Publications of Rytas J. Vilgalys    :chronological  alphabetical  combined  bibtex listing:

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Papers Published

  1. Bier, RL; Wernegreen, JJ; Vilgalys, RJ; Ellis, JC; Bernhardt, ES, Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage, Limnology and Oceanography, vol. 65 no. S1 (January, 2020), pp. S277-S292 [doi]  [abs].
  2. Liao, H-L; Bonito, G; Rojas, JA; Hameed, K; Wu, S; Schadt, CW; Labbé, J; Tuskan, GA; Martin, F; Grigoriev, IV; Vilgalys, R, Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition., Molecular Plant Microbe Interactions : Mpmi, vol. 32 no. 7 (July, 2019), pp. 853-864 [doi]  [abs].
  3. Veličkovic, D; Liao, H-L; Vilgalys, R; Chu, RK; Anderton, CR, Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization., Journal of Natural Products, vol. 82 no. 5 (May, 2019), pp. 1382-1386 [doi]  [abs].
  4. Policelli, N; Bruns, TD; Vilgalys, R; Nuñez, MA, Suilloid fungi as global drivers of pine invasions., The New Phytologist, vol. 222 no. 2 (April, 2019), pp. 714-725 [doi]  [abs].
  5. Bonito, G; Benucci, GMN; Hameed, K; Weighill, D; Jones, P; Chen, K-H; Jacobson, D; Schadt, C; Vilgalys, R, Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype., Frontiers in Microbiology, vol. 10 (January, 2019), pp. 481 [doi]  [abs].
  6. Uehling, JK; Entler, MR; Meredith, HR; Millet, LJ; Timm, CM; Aufrecht, JA; Bonito, GM; Engle, NL; Labbé, JL; Doktycz, MJ; Retterer, ST; Spatafora, JW; Stajich, JE; Tschaplinski, TJ; Vilgalys, RJ, Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange., Frontiers in Microbiology, vol. 10 (January, 2019), pp. 2163 [doi]  [abs].
  7. Hibbett, DS; Blackwell, M; James, TY; Spatafora, JW; Taylor, JW; Vilgalys, R, Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota, Ima Fungus, vol. 9 no. 2 (December, 2018), pp. 291-298, International Mycological Association (IMA) [doi]  [abs].
  8. Liao, H-L; Chen, Y; Vilgalys, R, 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, vol. 14 no. 10 (October, 2018), pp. e1007742 [doi]  [abs].
  9. Misztal, PK; Lymperopoulou, DS; Adams, RI; Scott, RA; Lindow, SE; Bruns, T; Taylor, JW; Uehling, J; Bonito, G; Vilgalys, R; Goldstein, AH, Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi., Environmental Science & Technology, vol. 52 no. 15 (August, 2018), pp. 8272-8282, American Chemical Society (ACS) [doi]  [abs].
  10. Vélez, JM; Tschaplinski, TJ; Vilgalys, R; Schadt, CW; Bonito, G; Hameed, K; Engle, N; 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](S1754504817300326)(10.1016/j.funeco.2017.03.001), Fungal Ecology, vol. 33 (June, 2018), pp. 143, Elsevier BV [doi]  [abs].
  11. Gryganskyi, AP; Golan, J; Dolatabadi, S; Mondo, S; Robb, S; Idnurm, A; Muszewska, A; Steczkiewicz, K; Masonjones, S; Liao, H-L; Gajdeczka, MT; Anike, F; Vuek, A; Anishchenko, IM; Voigt, K; de Hoog, GS; Smith, ME; Heitman, J; Vilgalys, R; Stajich, JE, Phylogenetic and Phylogenomic Definition of Rhizopus Species., G3 (Bethesda, Md.), vol. 8 no. 6 (May, 2018), pp. 2007-2018 [doi]  [abs].
  12. Cregger, MA; Veach, AM; Yang, ZK; Crouch, MJ; Vilgalys, R; Tuskan, GA; Schadt, CW, The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome., Microbiome, vol. 6 no. 1 (February, 2018), pp. 31 [doi]  [abs].
  13. Johansen, RB; Johnston, P; Mieczkowski, P; Perry, GLW; Robeson, MS; Vilgalys, R; 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, vol. 112 (September, 2017), pp. 177-190, Elsevier BV [doi]  [abs].
  14. 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; Bonito, G, Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens., Environmental Microbiology, vol. 19 no. 8 (August, 2017), pp. 2964-2983 [doi]  [abs].
  15. Smith, ME; Henkel, TW; Williams, GC; Aime, MC; Fremier, AK; Vilgalys, R, Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa., The New Phytologist, vol. 215 no. 1 (July, 2017), pp. 443-453 [doi]  [abs].
  16. Vélez, JM; Tschaplinski, TJ; Vilgalys, R; Schadt, CW; Bonito, G; Hameed, K; Engle, N; Hamilton, CE, Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees, Fungal Ecology, vol. 27 (June, 2017), pp. 78-86, Elsevier BV [doi]  [abs].
  17. Gryganskyi, AP; Mullens, BA; Gajdeczka, MT; Rehner, SA; Vilgalys, R; Hajek, AE, Hijacked: Co-option of host behavior by entomophthoralean fungi., edited by Sheppard, DC, Plos Pathogens, vol. 13 no. 5 (May, 2017), pp. e1006274 [doi] .
  18. Branco, S; Bi, K; Liao, H-L; Gladieux, P; Badouin, H; Ellison, CE; Nguyen, NH; Vilgalys, R; Peay, KG; Taylor, JW; Bruns, TD, Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes., edited by Giraud, T; Koskella, B; Laine, A-L, Molecular Ecology, vol. 26 no. 7 (April, 2017), pp. 2063-2076 [doi]  [abs].
  19. Li, Z; Yao, Q; Dearth, SP; Entler, MR; Castro Gonzalez, HF; Uehling, JK; Vilgalys, RJ; Hurst, GB; Campagna, SR; Labbé, JL; Pan, C, Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system., Environmental Microbiology, vol. 19 no. 3 (March, 2017), pp. 1041-1053 [doi]  [abs].
  20. 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; Bruns, TD, Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal., Mycologia, vol. 109 no. 1 (January, 2017), pp. 115-127 [doi]  [abs].
  21. Bonito, G; Hameed, K; Toome-Heller, M; Healy, R; Reid, C; Liao, H-L; Aime, MC; Schadt, C; Vilgalys, R, Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome., Mycologia, vol. 109 no. 1 (January, 2017), pp. 18-26 [doi]  [abs].
  22. Liao, H-L; Chen, Y; 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, vol. 12 no. 10 (October, 2016), pp. e1006348 [doi]  [abs].
