Most Recent Publications

Taylor, John W, and Bridget M Barker. 2019. “The Endozoan, Small-Mammal Reservoir Hypothesis and the Life Cycle of Coccidioides Species.” Medical Mycology 57 (Supplement_1): S16–20.

Vilela, Raquel, Richard A. Humber, John W. Taylor, and Leonel Mendoza. 2019. “Phylogenetic and Physiological Traits of Oomycetes Originally Identified as Lagenidium Giganteum from Fly and Mosquito Larvae.” Mycologia 111 (3): 408–22.

Gao, Cheng, Liliam Montoya, Ling Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Robert B. Hutmacher, et al. 2019. “Strong Succession in Arbuscular Mycorrhizal Fungal Communities.” The ISME Journal 13 (1): 214–26.

Sylvain, Iman A., Rachel I. Adams, and John W. Taylor. 2019. “A Different Suite: The Assemblage of Distinct Fungal Communities in Water-Damaged Units of a Poorly-Maintained Public Housing Building.” Edited by Vishnu Chaturvedi. PLoS ONE 14 (3): e0213355.

Hibbett, David S., Meredith Blackwell, Timothy Y. James, Joseph W. Spatafora, John W. Taylor, and Rytas Vilgalys. 2018. “Phylogenetic Taxon Definitions for Fungi, Dikarya, Ascomycota and Basidiomycota.” IMA Fungus 9 (2): 291–98.

Bruns, Thomas D., Nicolas Corradi, Dirk Redecker, John W. Taylor, and Maarja Öpik. 2018. “Glomeromycotina: What Is a Species and Why Should We Care?” New Phytologist 220 (4): 963–67.

Cernak, Paul, Raissa Estrela, Snigdha Poddar, Jeffrey M. Skerker, Ya-Fang Cheng, Annika K. Carlson, Berling Chen, et al. 2018. “Engineering Kluyveromyces Marxianus as a Robust Synthetic Biology Platform Host.” Edited by Sang Yup Lee. MBio 9 (5).

Xu, Ling, Dan Naylor, Zhaobin Dong, Tuesday Simmons, Grady Pierroz, Kim K. Hixson, Young-Mo Kim, et al. 2018. “Drought Delays Development of the Sorghum Root Microbiome and Enriches for Monoderm Bacteria.” Proceedings of the National Academy of Sciences 115 (18): E4284–93.

Allison, Steven D., Adriana L. Romero-Olivares, Ying Lu, John W. Taylor, and Kathleen K. Treseder. 2018. “Temperature Sensitivities of Extracellular Enzyme V max and K m across Thermal Environments.” Global Change Biology 24 (7): 2884–97.

Allison, Steven D., Adriana L. Romero-Olivares, Lucy Lu, John W. Taylor, and Kathleen K. Treseder. 2018. “Temperature Acclimation and Adaptation of Enzyme Physiology in Neurospora Discreta.” Fungal Ecology 35 (October): 78–86.

Hibbett, David S., Meredith Blackwell, Timothy Y. James, Joseph W. Spatafora, John W. Taylor, and Rytas Vilgalys. 2018. “Phylogenetic Taxon Definitions for Fungi, Dikarya, Ascomycota and Basidiomycota.” IMA Fungus 9 (2): 291–98.

Steidinger, Brian S., Jennifer M. Bhatnagar, Rytas Vilgalys, John W. Taylor, Thomas D. Bruns, and Kabir G. Peay. 2018. “Global Climate Changes Will Lead to Regionally Divergent Trajectories for Ectomycorrhizal Communities in North American Pinaceae Forests.” BioRxiv, August.

Hann-Soden, Christopher, Ian Holmes, and John W. Taylor. 2018. “Estimation of Rearrangement Break Rates Across the Genome.” BioRxiv, August

Taylor, John W., Sara Branco, Cheng Gao, Chris Hann-Soden, Liliam Montoya, Iman Sylvain, and Pierre Gladieux. 2017. “Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity.” Microbiology Spectrum 5 (5).

Branco, Sara, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Hélène Badouin, Christopher E. Ellison, Nhu H. Nguyen, et al. 2017. “Continental-Level Population Differentiation and Environmental Adaptation in the Mushroom Suillus Brevipes.” Molecular Ecology 26 (7): 2063–76.

Adams, Rachel I., Despoina S. Lymperopoulou, Pawel K. Misztal, Rita De Cassia Pessotti, Scott W. Behie, Yilin Tian, Allen H. Goldstein, et al. 2017. “Microbes and Associated Soluble and Volatile Chemicals on Periodically Wet Household Surfaces.” Microbiome 5 (1).

