Mushroom mating systems and population genetics
  • James, T. Y., S. Johannson, and H. Johannesson. (2009). Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum. Mycol. Res. 113: 583-590. pdf
  • James, T. Y., J. Stenlid, Å. Olson, and H. Johannesson. (2008). Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum. Evolution 62: 2279-2296. pdf
  • James, T. Y. (2007). Analysis of mating-type locus organization and synteny in mushroom fungi- beyond model species. pp. 317-331. In J. Heitman, J. Kronstad, J. W. Taylor, and L. A. Casselton [eds.]. Sex in fungi: molecular determination and evolutionary implications. ASM Press, Washington, D. C. pdf
  • James, T. Y., P. Srivilai, U. Kües, and R. Vilgalys. (2006). Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function. Genetics 172: 1877-1891. pdf
  • James, T. Y., S.-R. Liou, and R. Vilgalys. (2004). The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor. Fungal Genet. Biol. 41: 813-825. pdf
  • James, T. Y., U. Kües, S. A. Rehner, and R. Vilgalys. (2004). Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi. Fungal Genet. Biol. 41: 381-390. pdf
  • James, T. Y., and R. Vilgalys (2001). Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling. Mol. Ecol.10: 471-480. pdf
  • Kües, U., T. Y. James, R. Vilgalys, and M. Challen (2001). The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic basidiomycete Coprinus bilanatus. Curr. Genet. 39: 16-24. pdf
  • James, T. Y., J.-M. Moncalvo, S. Li, and R. Vilgalys (2001). Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics. 157: 149-161. pdf
  • James, T. Y., D. Porter, J. L. Hamrick, and R. Vilgalys. (1999). Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune. Evolution 53: 1665-1677. pdf

Fungal phylogeny
  • Hibbett, D. S., et al. (2007). A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111: 509-547. pdf
  • White, M. M., T. Y. James, K. O’Donnell, M. J. Cafaro, Y. Tanabe, and J. Sugiyama. (2006). Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98: 872-884. pdf
  • James, T. Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. Cox, G. Celio, and the AFTOL working group (2006). Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822. pdf
  • Lutzoni, F., et al. (2004). Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits Am. J. Bot. 91: 1446-1480. pdf
  • Moncalvo, J.-M., R. Vilgalys, S. A. Redhead, J. E. Johnson, T. Y. James, M. C. Aime, V. Hofstetter, S. Verduin, E. Larsen, T. J. Baroni, R. G. Thorn, S. Jacobsson, H. Clémençon, and O. K. Miller, Jr. (2002) One hundred and seventeen clades of euagarics. Mol. Phylogenet. Evol. 23: 357-400. pdf

Chytrid systematics
  • Simmons, D. R., T. Y. James, A. F. Meyer, and J. E. Longcore. (2009). Lobulomycetales, a new order in the Chytridiomycota. Mycol. Res. 113: 450-160. pdf
  • Hoffman, Y., C. Aflalo, A. Zarka, J. Gutman, T. Y. James, and S. Boussiba. (2008). Isolation and characterization of a novel chytrid species (Phylum Blastocladiomycota), parasitic on the green alga Haematococcus. Mycol. Res. 112: 70-81. pdf
  • James, T. Y., P. M. Letcher, J. E. Longcore, S. E. Mozley-Standridge, D. Porter, M. J. Powell, G. W. Griffith, R. Vilgalys (2006). A molecular phylogeny of the flagellated Fungi (Chytridiomycota) and a proposal for a new phylum (Blastocladiomycota). Mycologia 98: 860-871. pdf
  • James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. (2000) Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78: 336-350. pdf

Chytridiomycosis of amphibians
  • James T. Y., A. P. Litvintseva, , R. Vilgalys, J. A. T. Morgan, J. W. Taylor, M. C. Fisher, L. Berger, C. Weldon, L. du Preez, and J. E. Longcore. (2009) Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations. PLoS Pathog. 5: e1000458. pdf
  • Walker, S. F., J. Bosch, T. Y. James, A. P. Litvintseva, J. A. O. Valls, S. Piña, G. García, G. A. Rosa, A. A. Cunningham, S. Hole, R. Griffiths, and M. C. Fisher. (2008). Introduced pathogens threaten species recovery programs. Current Biology 18: R853-R854. pdf
  • Harris, R. N., T. Y. James, A. Lauer, M. A. Simon, and A. Patel. (2006). Amphibian pathogen Batrachochytrium dendrobatidis is inhibited by the cutaneous bacteria of amphibian species. EcoHealth 3: 53-56. pdf
  • James, T. Y., and R. Vilgalys. (2006). Amphibian chytridiomycosis as an emerging infectious disease of wildlife: what can we learn from the earliest diverging fungi? pp. 271-278. In J. Heitman, S. G. Filler, J. E. Edwards, Jr., and A. P. Mitchell [eds.]. Molecular Principals of Fungal Pathogenesis. ASM Press, Washington, D. C. pdf
  • Morehouse, E. A., T. Y. James, A. R. D. Ganley, R. Vilgalys, L. Berger, P. J. Murphy, and J. E. Longcore. (2003). Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone. Mol. Ecol. 12: 395-403. pdf