24, no. 11 (June 2015): 2747–58. https://doi.org/10.1111/mec.13132.
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  - Glassman, Sydney I., Kabir G. Peay, Jennifer M. Talbot, Dylan P. Smith, Judy A. Chung, John W. Taylor, Rytas Vilgalys, and Thomas D. Bruns. “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): 1619–31. https://doi.org/10.1111/nph.13240.
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  - Kuske, C. R., C. N. Hesse, J. F. Challacombe, D. Cullen, J. R. Herr, R. C. Mueller, A. Tsang, and R. Vilgalys. “Prospects and challenges for fungal metatranscriptomics of complex communities.” Fungal Ecology 14 (January 1, 2015): 133–37. https://doi.org/10.1016/j.funeco.2014.12.005.
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  - Liao, H. -. L., Y. Chen, T. D. Bruns, K. G. Peay, J. W. Taylor, S. Branco, J. M. Talbot, and R. Vilgalys. “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): 3730–42. https://doi.org/10.1111/1462-2920.12619.
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  - Bonito, Gregory, Hannah Reynolds, Michael S. Robeson, Jessica Nelson, Brendan P. Hodkinson, Gerald Tuskan, Christopher W. Schadt, and Rytas Vilgalys. “Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants..” Molecular Ecology 23, no. 13 (July 2014): 3356–70. https://doi.org/10.1111/mec.12821.
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  - Talbot, Jennifer M., Thomas D. Bruns, John W. Taylor, Dylan P. Smith, Sara Branco, Sydney I. Glassman, Sonya Erlandson, et al. “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): 6341–46. https://doi.org/10.1073/pnas.1402584111.
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  - Losada, Liliana, Suman B. Pakala, Natalie D. Fedorova, Vinita Joardar, Svetlana A. Shabalina, Jessica Hostetler, Suchitra M. Pakala, et al. “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): 165–73. https://doi.org/10.1111/1574-6968.12387.
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  - Cubeta, Marc A., Elizabeth Thomas, Ralph A. Dean, Suha Jabaji, Stephen M. Neate, Stellos Tavantzis, Takeshi Toda, et al. “Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP..” Genome Announcements 2, no. 5 (January 2014). https://doi.org/10.1128/genomeA.01072-14.
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  - Hofstetter, V., S. A. Redhead, F. Kauff, J. M. Moncalvo, P. B. Matheny, and R. Vilgalys. “Taxonomic revision and examination of ecological transitions of the Lyophyllaceae (Basidiomycota, Agaricales) based on a multigene phylogeny.” Cryptogamie, Mycologie 35, no. 4 (January 1, 2014): 399–425. https://doi.org/10.7872/crym.v35.iss4.2014.399.
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  - Lodge, D. J., M. Padamsee, P. B. Matheny, M. C. Aime, S. A. Cantrell, D. Boertmann, A. Kovalenko, et al. “Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales).” Fungal Diversity 64, no. 1 (January 1, 2014): 1–99. https://doi.org/10.1007/s13225-013-0259-0.
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  - Benítez, María-Soledad, Michelle H. Hersh, Rytas Vilgalys, and James S. Clark. “Pathogen regulation of plant diversity via effective specialization..” Trends in Ecology & Evolution 28, no. 12 (December 2013): 705–11. https://doi.org/10.1016/j.tree.2013.09.005.
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  - Gryganskyi, A. P., R. A. Humber, M. E. Smith, K. Hodge, B. Huang, K. Voigt, and R. Vilgalys. “Phylogenetic lineages in Entomophthoromycota..” Persoonia 30 (June 2013): 94–105. https://doi.org/10.3767/003158513X666330.
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  - Golonka, A. M., and R. Vilgalys. “Nectar inhabiting yeasts in Virginian populations of Silene latifolia (Caryophyllaceae) and coflowering species.” American Midland Naturalist 169, no. 2 (April 1, 2013): 235–58. https://doi.org/10.1674/0003-0031-169.2.235.
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  - Gryganskyi, A. P., R. A. Humber, M. E. Smith, J. Miadlikovska, S. Wu, K. Voigt, G. Walther, I. M. Anishchenko, and R. Vilgalys. “Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694].” Molecular Phylogenetics and Evolution 66, no. 3 (March 1, 2013). https://doi.org/10.1016/j.ympev.2012.11.001.
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  - Healy, R. A., M. E. Smith, G. M. Bonito, D. H. Pfister, Z. -. W. Ge, G. G. Guevara, G. Williams, et al. “High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales..” Molecular Ecology 22, no. 6 (March 2013): 1717–32. https://doi.org/10.1111/mec.12135.
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  - Husbands, Dillon R., Terry W. Henkel, Gregory Bonito, Rytas Vilgalys, and Matthew E. Smith. “New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence..” Mycologia 105, no. 2 (March 2013): 422–35. https://doi.org/10.3852/12-146.
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  - Talbot, J. M., T. D. Bruns, D. P. Smith, S. Branco, S. I. Glassman, S. Erlandson, R. Vilgalys, and K. G. Peay. “Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition.” Soil Biology and Biochemistry 57 (February 1, 2013): 282–91. https://doi.org/10.1016/j.soilbio.2012.10.004.