  23. Johansen, RB; Johnston, P; Mieczkowski, P; Perry, GLW; Robeson, MS; Burns, BR; Vilgalys, R, A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities, Fungal Ecology, vol. 23 (October, 2016), pp. 141-155, Elsevier BV [doi]  [abs].
  24. 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; Stajich, JE, A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data., Mycologia, vol. 108 no. 5 (September, 2016), pp. 1028-1046 [doi]  [abs].
  25. Ekblad, A; Mikusinska, A; Ågren, GI; Menichetti, L; Wallander, H; Vilgalys, R; Bahr, A; Eriksson, U, Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization., The New Phytologist, vol. 211 no. 3 (August, 2016), pp. 874-885 [doi]  [abs].
  26. Bonito, G; Hameed, K; Ventura, R; Krishnan, J; Schadt, CW; Vilgalys, R, Isolating a functionally relevant guild of fungi from the root microbiome of Populus, Fungal Ecology, vol. 22 (August, 2016), pp. 35-42, Elsevier BV [doi]  [abs].
  27. Gónzalez, D; Rodriguez-Carres, M; Boekhout, T; Stalpers, J; Kuramae, EE; Nakatani, AK; Vilgalys, R; Cubeta, MA, Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales., Fungal Biology, vol. 120 no. 4 (April, 2016), pp. 603-619 [doi]  [abs].
  28. Czaplicki, LM; Cooper, E; Ferguson, PL; Stapleton, HM; Vilgalys, R; 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.), vol. 26 no. 2 (January, 2016), pp. 59-72 [doi]  [abs].
  29. Branco, S; Gladieux, P; Ellison, CE; Kuo, A; LaButti, K; Lipzen, A; Grigoriev, IV; Liao, H-L; Vilgalys, R; Peay, KG; Taylor, JW; Bruns, TD, Genetic isolation between two recently diverged populations of a symbiotic fungus., Molecular Ecology, vol. 24 no. 11 (June, 2015), pp. 2747-2758 [doi]  [abs].
  30. Glassman, SI; Peay, KG; Talbot, JM; Smith, DP; Chung, JA; Taylor, JW; Vilgalys, R; Bruns, TD, A continental view of pine-associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern., The New Phytologist, vol. 205 no. 4 (March, 2015), pp. 1619-1631 [doi]  [abs].
  31. Kuske, CR; Hesse, CN; Challacombe, JF; Cullen, D; Herr, JR; Mueller, RC; Tsang, A; Vilgalys, R, Prospects and challenges for fungal metatranscriptomics of complex communities, Fungal Ecology, vol. 14 (January, 2015), pp. 133-137, Elsevier BV [doi]  [abs].
  32. Liao, H-L; Chen, Y; Bruns, TD; Peay, KG; Taylor, JW; Branco, S; Talbot, JM; Vilgalys, R, Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ., Environmental Microbiology, vol. 16 no. 12 (December, 2014), pp. 3730-3742 [doi]  [abs].
  33. Bonito, G; Reynolds, H; Robeson, MS; Nelson, J; Hodkinson, BP; Tuskan, G; Schadt, CW; Vilgalys, R, Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants., Molecular Ecology, vol. 23 no. 13 (July, 2014), pp. 3356-3370 [doi]  [abs].
  34. Talbot, JM; Bruns, TD; Taylor, JW; Smith, DP; Branco, S; Glassman, SI; Erlandson, S; Vilgalys, R; Liao, H-L; Smith, ME; 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, vol. 111 no. 17 (April, 2014), pp. 6341-6346 [doi]  [abs].
  35. 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; Cubeta, MA, Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3., Fems Microbiology Letters, vol. 352 no. 2 (March, 2014), pp. 165-173 [doi]  [abs].
  36. Hofstetter, V; Redhead, SA; Kauff, F; Moncalvo, JM; Matheny, PB; Vilgalys, R, Taxonomic revision and examination of ecological transitions of the Lyophyllaceae (Basidiomycota, Agaricales) based on a multigene phylogeny, Cryptogamie, Mycologie, vol. 35 no. 4 (January, 2014), pp. 399-425, BioOne [doi]  [abs].
  37. Lodge, DJ; Padamsee, M; Matheny, PB; Aime, MC; Cantrell, SA; Boertmann, D; Kovalenko, A; Vizzini, A; Dentinger, BTM; Kirk, PM; Ainsworth, AM; Moncalvo, JM; 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; Hattori, T, Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales), Fungal Diversity, vol. 64 no. 1 (January, 2014), pp. 1-99, Springer Nature [doi]  [abs].
  38. 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; Nierman, WC, Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP., Genome Announcements, vol. 2 no. 5 (January, 2014), pp. e01072-14-e01072-14 [doi]  [abs].
  39. Benítez, M-S; Hersh, MH; Vilgalys, R; Clark, JS, Pathogen regulation of plant diversity via effective specialization., Trends in Ecology and Evolution, vol. 28 no. 12 (December, 2013), pp. 705-711 [24091206], [doi]  [abs].
  40. Lodge, D Jean and Padamsee, M and Matheny, P B and Aime, M C and Cantrell, S A and Boertmann, D and Kovalenko, A, Vizzini, A, Dentinger, B T M and Kirk, P M and Ainsworth, A M and Moncalvo, J and Vilgalys, R and Larsson, E and Lucking, R and Griffith, G W and Smith, M E and Norvell, L L and Desjardin, D E and Redhead, S A and Ovrebo, C L and Lickey, E B and Ercole, E and Hughes, K W and Courtecuisse, R and Young, A and Binder, M and Minnis, A M and Lindner, D L and Ortiz-Santana, B and Haight, J and Laessoe, T and Baroni, T J and Geml, J and Hattori, T, Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales), Fungal Diversity (October, 2013) .
  41. Gryganskyi, A P and Humber, R A and Smith, M E and Hodge, K and Huang, B and Voigt, K and Vilgalys, R, Phylogenetic lineages in Entomophthoromycota, Persoonia - Molecular Phylogeny and Evolution of Fungi, vol. 30 no. 1 (June, 2013), pp. 94--105 .
  42. Gryganskyi, AP; Humber, RA; Smith, ME; Hodge, K; Huang, B; Voigt, K; Vilgalys, R, Phylogenetic lineages in Entomophthoromycota., Persoonia, vol. 30 (June, 2013), pp. 94-105 [doi]  [abs].
  43. Golonka, AM; Vilgalys, R, Nectar inhabiting yeasts in Virginian populations of Silene latifolia (Caryophyllaceae) and coflowering species, The American Midland Naturalist, vol. 169 no. 2 (April, 2013), pp. 235-258, University of Notre Dame [doi]  [abs].
