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

Papers Published

  1. Rush, TA; Wymore, AM; Rodríguez, M; Jawdy, S; Vilgalys, RJ; Martin, MZ; Andrews, HB, Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS)., mSystems, vol. 9 no. 9 (September, 2024), pp. e0091924 [doi]  [abs]
  2. Zhang, K; Wang, H; Tappero, R; Bhatnagar, JM; Vilgalys, R; Barry, K; Keymanesh, K; Tejomurthula, S; Grigoriev, IV; Kew, WR; Eder, EK; Nicora, CD; Liao, H-L, Ectomycorrhizal fungi enhance pine growth by stimulating iron-dependent mechanisms with trade-offs in symbiotic performance., The New phytologist, vol. 242 no. 4 (May, 2024), pp. 1645-1660 [doi]  [abs]
  3. Lofgren, L; Nguyen, NH; Kennedy, PG; Pérez-Pazos, E; Fletcher, J; Liao, H-L; Wang, H; Zhang, K; Ruytinx, J; Smith, AH; Ke, Y-H; Cotter, HVT; Engwall, E; Hameed, KM; Vilgalys, R; Branco, S, Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution., The New phytologist, vol. 242 no. 4 (May, 2024), pp. 1448-1475 [doi]  [abs]
  4. Marqués-Gálvez, JE; Pandharikar, G; Basso, V; Kohler, A; Lackus, ND; Barry, K; Keymanesh, K; Johnson, J; Singan, V; Grigoriev, IV; Vilgalys, R; Martin, F; Veneault-Fourrey, C, Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development., The New phytologist, vol. 242 no. 2 (April, 2024), pp. 658-674 [doi]  [abs]
  5. Mudbhari, S; Lofgren, L; Appidi, MR; Vilgalys, R; Hettich, RL; Abraham, PE, Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity., mSystems, vol. 9 no. 4 (April, 2024), pp. e0122523 [doi]  [abs]
  6. Swenie, RA; Looney, BP; Ke, Y-H; Alejandro Rojas, J; Cubeta, MA; Langer, GJ; Vilgalys, R; Matheny, PB, PacBio high-throughput multi-locus sequencing reveals high genetic diversity in mushroom-forming fungi., Molecular ecology resources, vol. 24 no. 1 (January, 2024), pp. e13885 [doi]  [abs]
  7. Hackman, J; Woodley, A; Carter, D; Strahm, B; Averill, C; Vilgalys, R; Garcia, K; Cook, R, Fungal biomass and ectomycorrhizal community assessment of phosphorus responsive Pinus taeda plantations, Frontiers in Fungal Biology, vol. 5 (January, 2024) [doi]  [abs]
  8. Gryganskyi, AP; Golan, J; Muszewska, A; Idnurm, A; Dolatabadi, S; Mondo, SJ; Kutovenko, VB; Kutovenko, VO; Gajdeczka, MT; Anishchenko, IM; Pawlowska, J; Tran, NV; Ebersberger, I; Voigt, K; Wang, Y; Chang, Y; Pawlowska, TE; Heitman, J; Vilgalys, R; Bonito, G; Benny, GL; Smith, ME; Reynolds, N; James, TY; Grigoriev, IV; Spatafora, JW; Stajich, JE, Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?, Microorganisms, vol. 11 no. 7 (July, 2023), pp. 1830 [doi]  [abs]
  9. Ke, Y-H; Branco, S; Bazzicalupo, AL; Nguyen, NH; Liao, H-L; Kennedy, P; Bruns, TD; Kuo, A; LaButti, K; Barry, K; Grigoriev, I; Vilgalys, R, Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi., Genetics, vol. 224 no. 2 (May, 2023), pp. iyad069 [doi]  [abs]
  10. Policelli, N; Hoeksema, JD; Moyano, J; Vilgalys, R; Vivelo, S; Bhatnagar, JM, Global pine tree invasions are linked to invasive root symbionts., The New phytologist, vol. 237 no. 1 (January, 2023), pp. 16-21 [doi]
  11. Milani, T; Hoeksema, JD; Jobbágy, EG; Rojas, JA; Vilgalys, R; Teste, FP, Co-invading ectomycorrhizal fungal succession in pine-invaded mountain grasslands, Fungal Ecology, vol. 60 (December, 2022) [doi]  [abs]
  12. Hackman, JJ; Rose, BD; Frank, HER; Vilgalys, R; Cook, RL; Garcia, K, NPK fertilizer use in loblolly pine plantations: Who are we really feeding?, Forest Ecology and Management, vol. 520 (September, 2022) [doi]  [abs]
  13. Gryganskyi, AP; Nie, Y; Hajek, AE; Hodge, KT; Liu, X-Y; Aadland, K; Voigt, K; Anishchenko, IM; Kutovenko, VB; Kava, L; Vuek, A; Vilgalys, R; Huang, B; Stajich, JE, The Early Terrestrial Fungal Lineage of Conidiobolus-Transition from Saprotroph to Parasitic Lifestyle., Journal of fungi (Basel, Switzerland), vol. 8 no. 8 (July, 2022), pp. 789 [doi]  [abs]
  14. Erlandson, SR; Margis, R; Ramirez, A; Nguyen, N; Lofgren, LA; Liao, H-L; Vilgalys, R; Kennedy, PG; Peay, KG, Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens., The New phytologist, vol. 234 no. 6 (June, 2022), pp. 1910-1913 [doi]  [abs]
  15. Fremin, BJ; Bhatt, AS; Kyrpides, NC; Global Phage Small Open Reading Frame (GP-SmORF) Consortium, Thousands of small, novel genes predicted in global phage genomes., Cell reports, vol. 39 no. 12 (June, 2022), pp. 110984 [doi]  [abs]