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  - Smith, Matthew E., Terry W. Henkel, Jessie K. Uehling, Alexander K. Fremier, H David Clarke, and Rytas Vilgalys. “The ectomycorrhizal fungal community in a neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea..” Plos One 8, no. 1 (January 31, 2013). https://doi.org/10.1371/journal.pone.0055160.
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  - Bonito, Gregory, Matthew E. Smith, Michael Nowak, Rosanne A. Healy, Gonzalo Guevara, Efren Cázares, Akihiko Kinoshita, et al. “Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage..” Plos One 8, no. 1 (January 2, 2013). https://doi.org/10.1371/journal.pone.0052765.
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  - Gryganskyi, Andrii P., Richard A. Humber, Jason E. Stajich, Bradley Mullens, Iryna M. Anishchenko, and Rytas Vilgalys. “Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex..” Plos One 8, no. 8 (January 2013). https://doi.org/10.1371/journal.pone.0071168.
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  - Guevara, Gonzalo, Gregory Bonito, James M. Trappe, Efren Cázares, Gwendolyn Williams, Rosanne A. Healy, Christopher Schadt, and Rytas Vilgalys. “New North American truffles (Tuber spp.) and their ectomycorrhizal associations..” Mycologia 105, no. 1 (January 2013): 194–209. https://doi.org/10.3852/12-087.
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  - Shakya, Migun, Neil Gottel, Hector Castro, Zamin K. Yang, Lee Gunter, Jessy Labbé, Wellington Muchero, et al. “A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees..” Plos One 8, no. 10 (January 2013). https://doi.org/10.1371/journal.pone.0076382.
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  - Weber, C. F., R. Vilgalys, and C. R. Kuske. “Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon.” Frontiers in Microbiology 4, no. APR (January 1, 2013). https://doi.org/10.3389/fmicb.2013.00078.
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  - Uehling, Jessie K., Terry W. Henkel, M Catherine Aime, Rytas Vilgalys, and Matthew E. Smith. “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 (December 2012): 1263–74. https://doi.org/10.1016/j.funbio.2012.09.004.
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  - Gryganskyi, Andrii P., Richard A. Humber, Matthew E. Smith, Jolanta Miadlikowska, Steven Wu, Kerstin Voigt, Grit Walther, Iryna M. Anishchenko, and Rytas Vilgalys. “Molecular phylogeny of the Entomophthoromycota..” Molecular Phylogenetics and Evolution 65, no. 2 (November 2012): 682–94. https://doi.org/10.1016/j.ympev.2012.07.026.
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  - Uehling, Jessie K., Terry W. Henkel, Rytas Vilgalys, and Matthew E. Smith. “Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests..” Mycorrhiza 22, no. 7 (October 2012): 577–81. https://doi.org/10.1007/s00572-012-0457-8.
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  - Henkel, T. W., M. C. Aime, M. M. L. Chin, S. L. Miller, R. Vilgalys, and M. E. Smith. “Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield.” Biodiversity and Conservation 21, no. 9 (August 1, 2012): 2195–2220. https://doi.org/10.1007/s10531-011-0166-1.
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  - Bonito, G., M. E. Smith, T. Brenneman, and R. Vilgalys. “Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants.” Plant and Soil 356, no. 1–2 (July 1, 2012): 357–66. https://doi.org/10.1007/s11104-012-1127-5.
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  - Dunbar, John, Stephanie A. Eichorst, La Verne Gallegos-Graves, Shannon Silva, Gary Xie, N. W. Hengartner, R David Evans, et al. “Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide..” Environmental Microbiology 14, no. 5 (May 2012): 1145–58. https://doi.org/10.1111/j.1462-2920.2011.02695.x.
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  - Thaler, A. D., C. L. Van Dover, and R. Vilgalys. “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 (April 1, 2012): 270–73. https://doi.org/10.1016/j.funeco.2011.07.002.
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  - Hersh, Michelle H., Rytas Vilgalys, and James S. Clark. “Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival..” Ecology 93, no. 3 (March 2012): 511–20. https://doi.org/10.1890/11-0598.1.
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  - Uehling, Jessie K., Terry W. Henkel, M Catherine Aime, Rytas Vilgalys, and Matthew E. Smith. “New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield..” Mycologia 104, no. 2 (March 2012): 547–56. https://doi.org/10.3852/11-130.
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  - Uehling, J. K., T. W. Henkel, M. C. Aime, R. Vilgalys, and M. E. Smith. “New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield.” Mycologia 103 (2012): 883–94.
  - Uehling, J. K., T. W. Henkel, M. C. Aime, R. Vilgalys, and M. E. Smith. “Four new species of Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, and a key to the lowland neotropical species..” Fungal Biology. in Press, 2012.
  - Baroni, T. J., V. Hofstetter, D. L. Largent, and R. Vilgalys. “Entocybe is proposed as a new genus in the Entolomataceae (Agaricomycetes, Basidiomycota) based on morphological and molecular evidence.” North American Fungi 6, no. 12 (December 1, 2011): 1–19. https://doi.org/10.2509/naf2011.006.012.