  44. Gryganskyi, AP; Humber, RA; Smith, ME; Miadlikovska, J; Wu, S; Voigt, K; Walther, G; Anishchenko, IM; Vilgalys, R, Corrigendum to "Molecular phylogeny of the Entomophthoromycota" [Mol. Phylogenet. Evol. 65 (2012) 682-694], Molecular Phylogenetics and Evolution, vol. 66 no. 3 (March, 2013), pp. 1099, Elsevier BV [doi] .
  45. 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; McLaughlin, DJ, High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales., Molecular Ecology, vol. 22 no. 6 (March, 2013), pp. 1717-1732 [doi]  [abs].
  46. Husbands, DR; Henkel, TW; Bonito, G; Vilgalys, R; Smith, ME, New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence., Mycologia, vol. 105 no. 2 (March, 2013), pp. 422-435 [doi]  [abs].
  47. Talbot, JM; Bruns, TD; Smith, DP; Branco, S; Glassman, SI; Erlandson, S; Vilgalys, R; Peay, KG, Independent roles of ectomycorrhizal and saprotrophic communities in soil organic matter decomposition, Soil Biology and Biochemistry, vol. 57 (February, 2013), pp. 282-291, Elsevier BV [doi]  [abs].
  48. Smith, ME; Henkel, TW; Uehling, JK; Fremier, AK; Clarke, HD; Vilgalys, R, The ectomycorrhizal fungal community in a neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea., Plos One, vol. 8 no. 1 (January, 2013), pp. e55160 [doi]  [abs].
  49. 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; Vilgalys, R, Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage., Plos One, vol. 8 no. 1 (January, 2013), pp. e52765 [23300990], [doi]  [abs].
  50. Smith, M E and Henkel, T W and Uehling, J K and Fremier, A K and Clarke, H D and Vilgalys, R, The Ectomycorrhizal Fungal Community in a Neotropical Forest Dominated by the Endemic Dipterocarp Pakaraimaea dipterocarpacea, PLoS ONE, vol. 8 no. 1 (January, 2013), pp. e55160 .
  51. Shakya, M; Gottel, N; Castro, H; Yang, ZK; Gunter, L; Labbé, J; Muchero, W; Bonito, G; Vilgalys, R; Tuskan, G; Podar, M; Schadt, CW, A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees., Plos One, vol. 8 no. 10 (January, 2013), pp. e76382 [doi]  [abs].
  52. Weber, CF; Vilgalys, R; Kuske, CR, Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon, Frontiers in Microbiology, vol. 4 no. APR (January, 2013), pp. 1--14, FRONTIERS MEDIA SA [doi]  [abs].
  53. Gryganskyi, AP; Humber, RA; Stajich, JE; Mullens, B; Anishchenko, IM; Vilgalys, R, Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex., Plos One, vol. 8 no. 8 (January, 2013), pp. e71168 [doi]  [abs].
  54. Guevara, G; Bonito, G; Trappe, JM; Cázares, E; Williams, G; Healy, RA; Schadt, C; Vilgalys, R, New North American truffles (Tuber spp.) and their ectomycorrhizal associations., Mycologia, vol. 105 no. 1 (January, 2013), pp. 194-209 [doi]  [abs].
  55. Uehling, JK; Henkel, TW; Aime, MC; Vilgalys, R; 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, vol. 116 no. 12 (December, 2012), pp. 1263-1274 [doi]  [abs].
  56. Gryganskyi, AP; Humber, RA; Smith, ME; Miadlikowska, J; Wu, S; Voigt, K; Walther, G; Anishchenko, IM; Vilgalys, R, Molecular phylogeny of the Entomophthoromycota., Molecular Phylogenetics and Evolution, vol. 65 no. 2 (November, 2012), pp. 682-694 [22877646], [doi]  [abs].
  57. Uehling, JK; Henkel, TW; Vilgalys, R; Smith, ME, Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests., Mycorrhiza, vol. 22 no. 7 (October, 2012), pp. 577-581 [doi]  [abs].
  58. Henkel, TW; Aime, MC; Chin, MML; Miller, SL; Vilgalys, R; Smith, ME, Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield, Biodiversity and Conservation, vol. 21 no. 9 (August, 2012), pp. 2195-2220, Springer Nature [doi]  [abs].
  59. Bonito, G; Smith, ME; Brenneman, T; Vilgalys, R, Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants, Plant and Soil, vol. 356 no. 1-2 (July, 2012), pp. 357-366, Springer Nature [doi]  [abs].
  60. 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; Kuske, CR, Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide., Environmental Microbiology, vol. 14 no. 5 (May, 2012), pp. 1145-1158 [doi]  [abs].
  61. Thaler, AD; Van Dover, CL; 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, vol. 5 no. 2 (April, 2012), pp. 270-273, Elsevier BV [doi]  [abs].
  62. Hersh, MH; Vilgalys, R; Clark, JS, Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival., Ecology, vol. 93 no. 3 (March, 2012), pp. 511-520 [22624206], [doi]  [abs].
  63. Uehling, JK; Henkel, TW; Aime, MC; Vilgalys, R; Smith, ME, New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield., Mycologia, vol. 104 no. 2 (March, 2012), pp. 547-556 [doi]  [abs].
  64. Bonito, G., Timothy Brenneman and Rytas Vilgalys., Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). ., Mycorrhiza. (2012), pp. 601-612 .
  65. Uehling, JK; Henkel, TW; Aime, MC; Vilgalys, R; 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)  [abs].
  66. Uehling, JK; Henkel, TW; Aime, MC; Vilgalys, R; Smith, ME, New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield, Mycologia, vol. 103 no. 2 (2012), pp. 883-894 [doi]  [abs].
  67. Baroni, TJ; Hofstetter, V; Largent, DL; Vilgalys, R, Entocybe is proposed as a new genus in the Entolomataceae (Agaricomycetes, Basidiomycota) based on morphological and molecular evidence, North American Fungi, vol. 6 no. 12 (December, 2011), pp. 1-19, Pacific Northwest Fungi Project [doi]  [abs].
  68. Smith, ME; Henkel, TW; Catherine Aime, M; Fremier, AK; Vilgalys, R, Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest., The New Phytologist, vol. 192 no. 3 (November, 2011), pp. 699-712 [entrez], [doi]  [abs].
  69. Bonito, G; Brenneman, T; Vilgalys, R, Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae)., Mycorrhiza, vol. 21 no. 7 (October, 2011), pp. 601-612 [doi]  [abs].
  70. Weber, CF; Zak, DR; Hungate, BA; Jackson, RB; Vilgalys, R; Evans, RD; Schadt, CW; Megonigal, JP; Kuske, CR, Responses of soil cellulolytic fungal communities to elevated atmospheric CO₂ are complex and variable across five ecosystems., Environmental Microbiology, vol. 13 no. 10 (October, 2011), pp. 2778-2793 [abstract], [doi]  [abs].