  16. Barge, EG; Leopold, DR; Rojas, A; Vilgalys, R; Busby, PE, Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism., Molecular ecology, vol. 31 no. 10 (May, 2022), pp. 3018-3030 [doi]  [abs]
  17. Wang, H; Tian, J; Chen, H; Ho, M; Vilgalys, R; Bu, ZJ; Liu, X; Richardson, CJ, Vegetation and microbes interact to preserve carbon in many wooded peatlands, Communications Earth and Environment, vol. 2 no. 1 (December, 2021) [doi]  [abs]
  18. Liao, HL; Bonito, G; Hameed, K; Wu, SH; Chen, KH; Labbé, J; Schadt, CW; Tuskan, GA; Martin, F; Kuo, A; Barry, K; Grigoriev, IV; Vilgalys, R, Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi, Frontiers in Microbiology, vol. 12 (November, 2021) [doi]  [abs]
  19. Tian, J; Wang, H; Vilgalys, R; Ho, M; Flanagan, N; Richardson, CJ, Response of fungal communities to fire in a subtropical peatland, Plant and Soil, vol. 466 no. 1-2 (September, 2021), pp. 525-543 [doi]  [abs]
  20. Peng, L; Shan, X; Wang, Y; Martin, F; Vilgalys, R; Yuan, Z, Hybrid Genome Assembly and Gene Repertoire of the Root Endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes)., Molecular plant-microbe interactions : MPMI, vol. 34 no. 6 (June, 2021), pp. 711-714 [doi]  [abs]
  21. Lofgren, LA; Nguyen, NH; Vilgalys, R; Ruytinx, J; Liao, H-L; Branco, S; Kuo, A; LaButti, K; Lipzen, A; Andreopoulos, W; Pangilinan, J; Riley, R; Hundley, H; Na, H; Barry, K; Grigoriev, IV; Stajich, JE; Kennedy, PG, Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi., The New phytologist, vol. 230 no. 2 (April, 2021), pp. 774-792 [doi]  [abs]
  22. Vélez, JM; Morris, RM; Vilgalys, R; Labbé, J; Schadt, CW, Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives., PloS one, vol. 16 no. 1 (January, 2021), pp. e0231367 [doi]  [abs]
  23. Bazzicalupo, AL; Ruytinx, J; Ke, Y-H; Coninx, L; Colpaert, JV; Nguyen, NH; Vilgalys, R; Branco, S, Fungal heavy metal adaptation through single nucleotide polymorphisms and copy-number variation., Molecular ecology, vol. 29 no. 21 (November, 2020), pp. 4157-4169 [doi]  [abs]
  24. Miyauchi, S; Kiss, E; Kuo, A; Drula, E; Kohler, A; Sánchez-García, M; Morin, E; Andreopoulos, B; Barry, KW; Bonito, G; Buée, M; Carver, A; Chen, C; Cichocki, N; Clum, A; Culley, D; Crous, PW; Fauchery, L; Girlanda, M; Hayes, RD; Kéri, Z; LaButti, K; Lipzen, A; Lombard, V; Magnuson, J; Maillard, F; Murat, C; Nolan, M; Ohm, RA; Pangilinan, J; Pereira, MDF; Perotto, S; Peter, M; Pfister, S; Riley, R; Sitrit, Y; Stielow, JB; Szöllősi, G; Žifčáková, L; Štursová, M; Spatafora, JW; Tedersoo, L; Vaario, L-M; Yamada, A; Yan, M; Wang, P; Xu, J; Bruns, T; Baldrian, P; Vilgalys, R; Dunand, C; Henrissat, B; Grigoriev, IV; Hibbett, D; Nagy, LG; Martin, FM, Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits., Nature communications, vol. 11 no. 1 (October, 2020), pp. 5125 [doi]  [abs]
  25. Peng, J; Rojas, JA; Sang, H; Proffer, TJ; Outwater, CA; Vilgalys, R; Sundin, GW, Draft Genome Sequence Resource for Blumeriella jaapii, the Cherry Leaf Spot Pathogen., Phytopathology, vol. 110 no. 9 (September, 2020), pp. 1507-1510 [doi]  [abs]
  26. Czaplicki, LM; Redfern, LK; Cooper, EM; Ferguson, PL; Vilgalys, R; Gunsch, CK, Investigating the mycobiome of the Holcomb Creosote Superfund Site., Chemosphere, vol. 252 (August, 2020), pp. 126208 [doi]  [abs]
  27. Hoeksema, JD; Averill, C; Bhatnagar, JM; Brzostek, E; Buscardo, E; Chen, KH; Liao, HL; Nagy, L; Policelli, N; Ridgeway, J; Rojas, JA; Vilgalys, R, Ectomycorrhizal Plant-Fungal Co-invasions as Natural Experiments for Connecting Plant and Fungal Traits to Their Ecosystem Consequences, Frontiers in Forests and Global Change, vol. 3 (July, 2020) [doi]  [abs]
  28. Zhang, K; Bonito, G; Hsu, CM; Hameed, K; Vilgalys, R; Liao, HL, Mortierella elongata increases plant biomass among non-leguminous crop species, Agronomy, vol. 10 no. 5 (May, 2020) [doi]  [abs]
  29. Steidinger, BS; Bhatnagar, JM; Vilgalys, R; Taylor, JW; Qin, C; Zhu, K; Bruns, TD; Peay, KG, Ectomycorrhizal fungal diversity predicted to substantially decline due to climate changes in North American Pinaceae forests, Journal of Biogeography, vol. 47 no. 3 (March, 2020), pp. 772-782 [doi]  [abs]
  30. 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]