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  - Smith, Matthew E., Terry W. Henkel, M. Catherine Aime, Alex K. Fremier, and Rytas Vilgalys. “Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest..” The New Phytologist 192, no. 3 (November 2011): 699–712. https://doi.org/10.1111/j.1469-8137.2011.03844.x.
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  - Bonito, Gregory, Timothy Brenneman, and Rytas Vilgalys. “Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae)..” Mycorrhiza 21, no. 7 (October 2011): 601–12. https://doi.org/10.1007/s00572-011-0368-0.
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  - Weber, Carolyn F., Donald R. Zak, Bruce A. Hungate, Robert B. Jackson, Rytas Vilgalys, R David Evans, Christopher W. Schadt, J Patrick Megonigal, and Cheryl R. Kuske. “Responses of soil cellulolytic fungal communities to elevated atmospheric CO₂ are complex and variable across five ecosystems..” Environmental Microbiology 13, no. 10 (October 2011): 2778–93. https://doi.org/10.1111/j.1462-2920.2011.02548.x.
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  - Gottel, Neil R., Hector F. Castro, Marilyn Kerley, Zamin Yang, Dale A. Pelletier, Mircea Podar, Tatiana Karpinets, et al. “Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types..” Applied and Environmental Microbiology 77, no. 17 (September 2011): 5934–44. https://doi.org/10.1128/AEM.05255-11.
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  - Porter, Teresita M., Wallace Martin, Timothy Y. James, Joyce E. Longcore, Frank H. Gleason, Peter H. Adler, Peter M. Letcher, and Rytas Vilgalys. “Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA..” Fungal Biology 115, no. 4–5 (April 2011): 381–92. https://doi.org/10.1016/j.funbio.2011.02.004.
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  - Bonito, G., J. M. Trappe, S. Donovan, and R. Vilgalys. “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 (February 1, 2011): 83–93. https://doi.org/10.1016/j.funeco.2010.08.003.
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  - Gryganskyi, Andrii P., Soo Chan Lee, Anastasia P. Litvintseva, Matthew E. Smith, Gregory Bonito, Teresita M. Porter, Iryna M. Anishchenko, Joseph Heitman, and Rytas Vilgalys. “Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex..” Plos One 5, no. 12 (December 9, 2010). https://doi.org/10.1371/journal.pone.0015273.
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  - Bonito, Gregory M., Andrii P. Gryganskyi, James M. Trappe, and Rytas Vilgalys. “A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal..” Molecular Ecology 19, no. 22 (November 2010): 4994–5008. https://doi.org/10.1111/j.1365-294x.2010.04855.x.
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  - Bonito, Gregory, James M. Trappe, Pat Rawlinson, and Rytas Vilgalys. “Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex..” Mycologia 102, no. 5 (September 2010): 1042–57. https://doi.org/10.3852/09-213.
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  - Bonito, Gregory, Omoanghe S. Isikhuemhen, and Rytas Vilgalys. “Identification of fungi associated with municipal compost using DNA-based techniques..” Bioresource Technology 101, no. 3 (February 2010): 1021–27. https://doi.org/10.1016/j.biortech.2009.08.109.
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  - McLaughlin, David J., David S. Hibbett, François Lutzoni, Joseph W. Spatafora, and Rytas Vilgalys. “The search for the fungal tree of life..” Trends in Microbiology 17, no. 11 (November 2009): 488–97. https://doi.org/10.1016/j.tim.2009.08.001.
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  - Parrent, Jeri Lynn, and Rytas Vilgalys. “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 (September 2009): 469–79. https://doi.org/10.1007/s00572-009-0250-5.
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  - James, Timothy Y., Anastasia P. Litvintseva, Rytas Vilgalys, Jess A. T. Morgan, John W. Taylor, Matthew C. Fisher, Lee Berger, Ché Weldon, Louis du Preez, and Joyce E. Longcore. “Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations..” Plos Pathogens 5, no. 5 (May 29, 2009). https://doi.org/10.1371/journal.ppat.1000458.
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  - Findley, Keisha, Marianela Rodriguez-Carres, Banu Metin, Johannes Kroiss, Alvaro Fonseca, Rytas Vilgalys, and Joseph Heitman. “Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales..” Eukaryot Cell 8, no. 3 (March 2009): 353–61. https://doi.org/10.1128/EC.00373-08.
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  - Hartman, Wyatt H., Curtis J. Richardson, Rytas Vilgalys, and Gregory L. Bruland. “Environmental and anthropogenic controls over bacterial communities in wetland soils..” Proceedings of the National Academy of Sciences of the United States of America 105, no. 46 (November 12, 2008): 17842–47. https://doi.org/10.1073/pnas.0808254105.
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  - Porter, T. M., C. W. Schadt, L. Rizvi, A. P. Martin, S. K. Schmidt, L. Scott-Denton, R. Vilgalys, and J. M. Moncalvo. “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 (February 2008): 635–44. https://doi.org/10.1016/j.ympev.2007.10.002.