  71. Gottel, NR; Castro, HF; Kerley, M; Yang, Z; Pelletier, DA; Podar, M; Karpinets, T; Uberbacher, E; Tuskan, GA; Vilgalys, R; Doktycz, MJ; Schadt, CW, Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types., Applied and Environmental Microbiology, vol. 77 no. 17 (September, 2011), pp. 5934-5944 [5934], [doi]  [abs].
  72. Porter, TM; Martin, W; James, TY; Longcore, JE; Gleason, FH; Adler, PH; Letcher, PM; Vilgalys, R, Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA., Fungal Biology, vol. 115 no. 4-5 (April, 2011), pp. 381-392 [S1878614611000250], [doi]  [abs].
  73. Bonito, G; Trappe, JM; Donovan, S; 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, vol. 4 no. 1 (February, 2011), pp. 83-93, Elsevier BV [doi]  [abs].
  74. Gryganskyi, AP; Lee, SC; Litvintseva, AP; Smith, ME; Bonito, G; Porter, TM; Anishchenko, IM; Heitman, J; Vilgalys, R, Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex., Plos One, vol. 5 no. 12 (December, 2010), pp. e15273 [repository], [doi]  [abs].
  75. Bonito, GM; Gryganskyi, AP; Trappe, JM; Vilgalys, R, A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal., Molecular Ecology, vol. 19 no. 22 (November, 2010), pp. 4994-5008 [doi]  [abs].
  76. Bonito, G; Trappe, JM; Rawlinson, P; Vilgalys, R, Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex., Mycologia, vol. 102 no. 5 (September, 2010), pp. 1042-1057 [doi]  [abs].
  77. Bonito, G; Isikhuemhen, OS; Vilgalys, R, Identification of fungi associated with municipal compost using DNA-based techniques., Bioresource Technology, vol. 101 no. 3 (February, 2010), pp. 1021-1027 [doi]  [abs].
  78. McLaughlin, DJ; Hibbett, DS; Lutzoni, F; Spatafora, JW; Vilgalys, R, The search for the fungal tree of life., Trends in Microbiology, vol. 17 no. 11 (November, 2009), pp. 488-497 [doi]  [abs].
  79. Parrent, JL; 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, vol. 19 no. 7 (September, 2009), pp. 469-479 [doi]  [abs].
  80. James, TY; Litvintseva, AP; Vilgalys, R; Morgan, JAT; Taylor, JW; Fisher, MC; Berger, L; Weldon, C; du Preez, L; Longcore, JE, Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations., Plos Pathogens, vol. 5 no. 5 (May, 2009), pp. e1000458 [doi]  [abs].
  81. Findley, K; Rodriguez-Carres, M; Metin, B; Kroiss, J; Fonseca, A; Vilgalys, R; Heitman, J, Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales., Eukaryot Cell, vol. 8 no. 3 (March, 2009), pp. 353-361 [doi]  [abs].
  82. Hartman, WH; Richardson, CJ; Vilgalys, R; Bruland, GL, Environmental and anthropogenic controls over bacterial communities in wetland soils., Proceedings of the National Academy of Sciences of the United States of America, vol. 105 no. 46 (November, 2008), pp. 17842-17847 [19004771], [doi]  [abs].
  83. Porter, TM; Schadt, CW; Rizvi, L; Martin, AP; Schmidt, SK; Scott-Denton, L; Vilgalys, R; 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, vol. 46 no. 2 (February, 2008), pp. 635-644 [doi]  [abs].
  84. PB Matheny, JM Curtis, V Hofstetter, MC Aime, JM Moncalvo, ZW Ge, JC Slot, JF Ammirati, TJ Baroni, NL Bougher, KW Hughes, DJ Lodge, RW Kerrigan, MT Seidl, DK Aanen, M DeNitis, GM Daniele, DE Desjardin, BR Kropp, LL Norvell, A Parker, EC Vellinga, R Vilgalys, DS Hibbett, Major clades of Agaricales: a multilocus phylogenetic overview., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 982-95  [abs].
  85. JM Moncalvo, RH Nilsson, B Koster, SM Dunham, T Bernauer, PB Matheny, TM Porter, S Margaritescu, M Weiss, S Garnica, E Danell, G Langer, E Langer, E Larsson, KH Larsson, R Vilgalys, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 937-48  [abs].
  86. TY James, PM Letcher, JE Longcore, SE Mozley-Standridge, D Porter, MJ Powell, GW Griffith, R Vilgalys, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)., Mycologia, United States, vol. 98 no. 6 (October, 2007), pp. 860-71  [abs].
  87. Ceresini, PC; Shew, HD; James, TY; Vilgalys, RJ; Cubeta, MA, Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci., Bmc Evolutionary Biology, vol. 7 (September, 2007), pp. 163 [17854492], [doi]  [abs].
  88. Henk, DA; 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, vol. 94 no. 9 (September, 2007), pp. 1515-1526, WILEY [doi]  [abs].
  89. AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, United States, vol. 99 no. 2 (September, 2007), pp. 185-206  [abs].
  90. AE Arnold, DA Henk, RL Eells, F Lutzoni, R Vilgalys, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, United States, vol. 99 no. 2 (September, 2007), pp. 185-206  [abs].
  91. Hibbett, DS; Binder, M; Bischoff, JF; Blackwell, M; Cannon, PF; Eriksson, OE; Huhndorf, S; James, T; Kirk, PM; Lücking, R; Thorsten Lumbsch, H; 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; Kurtzman, CP; Larsson, K-H; Lichtwardt, R; Longcore, J; Miadlikowska, J; Miller, A; Moncalvo, J-M; Mozley-Standridge, S; Oberwinkler, F; Parmasto, E; Reeb, V; Rogers, JD; Roux, C; Ryvarden, L; Sampaio, JP; Schüssler, A; Sugiyama, J; Thorn, RG; Tibell, L; Untereiner, WA; Walker, C; Wang, Z; Weir, A; Weiss, M; White, MM; Winka, K; Yao, Y-J; Zhang, N, A higher-level phylogenetic classification of the Fungi., Mycological Research, vol. 111 no. Pt 5 (May, 2007), pp. 509-547 [doi]  [abs].
  92. Arnold, AE; Henk, DA; Eells, RL; Lutzoni, F; Vilgalys, R, Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR., Mycologia, vol. 99 no. 2 (March, 2007), pp. 185-206 [17682771], [doi]  [abs].
  93. Parrent, JL; Vilgalys, R, Biomass and compositional responses of ectomycorrhizal fungal hyphae to elevated CO2 and nitrogen fertilization., The New Phytologist, vol. 176 no. 1 (January, 2007), pp. 164-174 [doi]  [abs].