Hagen, Ferry, H. Thorsten Lumbsch, Valentina Arsic Arsenijevic, Hamid Badali, Sebastien Bertout, R. Blake Billmyre, M. Rosa Bragulat, et al. 2017. “Importance of Resolving Fungal Nomenclature: The Case of Multiple Pathogenic Species in the Cryptococcus Genus.” Edited by Michael Lorenz. MSphere 2 (4).

Casadevall, Arturo, Joudeh B. Freij, Christopher Hann-Soden, and John Taylor. 2017. “Continental Drift and Speciation of the Cryptococcus Neoformans and Cryptococcus Gattii Species Complexes.” Edited by J. Andrew Alspaugh. MSphere 2 (2).

Rosenthal, Lisa M., Karl-Henrik Larsson, Sara Branco, Judy A. Chung, Sydney I. Glassman, Hui-Ling Liao, Kabir G. Peay, et al. 2017. “Survey of Corticioid Fungi in North American Pinaceous Forests Reveals Hyperdiversity, Underpopulated Sequence Databases, and Species That Are Potentially Ectomycorrhizal.” Mycologia 109 (1): 115–27.

Bruns, T. D., and J. W. Taylor. 2016. “Comment on ‘Global Assessment of Arbuscular Mycorrhizal Fungus Diversity Reveals Very Low Endemism.’” Science 351 (6275): 826–826.

Zhang, Yongjie, Ida Skaar, Michael Sulyok, Xingzhong Liu, Mingyong Rao, and John W. Taylor. 2016. “The Microbiome and Metabolites in Fermented Pu-Erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis.” Edited by Ulrich Melcher. PLoS ONE 11 (6): e0157847.

Muñoz, José F., Rhys A. Farrer, Christopher A. Desjardins, Juan E. Gallo, Sean Sykes, Sharadha Sakthikumar, Elizabeth Misas, et al. 2016. “Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.” Edited by Aaron P. Mitchell. MSphere 1 (5).

Hibbett, David, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, et al. 2017. “Sequence-Based Classification and Identification of Fungi,” 21.

Taylor, John W., Markus Göker, and John I. Pitt. 2016. “Choosing One Name for Pleomorphic Fungi: The Example of Aspergillus versus Eurotium , Neosartorya and Emericella.” Taxon 65 (3): 593–601.

Pitt, John I., and John W. Taylor. 2016. “Proposal to Conserve the Name Aspergillus ( Fungi : Eurotiales : Trichocomaceae ) with a Conserved Type to Maintain Also the Name Eurotium.” Taxon 65 (3): 631–32.

Mendoza, Leonel, John W. Taylor, Edward D. Walker, and Raquel Vilela. 2016. “Description of Three Novel Lagenidium (Oomycota) Species Causing Infection in Mammals.” Revista Iberoamericana de Micología 33 (2): 83–91.

Taylor, John W., Christopher Hann-Soden, Sara Branco, Iman Sylvain, and Christopher E. Ellison. 2015. “Clonal Reproduction in Fungi.” Proceedings of the National Academy of Sciences 112 (29): 8901–8.

Whiston, Emily, and John W. Taylor. 2016. “Comparative Phylogenomics of Pathogenic and Nonpathogenic Species.” G3: Genes|Genomes|Genetics 6 (2): 235–44.

Gladieux, Pierre, Benjamin A. Wilson, Fanny Perraudeau, Liliam A. Montoya, David Kowbel, Christopher Hann-Soden, Monika Fischer, Iman Sylvain, David J. Jacobson, and John W. Taylor. 2015. “Genomic Sequencing Reveals Historical, Demographic and Selective Factors Associated with the Diversification of the Fire-Associated Fungus Neurospora Discreta.” Molecular Ecology 24 (22): 5657–75.

Muñoz, José F., Gregory M. Gauthier, Christopher A. Desjardins, Juan E. Gallo, Jason Holder, Thomas D. Sullivan, Amber J. Marty, et al. 2015. “The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.” Edited by Sajeet Haridas. PLoS Genetics 11 (10): e1005493.

Romero-Olivares, Adriana L., John W. Taylor, and Kathleen K. Treseder. 2015. “Neurospora Discreta as a Model to Assess Adaptation of Soil Fungi to Warming.” BMC Evolutionary Biology 15 (1).

Adams, Rachel I., Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen, and Martin Täubel. 2015. “Passive Dust Collectors for Assessing Airborne Microbial Material.” Microbiome 3 (1).