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  - Ceresini, Paulo C., H David Shew, Timothy Y. James, Rytas J. Vilgalys, and Marc A. Cubeta. “Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci..” Bmc Evolutionary Biology 7 (September 13, 2007). https://doi.org/10.1186/1471-2148-7-163.
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  - Henk, D. A., and R. Vilgalys. “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 (September 1, 2007): 1515–26. https://doi.org/10.3732/ajb.94.9.1515.
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  - Hibbett, David S., Manfred Binder, Joseph F. Bischoff, Meredith Blackwell, Paul F. Cannon, Ove E. Eriksson, Sabine Huhndorf, et al. “A higher-level phylogenetic classification of the Fungi..” Mycological Research 111, no. Pt 5 (May 2007): 509–47. https://doi.org/10.1016/j.mycres.2007.03.004.
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  - Arnold, A Elizabeth, Daniel A. Henk, Rebecca L. Eells, François Lutzoni, and Rytas Vilgalys. “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. https://doi.org/10.1080/15572536.2007.11832578.
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  - Parrent, Jeri Lynn, and Rytas Vilgalys. “Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization..” The New Phytologist 176, no. 1 (January 2007): 164–74. https://doi.org/10.1111/j.1469-8137.2007.02155.x.
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  - James, Timothy Y., Peter M. Letcher, Joyce E. Longcore, Sharon E. Mozley-Standridge, David Porter, Martha J. Powell, Gareth W. Griffith, and Rytas Vilgalys. “A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)..” Mycologia 98, no. 6 (November 2006): 860–71. https://doi.org/10.1080/15572536.2006.11832616.
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  - Matheny, P Brandon, Judd M. Curtis, Valérie Hofstetter, M Catherine Aime, Jean-Marc Moncalvo, Zai-Wei Ge, Jason C. Slot, et al. “Major clades of Agaricales: a multilocus phylogenetic overview..” Mycologia 98, no. 6 (November 2006): 982–95. https://doi.org/10.1080/15572536.2006.11832627.
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  - Moncalvo, Jean-Marc, R Henrik Nilsson, Brenda Koster, Susie M. Dunham, Torsten Bernauer, P Brandon Matheny, Teresita M. Porter, et al. “The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods..” Mycologia 98, no. 6 (November 2006): 937–48. https://doi.org/10.1080/15572536.2006.11832623.
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  - James, Timothy Y., Frank Kauff, Conrad L. Schoch, P Brandon Matheny, Valérie Hofstetter, Cymon J. Cox, Gail Celio, et al. “Reconstructing the early evolution of Fungi using a six-gene phylogeny..” Nature 443, no. 7113 (October 2006): 818–22. https://doi.org/10.1038/nature05110.
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  - Yahr, R., R. Vilgalys, and P. T. DePriest. “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 (October 1, 2006). https://doi.org/10.1111/j.1469-8137.2006.01887.x.
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  - Parrent, Jeri Lynn, William F. Morris, and Rytas Vilgalys. “CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities..” Ecology 87, no. 9 (September 2006): 2278–87. https://doi.org/10.1890/0012-9658(2006)87[2278:canaae]2.0.co;2.
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  - González, Dolores, Marc A. Cubeta, and Rytas Vilgalys. “Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex..” Molecular Phylogenetics and Evolution 40, no. 2 (August 2006): 459–70. https://doi.org/10.1016/j.ympev.2006.03.022.
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  - Litvintseva, Anastasia P., Rameshwari Thakur, Rytas Vilgalys, and Thomas G. Mitchell. “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): 2223–38. https://doi.org/10.1534/genetics.105.046672.
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  - James, Timothy Y., Prayook Srivilai, Ursula Kües, and Rytas Vilgalys. “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 (March 2006): 1877–91. https://doi.org/10.1534/genetics.105.051128.
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  - Yahr, Rebecca, Rytas Vilgalys, and Paula T. DePriest. “Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis..” The New Phytologist 171, no. 4 (January 2006): 847–60. https://doi.org/10.1111/j.1469-8137.2006.01792.x.
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  - Wallenstein, M. D., and R. J. Vilgalys. “Quantitative analyses of nitrogen cycling genes in soils.” Pedobiologia 49, no. 6 (November 30, 2005): 665–72. https://doi.org/10.1016/j.pedobi.2005.05.005.
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  - O’Brien, Heath E., Jeri Lynn Parrent, Jason A. Jackson, Jean-Marc Moncalvo, and Rytas Vilgalys. “Fungal community analysis by large-scale sequencing of environmental samples..” Applied and Environmental Microbiology 71, no. 9 (September 2005): 5544–50. https://doi.org/10.1128/AEM.71.9.5544-5550.2005.
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  - Fierer, Noah, Jason A. Jackson, Rytas Vilgalys, and Robert B. Jackson. “Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays..” Applied and Environmental Microbiology 71, no. 7 (July 2005): 4117–20. https://doi.org/10.1128/AEM.71.7.4117-4120.2005.
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  - Didukh, Maryna, Rytas Vilgalys, Solomon P. Wasser, Omoanghe S. Isikhuemhen, and Eviatar Nevo. “Notes on Agaricus section Duploannulati using molecular and morphological data..” Mycological Research 109, no. Pt 6 (June 2005): 729–40.