  94. James, TY; Letcher, PM; Longcore, JE; Mozley-Standridge, SE; Porter, D; Powell, MJ; Griffith, GW; Vilgalys, R, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)., Mycologia, vol. 98 no. 6 (November, 2006), pp. 860-871 [doi]  [abs].
  95. 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; Vilgalys, R, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods., Mycologia, vol. 98 no. 6 (November, 2006), pp. 937-948 [doi]  [abs].
  96. Matheny, PB; Curtis, JM; Hofstetter, V; Aime, MC; Moncalvo, J-M; Ge, Z-W; 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; Hibbett, DS, Major clades of Agaricales: a multilocus phylogenetic overview., Mycologia, vol. 98 no. 6 (November, 2006), pp. 982-995 [doi]  [abs].
  97. Yahr, R; Vilgalys, R; 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)), The New Phytologist, vol. 172 no. 2 (October, 2006), pp. 377, WILEY [doi] .
  98. 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; Sugiyama, J; Rossman, AY; Rogers, JD; Pfister, DH; Hewitt, D; Hansen, K; Hambleton, S; Shoemaker, RA; Kohlmeyer, J; Volkmann-Kohlmeyer, B; Spotts, RA; Serdani, M; Crous, PW; Hughes, KW; Matsuura, K; Langer, E; Langer, G; Untereiner, WA; Lücking, R; Büdel, B; Geiser, DM; Aptroot, A; Diederich, P; Schmitt, I; Schultz, M; Yahr, R; Hibbett, DS; Lutzoni, F; McLaughlin, DJ; Spatafora, JW; Vilgalys, R, Reconstructing the early evolution of Fungi using a six-gene phylogeny., Nature, vol. 443 no. 7113 (October, 2006), pp. 818-822 [17051209], [doi]  [abs].
  99. JL Parrent, WF Morris, R Vilgalys, CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities., Ecology, United States, vol. 87 no. 9 (September, 2006), pp. 2278-87  [abs].
  100. Parrent, JL; Morris, WF; Vilgalys, R, CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities., Ecology, vol. 87 no. 9 (September, 2006), pp. 2278-2287 [16995628], [doi]  [abs].
  101. D González, MA Cubeta, R Vilgalys, Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex., Molecular phylogenetics and evolution, United States, vol. 40 no. 2 (August, 2006), pp. 459-70 [doi]  [abs].
  102. González, D; Cubeta, MA; Vilgalys, R, Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex., Molecular Phylogenetics and Evolution, vol. 40 no. 2 (August, 2006), pp. 459-470 [doi]  [abs].
  103. AP Litvintseva, R Thakur, R Vilgalys, TG Mitchell, Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana., Genetics, United States, vol. 172 no. 4 (April, 2006), pp. 2223-38 [doi]  [abs].
  104. Litvintseva, AP; Thakur, R; Vilgalys, R; Mitchell, TG, Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana., Genetics, vol. 172 no. 4 (April, 2006), pp. 2223-2238 [16322524], [doi]  [abs].
  105. TY James, P Srivilai, U Kües, R 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, United States, vol. 172 no. 3 (March, 2006), pp. 1877-91 [doi]  [abs].
  106. James, TY; Srivilai, P; Kües, U; 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, vol. 172 no. 3 (March, 2006), pp. 1877-1891 [doi]  [abs].
  107. Yahr, R; Vilgalys, R; DePriest, PT, Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis., The New Phytologist, vol. 171 no. 4 (January, 2006), pp. 847-860 [doi]  [abs].
  108. 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 GH, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schussler 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, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R, Reconstructing the early evolution of Fungi using a six-gene phylogeny, Nature, vol. 443 (2006), pp. 818-822 .
  109. R Yahr, R Vilgalys, PT DePriest, Geographic variation in algal partners of Cladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis., The New phytologist, England, vol. 171 no. 4 (2006), pp. 847-60 [doi]  [abs].
  110. Wallenstein, MD; Vilgalys, RJ, Quantitative analyses of nitrogen cycling genes in soils, Pedobiologia, vol. 49 no. 6 (November, 2005), pp. 665-672, Elsevier BV [doi]  [abs].
  111. O'Brien, HE; Parrent, JL; Jackson, JA; Moncalvo, J-M; Vilgalys, R, Fungal community analysis by large-scale sequencing of environmental samples., Applied and Environmental Microbiology, vol. 71 no. 9 (September, 2005), pp. 5544-5550 [16151147], [doi]  [abs].
  112. N Fierer, JA Jackson, R Vilgalys, RB Jackson, Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays., Applied and environmental microbiology, United States, vol. 71 no. 7 (July, 2005), pp. 4117-20 [doi]  [abs].
  113. Fierer, N; Jackson, JA; Vilgalys, R; Jackson, RB, Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays., Applied and Environmental Microbiology, vol. 71 no. 7 (July, 2005), pp. 4117-4120 [16000830], [doi]  [abs].
  114. Didukh, M; Vilgalys, R; Wasser, SP; Isikhuemhen, OS; Nevo, E, Notes on Agaricus section Duploannulati using molecular and morphological data., Mycological Research, vol. 109 no. Pt 6 (June, 2005), pp. 729-740 [doi]  [abs].
  115. AP Litvintseva, L Kestenbaum, R Vilgalys, TG Mitchell, Comparative analysis of environmental and clinical populations of Cryptococcus neoformans., Journal of clinical microbiology, United States, vol. 43 no. 2 (February, 2005), pp. 556-64 [doi]  [abs].
  116. Litvintseva, AP; Kestenbaum, L; Vilgalys, R; Mitchell, TG, Comparative analysis of environmental and clinical populations of Cryptococcus neoformans., Journal of Clinical Microbiology, vol. 43 no. 2 (February, 2005), pp. 556-564 [15695645], [doi]  [abs].
  117. Aime, MC; Vilgalys, R; Miller, OK, The crepidotaceae (Basidiomycota, Agaricales): Phylogeny and taxonomy of the genera and revision of the family based on molecular evidence, American Journal of Botany, vol. 92 no. 1 (January, 2005), pp. 74-82, WILEY [doi]  [abs].
  118. James, T. Y. and R. Vilgalys, Chytrid fungi as agents of amphibian decline- what can we learn from the earliest diverging fungi?, in Fungal Molecular principles of fungal pathogenesis, ASM Press. Joe Heitman, Scott Filler, and Aaron Mitchell-eds (2005) .
  119. Didukh, M; Vilgalys, R; Wasser, SP; Isikhuemhen, OS; Nevo, E, Notes on Agaricus section Duploannulati using molecular and morphological data, Mycological Research, vol. 109 no. 6 (2005), pp. 729-740 [doi]  [abs].