  31. 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]
  32. Millet, LJ; Aufrecht, J; Labbé, J; Uehling, J; Vilgalys, R; Estes, ML; Miquel Guennoc, C; Deveau, A; Olsson, S; Bonito, G; Doktycz, MJ; Retterer, ST, Increasing access to microfluidics for studying fungi and other branched biological structures, Fungal Biology and Biotechnology, vol. 6 no. 1 (June, 2019) [doi]  [abs]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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), vol. 8 no. 6 (May, 2018), pp. 2007-2018 [doi]  [abs]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. 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]
  47. 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]
  48. 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]
  49. 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]
  50. 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. 13 no. 1 (January, 2017), pp. e1006575 [doi]  [abs]
  51. 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]
  52. 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]
  53. 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]
  54. 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]
  55. 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]
  56. 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]
  57. 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]
  58. 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]
  59. 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]
  60. 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, ISSN 0962-1083 [doi]  [abs]
  61. 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 (April, 2015), pp. 133-137, Elsevier BV, ISSN 1754-5048 [doi]  [abs]
  62. 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, ISSN 0028-646X [doi]  [abs]
  63. 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 (December, 2014), pp. 399-425, BioOne, ISSN 0181-1584 [doi]  [abs]
  64. 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, ISSN 1462-2912 [doi]  [abs]
  65. 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 (October, 2014), pp. e01072-e01014 [doi]  [abs]
  66. 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, ISSN 0962-1083 [doi]  [abs]
  67. 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, ISSN 0027-8424 [doi]  [abs]
  68. 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, ISSN 0378-1097 [doi]  [abs]
  69. 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, ISSN 1560-2745 [doi]  [abs]
  70. Benítez, M-S; Hersh, MH; Vilgalys, R; Clark, JS, Pathogen regulation of plant diversity via effective specialization., Trends in ecology & evolution, vol. 28 no. 12 (December, 2013), pp. 705-711, ISSN 0169-5347 [24091206], [doi]  [abs]
  71. 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)
  72. 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
  73. Golonka, AM; Vilgalys, R, Nectar Inhabiting Yeasts in Virginian Populations of Silene latifolia (Caryophyllaceae) and Coflowering Species, American midland naturalist., vol. 169 no. 2 (April, 2013), pp. 235-258, University of Notre Dame, ISSN 0003-0031 [doi]  [abs]
  74. 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, ISSN 1055-7903 [doi]
  75. 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, ISSN 0962-1083 [doi]  [abs]
  76. 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, ISSN 0038-0717 [doi]  [abs]
  77. 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
  78. 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, ISSN 1932-6203 [doi]  [abs]
  79. 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. 78, FRONTIERS MEDIA SA, ISSN 1664-302X [doi]  [abs]
  80. 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, ISSN 1932-6203 [doi]  [abs]
  81. 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, ISSN 1878-6146 [doi]  [abs]
  82. 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, ISSN 0032-079X [doi]  [abs]
  83. 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, ISSN 1462-2912 [doi]  [abs]
  84. 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, ISSN 1754-5048 [doi]  [abs]
  85. 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, ISSN 0012-9658 [22624206], [doi]  [abs]
  86. 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]