Adams, Rachel I., Seema Bhangar, Wilmer Pasut, Edward A. Arens, John W. Taylor, Steven E. Lindow, William W. Nazaroff, and Thomas D. Bruns. 2015. “Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes.” PLoS ONE 10 (5).

Wang, Yizhou, Kristina M. Smith, John W. Taylor, Michael Freitag, and Jason E. Stajich. 2015. “Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon.” G3: Genes|Genomes|Genetics 5 (10): 1949–60.

Shrestha, Prachand, Ana B Ibáñez, Stefan Bauer, Sydney I Glassman, Timothy M Szaro, Thomas D Bruns, and John W Taylor. 2015. “Fungi Isolated from Miscanthus and Sugarcane: Biomass Conversion, Fungal Enzymes, and Hydrolysis of Plant Cell Wall Polymers.” Biotechnology for Biofuels 8 (1): 38.

Bhangar, S., R. I. Adams, W. Pasut, J. A. Huffman, E. A. Arens, J. W. Taylor, T. D. Bruns, and W. W. Nazaroff. 2016. “Chamber Bioaerosol Study: Human Emissions of Size-Resolved Fluorescent Biological Aerosol Particles.” Indoor Air 26 (2): 193–206.

Branco, Sara, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButti, Anna Lipzen, Igor V. Grigoriev, et al. 2015. “Genetic Isolation between Two Recently Diverged Populations of a Symbiotic Fungus.” Molecular Ecology 24 (11): 2747–58.

Natvig, Donald O., John W. Taylor, Adrian Tsang, Miriam I. Hutchinson, and Amy J. Powell. 2015. “Mycothermus Thermophilus Gen. et Comb. Nov., a New Home for the Itinerant Thermophile Scytalidium Thermophilum (Torula Thermophila).” Mycologia 107 (2): 319–27.

Taylor, John W. 2015. “Evolutionary Perspectives on Human Fungal Pathogens.” Cold Spring Harbor Perspectives in Medicine 5 (9): a019588.

Glassman, Sydney I., Kabir G. Peay, Jennifer M. Talbot, Dylan P. Smith, Judy A. Chung, John W. Taylor, Rytas Vilgalys, and Thomas D. Bruns. 2015. “A Continental View of Pine-Associated Ectomycorrhizal Fungal Spore Banks: A Quiescent Functional Guild with a Strong Biogeographic Pattern.” New Phytologist 205 (4): 1619–31.

Vilela, Raquel, John W. Taylor, Edward D. Walker, and Leonel Mendoza. 2015. “Lagenidium Giganteum Pathogenicity in Mammals.” Emerging Infectious Diseases 21 (2): 290–97.

Thompson III, George R., David A. Stevens, Karl V. Clemons, Josh Fierer, Royce H. Johnson, Jane Sykes, George Rutherford, Michael Peterson, John W. Taylor, and Vishnu Chaturvedi. 2015. “Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease.” Mycopathologia 179 (1–2): 1–9.

de Hoog, G. Sybren, Vishnu Chaturvedi, David W. Denning, Paul S. Dyer, Jens Christian Frisvad, David Geiser, Yvonne Gräser, et al. 2015. “Name Changes in Medically Important Fungi and Their Implications for Clinical Practice.” Edited by D. W. Warnock. Journal of Clinical Microbiology 53 (4): 1056–62.

Whiston, E., and J. W. Taylor. 2014. “Genomics in Coccidioides: Insights into Evolution, Ecology, and Pathogenesis.” Medical Mycology 52 (2): 149–55.

Corcoran, Pádraic, Jeremy R. Dettman, Yu Sun, Eva M. Luque, Luis M. Corrochano, John W. Taylor, Martin Lascoux, and Hanna Johannesson. 2014. “A Global Multilocus Analysis of the Model Fungus Neurospora Reveals a Single Recent Origin of a Novel Genetic System.” Molecular Phylogenetics and Evolution 78 (September): 136–47.

Liao, H.-L., Y. Chen, T. D. Bruns, K. G. Peay, J. W. Taylor, S. Branco, J. M. Talbot, and R. Vilgalys. 2014. “Metatranscriptomic Analysis of Ectomycorrhizal Roots Reveals Genes Associated with P Iloderma- P Inus Symbiosis: Improved Methodologies for Assessing Gene Expression in Situ: Metatranscriptomic Analysis of Ectomycorrhizae.” Environmental Microbiology 16 (12): 3730–42.