  120. Diezmann, S; Cox, CJ; Schönian, G; Vilgalys, RJ; Mitchell, TG, Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis., Journal of Clinical Microbiology, vol. 42 no. 12 (December, 2004), pp. 5624-5635 [15583292], [doi]  [abs].
  121. Yahr, R; Vilgalys, R; Depriest, PT, Strong fungal specificity and selectivity for algal symbionts in Florida scrub Cladonia lichens., Molecular Ecology, vol. 13 no. 11 (November, 2004), pp. 3367-3378 [doi]  [abs].
  122. 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; Stone, J; Sugiyama, J; Yahr, R; Vilgalys, R, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits., American Journal of Botany, vol. 91 no. 10 (October, 2004), pp. 1446-1480 [21652303], [doi]  [abs].
  123. James, TY; Liou, S-R; 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 : Fg & B, vol. 41 no. 8 (August, 2004), pp. 813-825 [doi]  [abs].
  124. Marra, RE; Huang, JC; Fung, E; Nielsen, K; Heitman, J; Vilgalys, R; Mitchell, TG, A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)., Genetics, vol. 167 no. 2 (June, 2004), pp. 619-631 [15238516], [doi]  [abs].
  125. James, TY; Kües, U; Rehner, SA; 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 : Fg & B, vol. 41 no. 3 (March, 2004), pp. 381-390 [doi]  [abs].
  126. Zervakis, GI; Moncalvo, J-M; Vilgalys, R, Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa., Microbiology, vol. 150 no. Pt 3 (March, 2004), pp. 715-726 [doi]  [abs].
  127. Peintner, U; Moncalvo, JM; Vilgalys, R, Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota), Mycologia, vol. 96 no. 5 (January, 2004), pp. 1042-1058, Informa UK Limited [doi]  [abs].
  128. Litvintseva, AP; Marra, RE; Nielsen, K; Heitman, J; Vilgalys, R; Mitchell, TG, Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa., Eukaryotic Cell, vol. 2 no. 6 (December, 2003), pp. 1162-1168 [14665451], [doi]  [abs].
  129. Davis, EC; Franklin, JB; Shaw, AJ; Vilgalys, R, Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis., American Journal of Botany, vol. 90 no. 11 (November, 2003), pp. 1661-1667 [21653342], [doi]  [abs].
  130. Vilgalys, R, Taxonomic misidentification in public DNA databases, The New Phytologist, vol. 160 no. 1 (October, 2003), pp. 4-5, WILEY [doi] .
  131. Pringle, A; Moncalvo, J-M; Vilgalys, R, Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica., Mycorrhiza, vol. 13 no. 4 (August, 2003), pp. 227-231 [doi]  [abs].
  132. Ceresini, PC; Shew, HD; Vilgalys, RJ; Gale, LR; Cubeta, MA, Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities., Phytopathology, vol. 93 no. 5 (May, 2003), pp. 610-615 [18942984], [doi]  [abs].
  133. Morehouse, EA; James, TY; Ganley, ARD; Vilgalys, R; Berger, L; Murphy, PJ; Longcore, JE, Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone., Molecular Ecology, vol. 12 no. 2 (February, 2003), pp. 395-403 [12535090], [doi]  [abs].
  134. Peintner, U; Horak, E; Moser, M; Vilgalys, R, Rozites, Cuphocybe and Rapacea are taxonomic synonyms of Cortinarius: New combinations and new names, Mycotaxon, vol. 83 (July, 2002), pp. 447-451  [abs].
  135. Redhead, SA; Lutzoni, F; Moncalvo, JM; Vilgalys, R, Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics), Mycotaxon, vol. 83 (July, 2002), pp. 19-57  [abs].
  136. Moncalvo, J-M; Vilgalys, R; Redhead, SA; Johnson, JE; James, TY; Catherine Aime, M; Hofstetter, V; Verduin, SJW; Larsson, E; Baroni, TJ; Greg Thorn, R; Jacobsson, S; Clémençon, H; Miller, OK, One hundred and seventeen clades of euagarics., Molecular Phylogenetics and Evolution, vol. 23 no. 3 (June, 2002), pp. 357-400 [doi]  [abs].
  137. Ceresini, PC; Shew, HD; Vilgalys, RJ; Cubeta, MA, Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina., Mycologia, vol. 94 no. 3 (May, 2002), pp. 437-449 [21156515]  [abs].
  138. Ceresini, PC; Shew, HD; Vilgalys, RJ; Rosewich, UL; Cubeta, MA, Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina., Mycologia, vol. 94 no. 3 (May, 2002), pp. 450-460 [21156516]  [abs].
  139. Peintner, U; Horak, E; Moser, MM; Vilgalys, R, Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences, Mycologia, vol. 94 no. 4 (January, 2002), pp. 620-629, Informa UK Limited [doi]  [abs].
  140. Peintner, U; Moser, M; Vilgalys, R, Thaxterogaster is a taxonomic synonym of Cortinarius: New combinations and new names, Mycotaxon, vol. 81 (January, 2002), pp. 177-184  [abs].
  141. Hofstetter, V; Clémençon, H; Vilgalys, R; Moncalvo, JM, Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences, Mycological Research, vol. 106 no. 9 (January, 2002), pp. 1043-1059, Elsevier BV [doi]  [abs].
  142. Henkel, TW; Terborgh, J; Vilgalys, RJ, Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana, Mycological Research, vol. 106 no. 5 (January, 2002), pp. 515-531, Elsevier BV [doi]  [abs].
  143. Xu, J; Luo, G; Vilgalys, RJ; Brandt, ME; Mitchell, TG, Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD., Microbiology, vol. 148 no. Pt 1 (January, 2002), pp. 203-212 [11782512], [doi]  [abs].
  144. Xu, J; Luo, G; Vilgalys, RJ; Brandt, ME; Mitchell, TG, Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD, Microbiology, vol. 148 no. 1 (2002), pp. 203-212  [abs].
  145. Mueller, GM; Wu, QX; Huang, YQ; Guo, SY; Aldana-Gomez, R; Vilgalys, R, Assessing biogeographic relationships between North American and Chinese macrofungi, Journal of Biogeography, vol. 28 no. 2 (July, 2001), pp. 271-281, WILEY [doi]  [abs].
  146. James, TY; Vilgalys, R, Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling., Molecular Ecology, vol. 10 no. 2 (February, 2001), pp. 471-479 [doi]  [abs].
  147. Kües, U; James, TY; Vilgalys, R; Challen, MP, The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic homobasidiomycete Coprinus bilanatus., Current Genetics, vol. 39 no. 1 (February, 2001), pp. 16-24 [doi]  [abs].
