Fungal mating systems and population genetics
  • James, T. Y., S. Sun, W. Li, J. Heitman, H.-C. Kuo, Y.-H. Lee, F. O. Asiegbu, and Å. Olson. (2013). Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Mycologia 105: 1374-1390. pdf
  • van Diepen, L. T. A., Å, Olson, K. Ihrmark, J. Stenlid, and T. Y. James. (2013). Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion. Mol. Biol. Evol. 30: 2286-2301. pdf
  • Heitman, J. E., S. Sun, and T. Y. James. (2013). Evolution of fungal sexual reproduction. Mycologia 105: 1-27. pdf
  • Malloure, B. M., and T. Y. James. (2013). Inbreeding depression in urban environments of the bird’s nest fungus Cyathus stercoreus (Basidiomycota). Heredity 110: 355-362. pdf
  • James, T. Y. (2012). Ancient yet fast: rapid evolution of mating genes and mating systems in Fungi. In R. S. Singh, J. Xu, and R. J. Kulathinal [eds]. pp. 187-200. Evolution in the Fast Lane: Rapidly Evolving Genes and Genetic Systems. Oxford University Press, Oxford, U.K. pdf
  • van Peer, A. F., S.-Y. Park, P.-G. Shin, K.-Y. Jang, Y.-B. Yoo, Y.-J. Park, B.-M. Lee, G.-H. Sung, T. Y. James, and W.-S. Kong. (2011). Comparative genomics of the mating-type loci of the mushroom Flammulina velutipes reveals widespread synteny and recent inversions. PLoS ONE 6: e22249. pdf
  • James, T. Y., M. Lee, and L. T. A. van Diepen. (2011). A single mating-type locus comprised of homeodomain genes promotes nuclear migration and heterokaryosis in the white-rot fungus Phanerochaete chrysosporium. Eukaryot. Cell 10: 249-261. pdf
  • Li, M. J. Liang, Y. Li, B. Feng, Z.-L. Yang, T. Y. James, and J. Xu. (2010). Genetic diversity of Dahongjun, the commercially important “Big Red Mushroom” from southern China. PLoS One 5: e10684. pdf
  • Strandberg, R., K. Nygren, A. Menkis, T. Y. James, L. Wik, J. E. Stajich, and H. Johannesson. 2010. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genet. Biol. 47: 869-878. pdf
  • 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


Chytridiomycosis of amphibians
  • Rosenblum, E. B., T. Y. James, K. R. Zamudio, T. J. Poorten, D. Ilut, D. Rodriguez, J. M. Eastman, K. Richards-Hrdlicka, S. Joneson, T. S. Jenkinson, J. E. Longcore, G. Parra Olea, L. F. Toledo, M. L. Arellano, E. M. Medina, S. Restrepo, S. V. Flechas, L. Berger, C. J. Briggs, J. E. Stajich. (2013). Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proc. Natl. Acad. Sci. U. S. A. 110: 9385-9390. pdf
  • Schloegel, L. M., L. F. Toledo, J. E. Longcore, S. E. Greenspan, C. A. Viera, M. Lee, S. Zhao, C. Wangen, C. M. Ferreira, M. Hipolito, A. J. Davies, P. Daszak, C. A. Cuomo, T. Y. James. (2012). Novel, panzootic, and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade. Mol. Ecol. 21: 5162-5177. pdf
  • Garland, S., T. Y. James, D. Blair, L. Berger, and L. F. Skerratt. (2011). Polymorphic repetitive loci of the amphibian pathogen Batrachochytrium dendrobatidis. Dis. Aquat. Organ. 97: 1-9. pdf
  • Rosenblum, E. B., M. C. Fisher, T. Y. James, J. E. Stajich, J. E. Longcore, L. R. Gentry, and T. J. Poorten. (2010). A molecular perspective on the biology of the emerging pathogen Batrachochytrium dendrobatidis. Dis. Aquat. Org. 92: 131-147. pdf
  • Schloegel, L. M., C. M. Ferreira, T. Y. James, M. Hipolito, J. E. Longcore, A. D. Hyatt, M. Yabsley, A. M. C. Martins-Martins, R. Mazzoni, A. J. Davies, and P. Daszak. (2010). The North American Bullfrog (Rana catesbeiana) as a reservoir for the spread of Batrachochytrium dendrobatidis in Brazil. Animal Conserv. 13: 53-61. pdf
  • 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


Fungal phylogeny
  • James, T. Y., A. Pelin, L. Bonen, S. Arhendt, D. Sain, N. Corradi, and J. E. Stajich. (2013). Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr. Biol. 23: 1548-1553. pdf
  • James, T. Y., M. L. Berbee. (2012). No jacket required- new fungal lineage defies dress code. BioEssays 34: 94-102. pdf
  • Rosling, A., F. Cox, K. Cruz-Martinez, K. Ihrmark, G.-A. Grelet, B. L. Lindahl, A. Menkis, and T. Y. James (2011). Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. Science 333: 876-879. pdf
  • Stajich, J. E., M. L. Berbee, M. Blackwell, D. S. Hibbett, T. Y. James, J. W. Spatafora, and J. W. Taylor. 2009. The Fungi. Curr. Biol. 19: R840-R845. pdf
  • 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
  • Longcore, J. E. P. M. Letcher, and T. Y. James. (2011). Homolaphlyctis polyrhiza gen. et sp. nov., a species in the Rhizophydiales (Chytridiomycetes) with multiple rhizoidal axes. MycoTaxon 118: 433-440. pdf
  • Porter, T. M., W. Martin, T. Y. James, J. E. Longcore, F. Gleason, P. H. Adler, P. M. Letcher, and R. Vilgalys (2011). Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal data. Fungal Biol. 115: 381-392. pdf
  • 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

Fungal genomics and molecular evolution
  • Ferandez-Fueyo, E., et al. (2012). Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc. Natl. Acad. Sci. U. S. A. 109: 5458-5463. pdf
  • Å. Olson, et al. (2012). Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol. 194: 1001-1013. pdf
  • Padamsee, M., et al. (2012). The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet. Biol. 49: 217-226. pdf
  • Stajich, J. E., (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc. Natl. Acad. Sci. U. S. A. 107:11889-11894. pdf
  • Parrent, J. L., T. Y. James, R. Vasaitis and A. F. S. Taylor. (2009). Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evol. Biol. 9: 148. pdf
  • Martinez, D., et al. (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA. 106: 1954-1959. pdf
  • Hoegger, P. J., S. Kilaru, T. Y. James, J. R. Thacker, and U. Kües. (2006). Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS Journal 273: 2308-2326. pdf

Fungal ecology
  • Diez, J. M., T. Y. James, McMunn, M., Ibáñez, I. (2013). Predicting species-specific responses of fungi to climatic variation using historical records. Global Change Biol. 19: 3145-3154. pdf
  • Henkel, T. W., T. Y. James, S. L. Miller, M. C. Aime, and O. K. Miller, Jr. 2006. The mycorrhizal status of Pseudotulostoma volvata (Elaphomycetaceae, Eurotiales, Ascomycota). Mycorrhiza 16: 241-244. pdf