  87. Bonito, G., Timothy Brenneman and Rytas Vilgalys., Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). ., Mycorrhiza. (2012), pp. 601-612
  88. Uehling, JK; Henkel, TW; Vilgalys, R; Smith, ME, Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests, Mycorrhiza (online), vol. 22 no. 7 (2012), pp. 577-581, ISSN 0940-6360 [doi]  [abs]
  89. 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]
  90. 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, ISSN 0027-5514 [doi]  [abs]
  91. Smith, ME; Henkel, TW; Uehling, JK; Fremier, AK; Clarke, HD; Vilgalys, R, Ectomycorrhizal fungal community in a tropical forest dominated by the Neotropical Dipterocarp, Pakaraimea dipterocarpaceae, PLOS ONE (in press), vol. 8 no. 1 (2012), pp. e55160 [doi]  [abs]
  92. Henkel, TW; Husbands, D; Bonito, GM; Vilgalys, R; Smith, ME, New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence, Mycologia, vol. in press no. 2 (2012), pp. 422-435 [doi]  [abs]
  93. Bonito; Gregory; Smith, ME; Nowak, M; Healy, RA; Guevara, G; Cázares, E; Kinoshita, A; Nouhra, ER; Domínguez, LS; Tedersoo, L; Murat, C; Wang, Y; Baldomero; Moreno, A; 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 (in press), vol. 8 no. 1 (2012), pp. e52765 [23300990], [doi]  [abs]
  94. 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 (2012), pp. 2195-2220, Springer Nature, ISSN 0960-3115 [doi]  [abs]
  95. Guevara; Gonzalo; Bonito, G; Trappe, JM; Cázares, E; Williams, G; Healy, RA; Schadt, CW; Vilgalys, R, New North American truffles (Tuber spp.) and their ectomycorrhizal associations., Mycologia, vol. 2012 no. 1 (2012), pp. 194-209 [doi]  [abs]
  96. Gryganskyi, AP; Humber, RA; Smith, ME; Hodge, K; Huang, B; Voigt, K; Vilgalys, R, Phylogenetic lineages in Entomophthoromycota., Persoonia., vol. 30 (2012), pp. 94-105 [doi]  [abs]
  97. 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 (2012), pp. 682.-694. [22877646], [doi]  [abs]
  98. 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, ISSN 1937-786X [doi]  [abs]
  99. Smith, ME; Henkel, TW; Aime, MC; Fremier, AK; Vilgalys, R, Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest, New Phytol, vol. 192 no. 3 (November, 2011), pp. 699-712, ISSN 0028-646X [entrez], [doi]  [abs]
  100. 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, ISSN 0940-6360 [doi]  [abs]
  101. 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, ISSN 1462-2912 [abstract], [doi]  [abs]
  102. 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, ISSN 0099-2240 [5934], [doi]  [abs]
  103. 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, ISSN 1878-6146 [S1878614611000250], [doi]  [abs]
  104. 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, ISSN 1754-5048 [doi]  [abs]
  105. 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, ISSN 1932-6203 [repository], [doi]  [abs]
  106. 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, ISSN 0962-1083 [doi]  [abs]
  107. 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, ISSN 0027-5514 [doi]  [abs]
  108. 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, ISSN 0960-8524 [doi]  [abs]
  109. 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, ISSN 0966-842X [doi]  [abs]
  110. 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, ISSN 1432-1890 [doi]  [abs]
  111. James, TY; Litvintseva, AP; Vilgalys, R; Morgan, JA; 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 Pathog, vol. 5 no. 5 (May, 2009), pp. e1000458, ISSN 1553-7366 [doi]  [abs]
  112. 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, ISSN 1535-9778 [doi]  [abs]
  113. 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, ISSN 1091-6490 [19004771], [doi]  [abs]
  114. 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, ISSN 1055-7903 [doi]  [abs]
  115. 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, ISSN 0027-5514  [abs]
  116. 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, ISSN 0027-5514  [abs]
  117. 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, ISSN 0027-5514  [abs]
  118. 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, ISSN 0002-9122 [doi]  [abs]
  119. 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, ISSN 1471-2148 [17854492], [doi]  [abs]
  120. 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, ISSN 0027-5514  [abs]