  - Litvintseva, Anastasia P., Lori Kestenbaum, Rytas Vilgalys, and Thomas G. Mitchell. “Comparative analysis of environmental and clinical populations of Cryptococcus neoformans..” J Clin Microbiol 43, no. 2 (February 2005): 556–64. https://doi.org/10.1128/JCM.43.2.556-564.2005.
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  - Aime, M. C., R. Vilgalys, and O. K. Miller. “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 (January 1, 2005): 74–82. https://doi.org/10.3732/ajb.92.1.74.
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  - Didukh, M., R. Vilgalys, S. P. Wasser, O. S. Isikhuemhen, and E. Nevo. “Notes on Agaricus section Duploannulati using molecular and morphological data.” Mycological Research 109, no. 6 (2005): 729–40. https://doi.org/10.1017/S0953756205002443.
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  - Diezmann, Stephanie, Cymon J. Cox, Gabriele Schönian, Rytas J. Vilgalys, and Thomas G. Mitchell. “Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis..” J Clin Microbiol 42, no. 12 (December 2004): 5624–35. https://doi.org/10.1128/JCM.42.12.5624-5635.2004.
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  - Yahr, Rebecca, Rytas Vilgalys, and Paula T. Depriest. “Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens..” Molecular Ecology 13, no. 11 (November 2004): 3367–78. https://doi.org/10.1111/j.1365-294x.2004.02350.x.
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  - Lutzoni, François, Frank Kauff, Cymon J. Cox, David McLaughlin, Gail Celio, Bryn Dentinger, Mahajabeen Padamsee, et al. “Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits..” American Journal of Botany 91, no. 10 (October 2004): 1446–80. https://doi.org/10.3732/ajb.91.10.1446.
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  - James, Timothy Y., Shian-Ren Liou, and Rytas Vilgalys. “The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor..” Fungal Genetics and Biology : Fg & B 41, no. 8 (August 2004): 813–25. https://doi.org/10.1016/j.fgb.2004.04.005.
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  - Marra, Robert E., Johnny C. Huang, Eula Fung, Kirsten Nielsen, Joseph Heitman, Rytas Vilgalys, and Thomas G. Mitchell. “A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)..” Genetics 167, no. 2 (June 2004): 619–31. https://doi.org/10.1534/genetics.103.023408.
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  - James, Timothy Y., Ursula Kües, Stephen A. Rehner, and Rytas Vilgalys. “Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi..” Fungal Genetics and Biology : Fg & B 41, no. 3 (March 2004): 381–90. https://doi.org/10.1016/j.fgb.2003.11.008.
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  - Zervakis, Georgios I., Jean-Marc Moncalvo, and Rytas Vilgalys. “Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa..” Microbiology 150, no. Pt 3 (March 2004): 715–26. https://doi.org/10.1099/mic.0.26673-0.
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  - Peintner, U., J. M. Moncalvo, and R. Vilgalys. “Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota).” Mycologia 96, no. 5 (January 1, 2004): 1042–58. https://doi.org/10.1080/15572536.2005.11832904.
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  - Litvintseva, Anastasia P., Robert E. Marra, Kirsten Nielsen, Joseph Heitman, Rytas Vilgalys, and Thomas G. Mitchell. “Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa..” Eukaryot Cell 2, no. 6 (December 2003): 1162–68. https://doi.org/10.1128/ec.2.6.1162-1168.2003.
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  - Davis, E Christine, Joseph B. Franklin, A Jonathan Shaw, and Rytas Vilgalys. “Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis..” American Journal of Botany 90, no. 11 (November 2003): 1661–67. https://doi.org/10.3732/ajb.90.11.1661.
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  - Vilgalys, R. “Taxonomic misidentification in public DNA databases.” New Phytologist 160, no. 1 (October 1, 2003): 4–5. https://doi.org/10.1046/j.1469-8137.2003.00894.x.
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  - Pringle, Anne, Jean-Marc Moncalvo, and Rytas Vilgalys. “Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica..” Mycorrhiza 13, no. 4 (August 2003): 227–31. https://doi.org/10.1007/s00572-003-0249-2.
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  - Ceresini, Paulo C., H David Shew, Rytas J. Vilgalys, Liane Rosewich Gale, and Marc A. Cubeta. “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): 610–15. https://doi.org/10.1094/phyto.2003.93.5.610.
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  - Morehouse, Erica A., Timothy Y. James, Austen R. D. Ganley, Rytas Vilgalys, Lee Berger, Peter J. Murphy, and Joyce E. Longcore. “Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone..” Molecular Ecology 12, no. 2 (February 2003): 395–403. https://doi.org/10.1046/j.1365-294x.2003.01732.x.
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  - Peintner, U., E. Horak, M. Moser, and R. Vilgalys. “Rozites, Cuphocybe and Rapacea are taxonomic synonyms of Cortinarius: New combinations and new names.” Mycotaxon 83 (July 1, 2002): 447–51.