Pitt, John I., and John W. Taylor. 2014. “Aspergillus, Its Sexual States and the New International Code of Nomenclature.” Mycologia 106 (5): 1051–62.

Ellison, Christopher E., David Kowbel, N. Louise Glass, John W. Taylor, and Rachel B. Brem. 2014. “Discovering Functions of Unannotated Genes from a Transcriptome Survey of Wild Fungal Isolates.” Edited by Judith Berman. MBio 5 (2).

Adams, Rachel I., Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen, and Martin Täubel. 2015. “Passive Dust Collectors for Assessing Airborne Microbial Material.” Microbiome 3. Microbiome: 46.

Adams, Rachel I., Marzia Miletto, Steven E. Lindow, John W. Taylor, and Thomas D. Bruns. 2014. “Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi.” PLoS ONE 9 (3).

Adams, Rachel I., Marzia Miletto, John W. Taylor, and Thomas D. Bruns. 2013. “The Diversity and Distribution of Fungi on Residential Surfaces.” PLoS ONE 8 (11).

Palma-Guerrero, Javier, Charles R. Hall, David Kowbel, Juliet Welch, John W. Taylor, Rachel B. Brem, and N. Louise Glass. 2013. “Genome Wide Association Identifies Novel Loci Involved in Fungal Communication.” Edited by Joshua M. Akey. PLoS Genetics 9 (8): e1003669.

Adams, Rachel I., Marzia Miletto, John W. Taylor, and Thomas D. Bruns. 2013. “Dispersal in Microbes: Fungi in Indoor Air Are Dominated by Outdoor Air and Show Dispersal Limitation at Short Distances.” ISME Journal 7 (7): 1262–73.

Wise, Hua Zhang, Chiung-Yu Hung, Emily Whiston, John W. Taylor, and Garry T. Cole. 2013. “Extracellular Ammonia at Sites of Pulmonary Infection with Coccidioides Posadasii Contributes to Severity of the Respiratory Disease.” Microbial Pathogenesis 59–60 (June): 19–28.

Adams, Rachel I., Anthony S. Amend, John W. Taylor, and Thomas D. Bruns. 2013. “A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: A Case Study of Fungi in Indoor Dust.” Microbial Ecology 66 (4): 735–41.

Jennifer M. Talbot, Thomas D. Bruns, John W. Taylor, Dylan P. Smith, Sara Branco, Sydney I. Glassman, Sonya Erlandson, Rytas Vilgalys, Hui-Ling Liao, Matthew E. Smith, and Kabir G. Peay. 2014. Endemism and functional convergence across the North American soil mycobiome. PNAS 111(17): 6341-6346.
 

Rachel I. Adams, Marzia Miletto, John W. Taylor and Thomas D. Bruns. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. The ISME Journal doi:10.1038/ismej.2013.28.
 

David S. Hibbett and John W. Taylor. 2013. Fungal systematics: is a new age of enlightenment at hand? Nature Reviews Microbiology 11: 129-133.
 

Whiston, E., Wise, H.-Z., Jui, G., Sharpton, T. J., Cole, G. T., J. W. Taylor. 2012. Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PLoS One 7: e41034.

Corcoran, Pádraic, David J. Jacobson, Martin I. Bidartondo, Patrick C. Hickey, Jennifer F. Kerekes, John W. Taylor, and Hanna Johannesson. 2012. “Quantifying Functional Heterothallism in the Pseudohomothallic Ascomycete Neurospora Tetrasperma.” Fungal Biology 116 (9): 962–75.

Turner, E., Jacobson, D. J. and J. W. Taylor. 2011. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurosporaspecies indicates evolution via natural selection. PLoS Genetics 7(8): e1002204. doi: 10.1371/journal.pgen.1002204
 

Ellison, C. E., Stajich, J. E., Jacobson D. J., Lapidus, A., Foster, B., Aerts. A., Riley, R., Lindquist, E. A., Grigoriev, I. V., and J. W. Taylor. 2011. Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics 189:55-69. doi: 10.1534/genetics.111.130690
 

Gilbert, L. B., Kasuga, T., Glass, N. L., Taylor, J. W. 2011. Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees? BMC Genomics. 12: Article Number: 487 doi: 10.1186/1471-2164-12-487
 

Gilbert, L. B., Chae, L., Kasuga, T., Taylor, J. W. 2011. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach. BMC Genomics. 12: Article Number: 456 . doi: 10.1186/1471-2164-12-456
 

Anna Muszewska, A., Taylor, J. W., Szczęsny, P. and M. Grynberg. 2011. Independent subtilases expansions in fungi associated with animals. Molecular Biology and Evolution 28: 3395-3404. doi:10.1093/molbev/msr176
 

Roper, M., Ellison, C., Taylor, J., and N. L. Glass. 2011. Nuclear and genome dynamics in multinucleate ascomycete fungi. Current Biology 21(18): R786-R793.
 