  121. 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, ISSN 0027-5514  [abs]
  122. 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, ISSN 0027-5514 [17682771], [doi]  [abs]
  123. 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, ISSN 0028-646X [doi]  [abs]
  124. Hibbett, DS; Binder, M; Bischoff, JF; Blackwell, M; Cannon, PF; Eriksson, O; Huhndorf, S; James, T; Kirk, PM; Lücking, R; Lumbsch, T; 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, YC; Gams, W; Geiser, DM; Griffith, GW; Gueidan, C; Hawksworth, DL; Hestmark, G; Hosaka, K; Humber, RA; Hyde, K; Koljalg, U; Kurtzman, CP; Larsson, KH; Lichtward, R; Longcore, J; Miadlikowska, J; Miller, A; Monclavo, JM; Mozley Standridge, S; Oberwinkler, F; Parmasto, E; Reeb, V; Rogers, JD; Roux, C; Ryvarden, L; Sampaio, JP; Schuessler, A; Sugiyama, J; Thorn, RG; Tibell, L; Untereiner, WA; Walker, C; Wang, Z; Weir, A; Weiss, M; White, M; Winka, K; Yao, YJ; Zhang, N, A higher-level phylogenetic classification of the Fungi, Mycological Research, vol. 111 no. Pt 5 (2007), pp. 509-547, ISSN 0953-7562 [doi]  [abs]
  125. 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, ISSN 0027-5514 [doi]  [abs]
  126. 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, ISSN 0027-5514 [doi]  [abs]
  127. 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, ISSN 0027-5514 [doi]  [abs]
  128. 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)), New Phytologist, vol. 172 no. 2 (October, 2006), pp. 377, WILEY, ISSN 0028-646X [doi]
  129. 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, ISSN 0012-9658  [abs]
  130. 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, ISSN 0012-9658 [16995628], [doi]  [abs]
  131. 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, ISSN 1055-7903 [doi]  [abs]
  132. 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, ISSN 1055-7903 [doi]  [abs]
  133. 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, ISSN 0016-6731 [doi]  [abs]
  134. 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, ISSN 0016-6731 [16322524], [doi]  [abs]
  135. 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, ISSN 0016-6731 [doi]  [abs]
  136. 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, ISSN 0016-6731 [doi]  [abs]
  137. 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, ISSN 0028-646X [doi]  [abs]
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  139. James, TY; Kauff, F; Schoch, C; Matheny, PB; Hofstetter, V; Cox, CJ; Celio, G; Gueidan, C; Fraker, E; Miadlikowska, J; Lumbsch, T; Rauhut, A; Reeb, V; Arnold, AE; Amtoft, A; Stajich, JE; Hosaka, K; Sung, GH; Johnson, D; O’Rourke, B; 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; 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; Buck, WR; Cole, MS; Diederich, P; Printzen, C; Schmitt, I; Schultz, M; Yahr, R; Zavarzin, A; Hibbett, DH; Lutzoni, F; McLaughlin, DJ; Spatafora, JW; Vilgalys, R, Reconstructing the early evolution of the Fungi using a six-gene phylogeny, Nature, vol. 443 no. 7113 (2006), pp. 818-822, ISSN 1476-4687 [17051209], [doi]  [abs]
  140. 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, ISSN 0028-646X [doi]  [abs]
  141. Wallenstein, MD; Vilgalys, RJ, Quantitative analyses of nitrogen cycling genes in soils, Pedobiologia, vol. 49 no. 6 (November, 2005), pp. 665-672, Elsevier BV, ISSN 0031-4056 [doi]  [abs]
  142. 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, ISSN 0099-2240 [16151147], [doi]  [abs]
  143. 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, ISSN 0099-2240 [16000830], [doi]  [abs]
  144. 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, ISSN 0099-2240 [doi]  [abs]
  145. 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, ISSN 0953-7562 [doi]  [abs]
  146. 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, ISSN 0095-1137 [doi]  [abs]
  147. Litvintseva, AP; Kestenbaum, L; Vilgalys, R; Mitchell, TG, Comparative analysis of environmental and clinical populations of Cryptococcus neoformans., J Clin Microbiol, vol. 43 no. 2 (February, 2005), pp. 556-564, ISSN 0095-1137 [15695645], [doi]  [abs]
  148. 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, ISSN 0002-9122 [doi]  [abs]
  149. 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)