  - Redhead, S. A., F. Lutzoni, J. M. Moncalvo, and R. Vilgalys. “Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics).” Mycotaxon 83 (July 1, 2002): 19–57.
  - Moncalvo, Jean-Marc, Rytas Vilgalys, Scott A. Redhead, James E. Johnson, Timothy Y. James, M. Catherine Aime, Valerie Hofstetter, et al. “One hundred and seventeen clades of euagarics..” Molecular Phylogenetics and Evolution 23, no. 3 (June 2002): 357–400. https://doi.org/10.1016/s1055-7903(02)00027-1.
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  - Ceresini, Paulo C., H David Shew, Rytas J. Vilgalys, U Liane Rosewich, and Marc A. Cubeta. “Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina..” Mycologia 94, no. 3 (May 2002): 450–60.
  - Ceresini, Paulo C., H David Shew, Rytas J. Vilgalys, and Marc A. Cubeta. “Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina..” Mycologia 94, no. 3 (May 2002): 437–49.
  - Henkel, T. W., J. Terborgh, and R. J. Vilgalys. “Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana.” Mycological Research 106, no. 5 (January 1, 2002): 515–31. https://doi.org/10.1017/S0953756202005919.
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  - Hofstetter, V., H. Clémençon, R. Vilgalys, and J. M. Moncalvo. “Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences.” Mycological Research 106, no. 9 (January 1, 2002): 1043–59. https://doi.org/10.1017/S095375620200641X.
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  - Peintner, U., E. Horak, M. M. Moser, and R. Vilgalys. “Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences.” Mycologia 94, no. 4 (January 1, 2002): 620–29. https://doi.org/10.1080/15572536.2003.11833190.
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  - Peintner, U., M. Moser, and R. Vilgalys. “Thaxterogaster is a taxonomic synonym of Cortinarius: New combinations and new names.” Mycotaxon 81 (January 1, 2002): 177–84.
  - Xu, J., G. Luo, R. J. Vilgalys, M. E. Brandt, and T. G. Mitchell. “Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD.” Microbiology 148, no. 1 (2002): 203–12.
  - Xu, Jianping, Guizhen Luo, Rytas J. Vilgalys, Mary E. Brandt, and Thomas G. Mitchell. “Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD..” Microbiology 148, no. Pt 1 (January 2002): 203–12. https://doi.org/10.1099/00221287-148-1-203.
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  - Mueller, G. M., Q. X. Wu, Y. Q. Huang, S. Y. Guo, R. Aldana-Gomez, and R. Vilgalys. “Assessing biogeographic relationships between North American and Chinese macrofungi.” Journal of Biogeography 28, no. 2 (July 16, 2001): 271–81. https://doi.org/10.1046/j.1365-2699.2001.00540.x.
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  - James, T. Y., and R. Vilgalys. “Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling..” Molecular Ecology 10, no. 2 (February 2001): 471–79. https://doi.org/10.1046/j.1365-294x.2001.01224.x.
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  - Kües, U., T. Y. James, R. Vilgalys, and M. P. Challen. “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 (February 2001): 16–24. https://doi.org/10.1007/s002940000176.
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  - Xu, J., C. Onyewu, H. J. Yoell, R. Y. Ali, R. J. Vilgalys, and T. G. Mitchell. “Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans..” Antimicrob Agents Chemother 45, no. 2 (February 2001): 420–27. https://doi.org/10.1128/AAC.45.2.420-427.2001.
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  - Gonzalez, D., D. E. Carling, S. Kuninaga, R. Vilgalys, and M. A. Cubetae. “Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs.” Mycologia 93, no. 6 (January 1, 2001): 1138–50. https://doi.org/10.2307/3761674.
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  - Hughes, K. W., R. H. Petersen, J. E. Johnson, J. M. Moncalvo, R. Vilgalys, S. A. Redhead, T. Thomas, and L. L. McGhee. “Infragenic phylogeny of Collybia s. str. based on sequences of ribosomal ITS and LSU regions.” Mycological Research 105, no. 2 (January 1, 2001): 164–72. https://doi.org/10.1017/S0953756200003415.
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  - James, T. Y., J. M. Moncalvo, S. Li, and R. Vilgalys. “Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune..” Genetics 157, no. 1 (January 2001): 149–61.
  - Peintner, U., N. L. Bougher, M. A. Castellano, J. M. Moncalvo, M. M. Moser, J. M. Trappe, and R. Vilgalys. “Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae).” American Journal of Botany 88, no. 12 (January 1, 2001): 2168–79. https://doi.org/10.2307/3558378.
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  - Redhead, S. A., R. Vilgalys, J. M. Moncalvo, J. Johnson, and J. Hopple. “Coprinus Pers. and the disposition of Coprinus species sensu lato.” Taxon 50, no. 1 (January 1, 2001): 203–41. https://doi.org/10.2307/1224525.
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  - Wagner, R. P., and J. F. Crow. “The other fly room: J. T. Patterson and Texas genetics..” Genetics 157, no. 1 (January 2001): 1–5.
  - Forche, A., J. Xu, R. Vilgalys, and T. G. Mitchell. “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. https://doi.org/10.1006/fgbi.2000.1240.