  148. Xu, J; Onyewu, C; Yoell, HJ; Ali, RY; Vilgalys, RJ; Mitchell, TG, Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans., Antimicrobial Agents and Chemotherapy, vol. 45 no. 2 (February, 2001), pp. 420-427 [11158735], [doi]  [abs].
  149. Redhead, SA; Vilgalys, R; Moncalvo, JM; Johnson, J; Hopple, J, Coprinus Pers. and the disposition of Coprinus species sensu lato, Taxon, vol. 50 no. 1 (January, 2001), pp. 203-241, WILEY [doi]  [abs].
  150. Hughes, KW; Petersen, RH; Johnson, JE; Moncalvo, JM; Vilgalys, R; Redhead, SA; Thomas, T; McGhee, LL, Infragenic phylogeny of Collybia s. str. based on sequences of ribosomal ITS and LSU regions, Mycological Research, vol. 105 no. 2 (January, 2001), pp. 164-172, Elsevier BV [doi]  [abs].
  151. Wagner, RP; Crow, JF, The other fly room: J. T. Patterson and Texas genetics., Genetics, vol. 157 no. 1 (January, 2001), pp. 1-5 .
  152. Peintner, U; Bougher, NL; Castellano, MA; Moncalvo, JM; Moser, MM; Trappe, JM; Vilgalys, R, Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae), American Journal of Botany, vol. 88 no. 12 (January, 2001), pp. 2168-2179, WILEY [doi]  [abs].
  153. Gonzalez, D; Carling, DE; Kuninaga, S; Vilgalys, R; Cubetae, MA, Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs, Mycologia, vol. 93 no. 6 (January, 2001), pp. 1138-1150, JSTOR [doi]  [abs].
  154. James, TY; Moncalvo, JM; Li, S; Vilgalys, R, Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune., Genetics, vol. 157 no. 1 (January, 2001), pp. 149-161  [abs].
  155. Forche, A; Xu, J; Vilgalys, R; Mitchell, TG, Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms and other markers., Fungal Genetics and Biology : Fg & B, vol. 31 no. 3 (December, 2000), pp. 189-203 [11273681], [doi]  [abs].
  156. Xu, J; Vilgalys, R; Mitchell, TG, Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans., Molecular Ecology, vol. 9 no. 10 (October, 2000), pp. 1471-1481 [11050543], [doi]  [abs].
  157. Moncalvo, JM; Drehmel, D; 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, vol. 16 no. 1 (July, 2000), pp. 48-63 [doi]  [abs].
  158. Moncalvo, JM; Lutzoni, FM; Rehner, SA; Johnson, J; Vilgalys, R, Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences., Systematic Biology, vol. 49 no. 2 (June, 2000), pp. 278-305 [12118409], [doi]  [abs].
  159. Xu, J; Ali, RY; Gregory, DA; Amick, D; Lambert, SE; Yoell, HJ; Vilgalys, RJ; Mitchell, TG, Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans., Current Microbiology, vol. 40 no. 4 (April, 2000), pp. 269-273 [10688697], [doi]  [abs].
  160. Xu, J; Ramos, AR; Vilgalys, R; Mitchell, TG, Clonal and spontaneous origins of fluconazole resistance in Candida albicans., Journal of Clinical Microbiology, vol. 38 no. 3 (March, 2000), pp. 1214-1220 [10699025]  [abs].
  161. James, TY; Porter, D; Leander, CA; Vilgalys, R; Longcore, JE, Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics, Canadian Journal of Botany, vol. 78 no. 3 (January, 2000), pp. 336-350, Canadian Science Publishing [doi]  [abs].
  162. Redhead, SA; Seifert, KA; Vilgalys, R; Moncalvo, JM, Rhacophyllus and Zerovaemyces - Teleomorphs or anamorphs?, Taxon, vol. 49 no. 4 (January, 2000), pp. 789-798, WILEY [doi]  [abs].
  163. Thorn, RG; Moncalvo, JM; Reddy, CA; Vilgalys, R, Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi, Mycologia, vol. 92 no. 2 (January, 2000), pp. 241-252, JSTOR [doi]  [abs].
  164. Pringle, A; Moncalvo, JM; 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, vol. 92 no. 2 (January, 2000), pp. 259-268, JSTOR [doi]  [abs].
  165. Isikhuemhen, OS; Moncalvo, JM; Nerud, F; Vilgalys, R, Mating compatibility and phylogeography in Pleurotus tuberregium, Mycological Research, vol. 104 no. 6 (January, 2000), pp. 732-737, Elsevier BV [doi]  [abs].
  166. Isikhuemhen, OS; Nerud, F; Vilgalys, R, Cultivation studies on wild and hybrid strains of Pleurotus tuberregium (Fr.) Sing. on wheat straw substrate, World Journal of Microbiology & Biotechnology, vol. 16 no. 5 (2000), pp. 431-435 [doi]  [abs].
  167. McEwen, JG; Taylor, JW; Carter, D; Xu, J; Felipe, MS; Vilgalys, R; Mitchell, TG; Kasuga, T; White, T; Bui, T; Soares, CM, Molecular typing of pathogenic fungi., Medical Mycology, vol. 38 Suppl 1 (2000), pp. 189-197 [11204145], [doi]  [abs].
  168. Schönian, G; Forche, A; Tietz, HJ; Müller, M; Gräser, Y; Vilgalys, R; Mitchell, TG; Presber, W, [Genetic structure of geographically different populations of candida albicans]., Mycoses, vol. 43 Suppl 2 (2000), pp. 51-56 [11291578]  [abs].
  169. James, TY; Porter, D; Hamrick, JL; Vilgalys, R, Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune, Evolution; International Journal of Organic Evolution, vol. 53 no. 6 (December, 1999), pp. 1665-1677, WILEY [doi]  [abs].
  170. Forche, A; Schönian, G; Gräser, Y; Vilgalys, R; Mitchell, TG, Genetic structure of typical and atypical populations of Candida albicans from Africa., Fungal Genetics and Biology : Fg & B, vol. 28 no. 2 (November, 1999), pp. 107-125 [10587473], [doi]  [abs].
  171. Hopple, JS; 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, vol. 13 no. 1 (October, 1999), pp. 1-19 [doi]  [abs].
  172. Gräser, Y; El Fari, M; Vilgalys, R; Kuijpers, AF; De Hoog, GS; Presber, W; Tietz, H, Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region., Medical Mycology, vol. 37 no. 2 (April, 1999), pp. 105-114 [doi]  [abs].
  173. Xu, J; Vilgalys, R; Mitchell, TG, Lack of genetic differentiation between two geographically diverse samples of Candida albicans isolated from patients infected with human immunodeficiency virus., Journal of Bacteriology, vol. 181 no. 4 (February, 1999), pp. 1369-1373 [9973371]  [abs].