  150. Diezmann, S; Cox, CJ; Schönian, G; Vilgalys, RJ; Mitchell, TG, Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis., J Clin Microbiol, vol. 42 no. 12 (December, 2004), pp. 5624-5635, ISSN 0095-1137 [15583292], [doi]  [abs]
  151. 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, ISSN 0962-1083 [doi]  [abs]
  152. 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, ISSN 0002-9122 [21652303], [doi]  [abs]
  153. Peintner, U; Moncalvo, JM; Vilgalys, R, Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota)., Mycologia, vol. 96 no. 5 (September, 2004), pp. 1042-1058, Informa UK Limited [doi]  [abs]
  154. 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, ISSN 1087-1845 [doi]  [abs]
  155. 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, ISSN 0016-6731 [15238516], [doi]  [abs]
  156. 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, ISSN 1087-1845 [doi]  [abs]
  157. Zervakis, GI; Moncalvo, J-M; Vilgalys, R, Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa., Microbiology (Reading, England), vol. 150 no. Pt 3 (March, 2004), pp. 715-726, ISSN 1350-0872 [doi]  [abs]
  158. 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., Eukaryot Cell, vol. 2 no. 6 (December, 2003), pp. 1162-1168, ISSN 1535-9778 [14665451], [doi]  [abs]
  159. 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, ISSN 0002-9122 [21653342], [doi]  [abs]
  160. Vilgalys, R, Taxonomic misidentification in public DNA databases., The New phytologist, vol. 160 no. 1 (October, 2003), pp. 4-5, WILEY [doi]  [abs]
  161. 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, ISSN 0940-6360 [doi]  [abs]
  162. 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, ISSN 0031-949X [18942984], [doi]  [abs]
  163. 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 [doi]  [abs]
  164. 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, ISSN 0962-1083 [12535090], [doi]  [abs]
  165. Hofstetter, V; Clemencon, 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 (September, 2002), pp. 1043-1059, Elsevier BV [doi]  [abs]
  166. 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 (July, 2002), pp. 620-629, Informa UK Limited, ISSN 0027-5514 [doi]  [abs]
  167. 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]
  168. 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]
  169. Moncalvo, JM; Vilgalys, R; Redhead, SA; Johnson, JE; James, TY; Catherine Aime, M; Hofstetter, V; Verduin, SJ; Larsson, E; Baroni, TJ; Greg Thorn, R; Jacobsson, S; Clémençon, H; Miller, OK, One hundred and seventeen clades of euagarics., Mol Phylogenet Evol, vol. 23 no. 3 (June, 2002), pp. 357-400, ISSN 1055-7903 [doi]  [abs]
  170. Redhead, SA; Moncalvo, JM; Vilgalys, R; Lutzoni, F, Phylogeny of agarics: partial systematics solutions for bryophilous omphalinoid agarics outside of the Agaricales (Euagarics)., Mycotaxon., vol. 82 (June, 2002), pp. 151-168  [abs]
  171. 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, ISSN 0027-5514 [21156515], [doi]  [abs]
  172. 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, ISSN 0027-5514 [21156516], [doi]  [abs]
  173. Henkel, TW; Terborgh, J; Vilgalys, RJ, Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana., Mycological research., vol. 106 no. 5 (May, 2002), pp. 515-531, Elsevier BV [doi]  [abs]
  174. Peintner, U; Moser, M; Vilgalys, R, Thaxterogaster is a taxonomic synonym of Cortinarius: new combinations and new names., Mycotaxon., vol. 81 (March, 2002), pp. 177-184  [abs]
  175. Xu, J; Luo, G; Vilgalys, RJ; Brandt, ME; Mitchell, TG, Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD., Microbiology (Reading), vol. 148 no. Pt 1 (January, 2002), pp. 203-212, ISSN 1350-0872 [11782512], [doi]  [abs]
  176. 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]
  177. 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 (December, 2001), pp. 2168-2179, WILEY [doi]  [abs]
  178. Gonzalez, D; Carling, DE; Kuninaga, S; Vilgalys, R; Cubeta, MA, Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs., Mycologia, vol. 93 no. 6 (November, 2001), pp. 1138-1150, JSTOR, ISSN 0027-5514 [doi]  [abs]
  179. Mueller, GM; Wu, Q; Huang, Y; Guo, S; Aldana‐Gomez, R; Vilgalys, R, Assessing biogeographic relationships between North American and Chinese macrofungi, Journal of biogeography, vol. 28 no. 2 (February, 2001), pp. 271-281, WILEY, ISSN 0305-0270 [doi]  [abs]