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  - Xu, J., R. Vilgalys, and T. G. Mitchell. “Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans..” Mol Ecol 9, no. 10 (October 2000): 1471–81. https://doi.org/10.1046/j.1365-294x.2000.01021.x.
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  - Moncalvo, J. M., D. Drehmel, and R. Vilgalys. “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 (July 2000): 48–63. https://doi.org/10.1006/mpev.2000.0782.
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  - Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. “Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences..” Systematic Biology 49, no. 2 (June 2000): 278–305. https://doi.org/10.1093/sysbio/49.2.278.
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  - Xu, J., R. Y. Ali, D. A. Gregory, D. Amick, S. E. Lambert, H. J. Yoell, R. J. Vilgalys, and T. G. Mitchell. “Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans..” Curr Microbiol 40, no. 4 (April 2000): 269–73.
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  - Xu, J., A. R. Ramos, R. Vilgalys, and T. G. Mitchell. “Clonal and spontaneous origins of fluconazole resistance in Candida albicans..” J Clin Microbiol 38, no. 3 (March 2000): 1214–20.
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  - Isikhuemhen, O. S., J. M. Moncalvo, F. Nerud, and R. Vilgalys. “Mating compatibility and phylogeography in Pleurotus tuberregium.” Mycological Research 104, no. 6 (January 1, 2000): 732–37. https://doi.org/10.1017/S0953756299001926.
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  - James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. “Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics.” Canadian Journal of Botany 78, no. 3 (January 1, 2000): 336–50. https://doi.org/10.1139/b00-009.
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  - McEwen, J. G., J. W. Taylor, D. Carter, J. Xu, M. S. Felipe, R. Vilgalys, T. G. Mitchell, et al. “Molecular typing of pathogenic fungi..” Med Mycol 38 Suppl 1 (2000): 189–97.
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  - Pringle, A., J. M. Moncalvo, and R. Vilgalys. “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 (January 1, 2000): 259–68. https://doi.org/10.2307/3761559.
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  - Redhead, S. A., K. A. Seifert, R. Vilgalys, and J. M. Moncalvo. “Rhacophyllus and Zerovaemyces - Teleomorphs or anamorphs?.” Taxon 49, no. 4 (January 1, 2000): 789–98. https://doi.org/10.2307/1223980.
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  - Schönian, G., A. Forche, H. J. Tietz, M. Müller, Y. Gräser, R. Vilgalys, T. G. Mitchell, and W. Presber. “[Genetic structure of geographically different populations of candida albicans]..” Mycoses 43 Suppl 2 (2000): 51–56.
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  - Thorn, R. G., J. M. Moncalvo, C. A. Reddy, and R. Vilgalys. “Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi.” Mycologia 92, no. 2 (January 1, 2000): 241–52. https://doi.org/10.2307/3761557.
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  - 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, T. Y., D. Porter, J. L. Hamrick, and R. Vilgalys. “Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune.” Evolution 53, no. 6 (December 1, 1999): 1665–77.
  - Forche, A., G. Schönian, Y. Gräser, R. Vilgalys, and T. G. Mitchell. “Genetic structure of typical and atypical populations of Candida albicans from Africa..” Fungal Genet Biol 28, no. 2 (November 1999): 107–25. https://doi.org/10.1006/fgbi.1999.1164.
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  - Hopple, J. S., and R. Vilgalys. “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 (October 1999): 1–19. https://doi.org/10.1006/mpev.1999.0634.
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  - Gräser, Y., M. El Fari, R. Vilgalys, A. F. Kuijpers, G. S. De Hoog, W. Presber, and H. Tietz. “Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region..” Medical Mycology 37, no. 2 (April 1999): 105–14. https://doi.org/10.1046/j.1365-280x.1999.00203.x.
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  - Xu, J., R. Vilgalys, and T. G. Mitchell. “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): 1369–73.
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  - Baroni, T. J., N. W. Legon, R. Vilgalys, and D. J. Lodge. “Calocybe cyanea - A rare and beautiful agaric is discovered in Puerto Rico.” Mycologist 13, no. 1 (January 1, 1999): 7–10. https://doi.org/10.1016/S0269-915X(99)80065-2.
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  - Drehmel, D., J. M. Moncalvo, and R. Vilgalys. “Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: Implications for taxonomy and character evolution.” Mycologia 91, no. 4 (January 1, 1999): 610–18. https://doi.org/10.2307/3761246.
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  - Xu, J., T. G. Mitchell, and R. Vilgalys. “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. https://doi.org/10.1046/j.1365-294x.1999.00523.x.
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  - Johnson, J., and R. Vilgalys. “Phylogenetic systematics of Lepiota sensu lato based on nuclear large subunit rDNA evidence.” Mycologia 90, no. 6 (December 15, 1998): 971–79. https://doi.org/10.2307/3761269.
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  - Xu, J., R. Vilgalys, and T. G. Mitchell. “Colony size can be used to determine the MIC of fluconazole for pathogenic yeasts..” J Clin Microbiol 36, no. 8 (August 1998): 2383–85.