  174. Baroni, TJ; Legon, NW; Vilgalys, R; Lodge, DJ, Calocybe cyanea - A rare and beautiful agaric is discovered in Puerto Rico, Mycologist, vol. 13 no. 1 (January, 1999), pp. 7-10, Elsevier BV [doi]  [abs].
  175. Drehmel, D; Moncalvo, JM; Vilgalys, R, Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: Implications for taxonomy and character evolution, Mycologia, vol. 91 no. 4 (January, 1999), pp. 610-618, JSTOR [doi]  [abs].
  176. Xu, J; Mitchell, TG; Vilgalys, R, PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans., Molecular Ecology, vol. 8 no. 1 (January, 1999), pp. 59-73 [9919698], [doi]  [abs].
  177. Johnson, J; Vilgalys, R, Phylogenetic systematics of Lepiota sensu lato based on nuclear large subunit rDNA evidence, Mycologia, vol. 90 no. 6 (December, 1998), pp. 971-979, JSTOR [doi]  [abs].
  178. Xu, J; Vilgalys, R; Mitchell, TG, Colony size can be used to determine the MIC of fluconazole for pathogenic yeasts., Journal of Clinical Microbiology, vol. 36 no. 8 (August, 1998), pp. 2383-2385 [9666032]  [abs].
  179. Lewis, LA; Mishler, BD; Vilgalys, R, Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL., Molecular Phylogenetics and Evolution, vol. 7 no. 3 (June, 1997), pp. 377-393 [doi]  [abs].
  180. Cubeta, MA; Vilgalys, R, Population biology of the Rhizoctonia solani complex, Phytopathology, vol. 87 no. 4 (April, 1997), pp. 480-483 .
  181. McPartland, JM; Vilgalys, RJ; Cubeta, MA, Mushroom poisoning., American Family Physician, vol. 55 no. 5 (April, 1997), pp. 1797-1812 [9105206]  [abs].
  182. Yoder, AD; Vilgalys, R; Ruvolo, M, Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions., Molecular Biology and Evolution, vol. 13 no. 10 (December, 1996), pp. 1339-1350 [doi]  [abs].
  183. Gräser, Y; Volovsek, M; Arrington, J; Schönian, G; Presber, W; Mitchell, TG; Vilgalys, R, Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination., Proceedings of the National Academy of Sciences of the United States of America, vol. 93 no. 22 (October, 1996), pp. 12473-12477 [8901606], [doi]  [abs].
  184. Haase, G, Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens., Journal of Clinical Microbiology, vol. 34 no. 8 (August, 1996), pp. 2049-2050 [7615749]  [abs].
  185. Yoder, AD; Cartmill, M; Ruvolo, M; Smith, K; Vilgalys, R, Ancient single origin for Malagasy primates., Proceedings of the National Academy of Sciences of the United States of America, vol. 93 no. 10 (May, 1996), pp. 5122-5126 [doi]  [abs].
  186. Spatafora, JW; Mitchell, TG; Vilgalys, R, Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens., Journal of Clinical Microbiology, vol. 33 no. 5 (May, 1995), pp. 1322-1326 [7615749]  [abs].
  187. Vilgalys, 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, vol. 91 no. 16 (August, 1994), pp. 7832, Proceedings of the National Academy of Sciences [doi] .
  188. Vilgalys, R; 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, vol. 91 no. 10 (May, 1994), pp. 4599-4603 [doi]  [abs].
  189. Vilgalys, R; Sun Bao Lin,, Assessment of species distributions in Pleurotus based on trapping of airborne basidiospores, Mycologia, vol. 86 no. 2 (January, 1994), pp. 270-274, JSTOR [doi] .
  190. Vilgalys, R; Cubeta, MA, Molecular systematics and population biology of Rhizoctonia, Annual Review of Phytopathology, vol. 32 no. 1 (January, 1994), pp. 135-155, ANNUAL REVIEWS [doi] .
  191. Meyer, W; Mitchell, TG; Freedman, EZ; Vilgalys, R, Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans., Journal of Clinical Microbiology, vol. 31 no. 9 (September, 1993), pp. 2274-2280 [8408543]  [abs].
  192. Vilgalys, R; Smith, A; Bao Lin Sun, ; Miller, OK, Intersterility groups in the Pleurotus ostreatus complex from the continental United States and adjacent Canada, Canadian Journal of Botany, vol. 71 no. 1 (January, 1993), pp. 113-128, Canadian Science Publishing [doi]  [abs].
  193. Moncalvo, JM; Rehner, SA; Vilgalys, R, Systematics of Lyophyllum section difformia based on evidence from culture studies and ribosomal DNA sequences, Mycologia, vol. 85 no. 5 (January, 1993), pp. 788-794, JSTOR [doi] .
  194. Bruns, TD; Vilgalys, R; Barns, SM; Gonzalez, D; Hibbett, DS; Lane, DJ; Simon, L; Stickel, S; Szaro, TM; Weisburg, WG, Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences., Molecular Phylogenetics and Evolution, vol. 1 no. 3 (September, 1992), pp. 231-241 [doi]  [abs].
  195. Kay, E; Vilgalys, R, Spatial distribution and genetic relationships among individuals in a natural population of the oyster mushroom Pleurotus ostreatus, Mycologia, vol. 84 no. 2 (January, 1992), pp. 173-182, JSTOR [doi]  [abs].
  196. Hibbett, DS; Vilgalys, R, Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA, Mycologia, vol. 83 no. 4 (January, 1991), pp. 425-439  [abs].
  197. Vilgalys, R, Speciation and species concepts in the Collybia dryophila complex, Mycologia, vol. 83 no. 6 (January, 1991), pp. 758-773, JSTOR [doi]  [abs].
  198. Vilgalys, D; Gonzalez, D, Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola., Current Genetics, vol. 18 no. 3 (October, 1990), pp. 277-280 [doi]  [abs].
  199. Vilgalys, R; Hester, M, Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species., Journal of Bacteriology, vol. 172 no. 8 (August, 1990), pp. 4238-4246 [doi]  [abs].

Book Chapters

  1. Idnurm, A., T. Y. James, and R. Vilgalys, Sex in the rest: mysterious mating in the Chytridiomycota and Zygomycota, in Sex in fungi: molecular determination and evolutionary implications, edited by Joe Heitman, Jim Kronstad, John Taylor, and Lorna Casselton eds (2007), ASM Press, Washington, D.C. .
  2. James, T. Y. and R. Vilgalys, Amphibian chytridiomycosis as an emerging infectious disease of wildlife: what can we learn from the earliest diverging fungi?, in Molecular principles of fungal pathogenesis, edited by J. Heitman, S.G. Filler, J.E. Edwards, Jr, and A.P. Mitchell (2006), ASM Press, Washington, D.C. .