  180. 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 (February, 2001), pp. 164-172, Elsevier BV [doi]  [abs]
  181. 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, ISSN 0962-1083 [doi]  [abs]
  182. 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, ISSN 0172-8083 [doi]  [abs]
  183. Xu, J; Onyewu, C; Yoell, HJ; Ali, RY; Vilgalys, RJ; Mitchell, TG, Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans., Antimicrob Agents Chemother, vol. 45 no. 2 (February, 2001), pp. 420-427, ISSN 0066-4804 [11158735], [doi]  [abs]
  184. Wagner, RP; Crow, JF, The other fly room: J. T. Patterson and Texas genetics., Genetics, vol. 157 no. 1 (January, 2001), pp. 1-5, ISSN 0016-6731 [doi]
  185. 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, ISSN 0040-0262 [doi]  [abs]
  186. 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, ISSN 0016-6731  [abs]
  187. 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 Genet Biol, vol. 31 no. 3 (December, 2000), pp. 189-203, ISSN 1087-1845 [11273681], [doi]  [abs]
  188. Xu, J; Vilgalys, R; Mitchell, TG, Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans., Mol Ecol, vol. 9 no. 10 (October, 2000), pp. 1471-1481, ISSN 0962-1083 [11050543], [doi]  [abs]
  189. 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 (July, 2000), pp. 431-435, ISSN 0959-3993 [doi]  [abs]
  190. 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]
  191. Isikhuemhen, OS; Moncalvo, JM; Nerud, F; Vilgalys, R, Mating compatibility and phylogeography in Pleurotus tuberregium., Mycological research., vol. 104 no. 6 (June, 2000), pp. 732-737, Elsevier BV [doi]  [abs]
  192. 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, ISSN 1063-5157 [12118409], [doi]  [abs]
  193. 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., Curr Microbiol, vol. 40 no. 4 (April, 2000), pp. 269-273, ISSN 0343-8651 [10688697], [doi]  [abs]
  194. 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 (March, 2000), pp. 336-350, Canadian Science Publishing [doi]  [abs]
  195. Xu, J; Ramos, AR; Vilgalys, R; Mitchell, TG, Clonal and spontaneous origins of fluconazole resistance in Candida albicans., J Clin Microbiol, vol. 38 no. 3 (March, 2000), pp. 1214-1220, ISSN 0095-1137 [10699025], [doi]  [abs]
  196. 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]
  197. 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]
  198. 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]
  199. 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., Med Mycol, vol. 38 Suppl 1 (2000), pp. 189-197, ISSN 1369-3786 [11204145], [doi]  [abs]
  200. 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, ISSN 0933-7407 [11291578]  [abs]
  201. 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]
  202. Forche, A; Schönian, G; Gräser, Y; Vilgalys, R; Mitchell, TG, Genetic structure of typical and atypical populations of Candida albicans from Africa., Fungal Genet Biol, vol. 28 no. 2 (November, 1999), pp. 107-125, ISSN 1087-1845 [10587473], [doi]  [abs]
  203. 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]
  204. 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, ISSN 1369-3786 [doi]  [abs]
  205. 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., J Bacteriol, vol. 181 no. 4 (February, 1999), pp. 1369-1373, ISSN 0021-9193 [9973371], [doi]  [abs]
  206. 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]
  207. 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]
  208. Xu, J; Mitchell, TG; Vilgalys, R, PCR-restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candida albicans., Mol Ecol, vol. 8 no. 1 (January, 1999), pp. 59-73, ISSN 0962-1083 [9919698], [doi]  [abs]
  209. 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]
  210. Xu, J; Vilgalys, R; Mitchell, TG, Colony size can be used to determine the MIC of fluconazole for pathogenic yeasts., J Clin Microbiol, vol. 36 no. 8 (August, 1998), pp. 2383-2385, ISSN 0095-1137 [9666032], [doi]  [abs]
  211. 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]
  212. Cubeta, MA; Vilgalys, R, Population Biology of the Rhizoctonia solani Complex., Phytopathology, vol. 87 no. 4 (April, 1997), pp. 480-484 [doi]
  213. McPartland, JM; Vilgalys, RJ; Cubeta, MA, Mushroom poisoning., American family physician, vol. 55 no. 5 (April, 1997), pp. 1797-1812, ISSN 0002-838X [9105206]  [abs]