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  - Lewis, L. A., B. D. Mishler, and R. Vilgalys. “Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL..” Molecular Phylogenetics and Evolution 7, no. 3 (June 1997): 377–93. https://doi.org/10.1006/mpev.1996.0395.
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  - Cubeta, M. A., and R. Vilgalys. “Population biology of the Rhizoctonia solani complex.” Phytopathology 87, no. 4 (April 1, 1997): 480–83.
  - McPartland, J. M., R. J. Vilgalys, and M. A. Cubeta. “Mushroom poisoning..” American Family Physician 55, no. 5 (April 1997): 1797–1812.
  - Yoder, A. D., R. Vilgalys, and M. Ruvolo. “Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions..” Molecular Biology and Evolution 13, no. 10 (December 1996): 1339–50. https://doi.org/10.1093/oxfordjournals.molbev.a025580.
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  - Gräser, Y., M. Volovsek, J. Arrington, G. Schönian, W. Presber, T. G. Mitchell, and R. Vilgalys. “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): 12473–77. https://doi.org/10.1073/pnas.93.22.12473.
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  - Haase, G. “Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens..” J Clin Microbiol 34, no. 8 (August 1996): 2049–50.
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  - Yoder, A. D., M. Cartmill, M. Ruvolo, K. Smith, and R. Vilgalys. “Ancient single origin for Malagasy primates..” Proceedings of the National Academy of Sciences of the United States of America 93, no. 10 (May 1996): 5122–26. https://doi.org/10.1073/pnas.93.10.5122.
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  - Spatafora, J. W., T. G. Mitchell, and R. Vilgalys. “Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens..” J Clin Microbiol 33, no. 5 (May 1995): 1322–26.
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  - Vilgalys, R., and R. Bao Lin Sun. “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 (August 10, 1994). https://doi.org/10.1073/pnas.91.16.7832.
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  - Vilgalys, R., and B. L. Sun. “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 (May 1994): 4599–4603. https://doi.org/10.1073/pnas.91.10.4599.
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  - Vilgalys, R., and M. A. Cubeta. “Molecular systematics and population biology of Rhizoctonia.” Annual Review of Phytopathology 32 (January 1, 1994): 135–55. https://doi.org/10.1146/annurev.py.32.090194.001031.
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  - Vilgalys, R., and R. Sun Bao Lin. “Assessment of species distributions in Pleurotus based on trapping of airborne basidiospores.” Mycologia 86, no. 2 (January 1, 1994): 270–74. https://doi.org/10.2307/3760649.
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  - Meyer, W., T. G. Mitchell, E. Z. Freedman, and R. Vilgalys. “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): 2274–80.
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  - Moncalvo, J. M., S. A. Rehner, and R. Vilgalys. “Systematics of Lyophyllum section difformia based on evidence from culture studies and ribosomal DNA sequences.” Mycologia 85, no. 5 (January 1, 1993): 788–94. https://doi.org/10.2307/3760610.
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  - Vilgalys, R., A. Smith, A. Bao Lin Sun, and O. K. Miller. “Intersterility groups in the Pleurotus ostreatus complex from the continental United States and adjacent Canada.” Canadian Journal of Botany 71, no. 1 (January 1, 1993): 113–28. https://doi.org/10.1139/b93-013.
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  - Bruns, T. D., R. Vilgalys, S. M. Barns, D. Gonzalez, D. S. Hibbett, D. J. Lane, L. Simon, S. Stickel, T. M. Szaro, and W. G. Weisburg. “Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences..” Molecular Phylogenetics and Evolution 1, no. 3 (September 1992): 231–41. https://doi.org/10.1016/1055-7903(92)90020-h.
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  - Kay, E., and R. Vilgalys. “Spatial distribution and genetic relationships among individuals in a natural population of the oyster mushroom Pleurotus ostreatus.” Mycologia 84, no. 2 (January 1, 1992): 173–82. https://doi.org/10.2307/3760248.
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  - Hibbett, D. S., and R. Vilgalys. “Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA.” Mycologia 83, no. 4 (January 1, 1991): 425–39.
  - Vilgalys, R. “Speciation and species concepts in the Collybia dryophila complex.” Mycologia 83, no. 6 (January 1, 1991): 758–73. https://doi.org/10.2307/3760433.
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  - Vilgalys, D., and D. Gonzalez. “Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola..” Current Genetics 18, no. 3 (October 1990): 277–80. https://doi.org/10.1007/bf00318394.
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  - Vilgalys, R., and M. Hester. “Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species..” Journal of Bacteriology 172, no. 8 (August 1990): 4238–46. https://doi.org/10.1128/jb.172.8.4238-4246.1990.
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Teaching & Mentoring
Recent Courses
- BIOLOGY 293: Research Independent Study 2019
- BIOLOGY 493: Research Independent Study 2019
- BIOLOGY 540L: Mycology 2019
- BIOLOGY 557L: Microbial Ecology and Evolution 2019
- BIOLOGY 792: Research 2019
Scholarly, Clinical, & Service Activities
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Outreach & Engaged Scholarship
- Unknown. Mushroom Identification. December 22, 2013 2013
- Unknown. Mushroom classes and workshops. December 22, 2013 2013

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