  214. 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, ISSN 0737-4038 [doi]  [abs]
  215. 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., Proc Natl Acad Sci U S A, vol. 93 no. 22 (October, 1996), pp. 12473-12477, ISSN 0027-8424 [8901606], [doi]  [abs]
  216. Haase, G, Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens., J Clin Microbiol, vol. 34 no. 8 (August, 1996), pp. 2049-2050, ISSN 0095-1137 [7615749], [doi]  [abs]
  217. 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, ISSN 0027-8424 [doi]  [abs]
  218. Spatafora, JW; Mitchell, TG; Vilgalys, R, Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens., J Clin Microbiol, vol. 33 no. 5 (May, 1995), pp. 1322-1326, ISSN 0095-1137 [7615749], [doi]  [abs]
  219. Lutzoni, F; Vilgalys, R, Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichens., Cryptogamic botany., vol. 5 no. 1 (February, 1995), pp. 71-81
  220. 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, ISSN 0027-8424 [doi]
  221. 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]
  222. Hopple, JSJR; Vilgalys, R, Phylogenetic relationships among coprinoid taxa and allies based on data from restriction site mapping of nuclear rDNA., Mycologia, vol. 86 no. 1 (February, 1994), pp. 96-107 [doi]
  223. 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]
  224. 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]
  225. Steele, KP; Vilgalys, R, Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK, Systematic botany., vol. 19 no. 1 (January, 1994), pp. 126-142 [doi]  [abs]
  226. Cubeta, MA; Briones-Ortega, R; Vilgalys, R, Reassessment of heterokaryon formation in Rhizoctonia solani anastomosis group 4., Mycologia, vol. 85 no. 5 (September, 1993), pp. 777-787 [doi]
  227. 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., J Clin Microbiol, vol. 31 no. 9 (September, 1993), pp. 2274-2280, ISSN 0095-1137 [8408543], [doi]  [abs]
  228. 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]
  229. 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]
  230. Hibbett, DS; Vilgalys, R, Phylogenetic relationships of Lentinus (Basidiomycotina) inferred from molecular and morphological characters, Systematic botany., vol. 18 no. 3 (January, 1993), pp. 407-433 [doi]  [abs]
  231. 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, ISSN 1055-7903 [doi]  [abs]
  232. 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]
  233. Mishler, BD; Thrall, PH; Hopple, JSJR; De Luna, E; Vilgalys, R, A molecular approach to the phylogeny of bryophytes: cladistic analysis of chloroplast-encoded 16S and 23S ribosomal RNA genes., Bryologist., vol. 95 no. 2 (January, 1992), pp. 172-180 [doi]
  234. Cubeta, MA; Echandi, E; Abernethy, T; Vilgalys, R, Characterization of anastomosis groups of binucleate Rhizoctonia species using restriction analysis of an amplified ribosomal RNA gene, Phytopathology, vol. 81 no. 11 (November, 1991), pp. 1395-1400 [doi]  [abs]
  235. 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 (July, 1991), pp. 425-439, ISSN 0027-5514 [doi]  [abs]
  236. Vilgalys, R, Speciation and species concepts in the Collybia dryophila complex, Mycologia, vol. 83 no. 6 (January, 1991), pp. 758-773, JSTOR [doi]  [abs]
  237. Vilgalys, D; Gonzalez, D, Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola., Current genetics, vol. 18 no. 3 (October, 1990), pp. 277-280, ISSN 0172-8083 [doi]  [abs]
  238. 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, ISSN 0021-9193 [doi]  [abs]
  239. Vilgalys, R; Gonzalez, D, Ribosomal DNA restriction fragment length polymorphisms in Rhizoctonia solani, Phytopathology, vol. 80 no. 2 (February, 1990), pp. 151-158 [doi]  [abs]
  240. Vilgalys, R, Genetic relatedness among anastomosis groups in Rhizoctonia as measured by DNA/DNA hybridization., Phytopathology, vol. 78 no. 6 (June, 1988), pp. 698-702 [doi]  [abs]
  241. Vilgalys, RJ; Johnson, JL, Extensive genetic divergence associated with speciation in filamentous fungi., Proceedings of the National Academy of Sciences of the United States of America, vol. 84 no. 8 (April, 1987), pp. 2355-2358 [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.
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