Prachand Shrestha, Timothy M. Szaro, Thomas D. Bruns and John W. Taylor. 2011. Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field. Applied Environmental Microbiology 77(15): 5490–5504. doi:10.1128/AEM.02996-10.
 

Taylor, J. W., 2011. One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2: 113-120.
 

Hawksworth, D. L., Crous, P. W., Redhead, S. A., Reynolds, D. R., Samson, R. A., Seifert, K. A., Taylor, J. W., Wingfield, M. J., et al. 2011. The Amsterdam declaration on fungal nomenclature. IMA Fungus. 2: 105-112.
 

John W. Taylor. 2011. Keynote paper: The poetry of mycological accomplishment and challenge. Fungal Biology Reviews 25: 3-13.
 

Ellison, C. E., C. Hall, D. Kowbel, J. Welch, R. B. Brem, N. L. Glass, and J. W. Taylor. 2011. Population genomics and local adaptation in wild isolates of a model microbial eukaryote. Proceedings of the National Academy of Science (USA) 108 (7): 2831-2836. [Neurospora SNP data]
 

John W. Taylor and Christopher E. Ellison. 2010. Mushrooms: Morphological complexity in the fungi. PNAS 107 (26): 11655-11656.
 

E. Turner, D.J. Jacobson and J.W Taylor. 2010. Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus. Journal of Evolutionary Biology 23: 1642–1656.
 

Hawksworth, D. L., J. A. Cooper, et al. 2010. Proposals 117-119: To make the pre-publication deposit of key nomenclatural information in a recognized repository a requirement for valid publication of organisms treated as fungi under the CODE. Mycotaxon 111: 514-519.
 

Daniel E. Neafsey, Bridget M. Barker, Thomas J. Sharpton, Jason E. Stajich, Daniel J. Park, Emily Whiston, Chiung-Yu Hung, Cody McMahan, Jared White, Sean Sykes, David Heiman, Sarah Young, Qiandong Zeng, Amr Abouelleil, Lynne Aftuck, Daniel Bessette, Adam Brown, Michael FitzGerald, Annie Lui, J. Pendexter Macdonald, Margaret Priest, Marc J. Orbach, John N. Galgiani, Theo N. Kirkland, Garry T. Cole, Bruce W. Birren, Matthew R. Henn, John W. Taylor and Steven D. Rounsley. 2009. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Geneome Research 19: 1722-1731.
 

Berbee ML & Taylor JW. 2010. Dating the molecular clock in fungi -- how close are we? Fungal Biology Reviews 24: 1–16.
 

Stajich, JE, Berbee, ML, Blackwell, M, Hibbett, DS, James, TY, Spatafora, JW, Taylor, JW. 2009. The Fungi. Current Biology 19(18): R840-845.
 

James TY, Litvintseva AP, Vilgalys R, Morgan JAT, Taylor JW, Fisher MC, Berger L, Weldon C, du Preez L, Longcore JE. 2009. Rapid global expansion of the fungal disease Chytridiomycosis into declining and healthy amphibian populations. PLoS Pathogens 5: e1000458.
 

Thomas J. Sharpton, Jason E. Stajich, Steven D. Rounsley, Malcolm J. Gardner, Jennifer R. Wortman, Vinita S. Jordar, Rama Maiti, Chinnappa D. Kodira, Daniel E. Neafsey, Qiandong Zeng, Chiung-Yu Hung, Cody McMahan, Anna Muszewska, Marcin Grynberg, M. Alejandra Mandel, Ellen M. Kellner, Bridget M. Barker, John N. Galgiani, Marc J. Orbach, Theo N. Kirkland, Garry T. Cole, Matthew R. Henn, Bruce W. Birren, and John W. Taylor. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19(10): 1722-1731. doi: 10.1101/gr.087551.108.
 

Christopher F. Villalta, David J. Jacobson and John W. Taylor. 2009. Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii. Mycologia 101(6): 777-789.
 

Vilela, R., Rosa, PS, Belone, AFF, Taylor JW, Diorio SM, Mendoza, L. 2009. Molecular phylogeny of animal pathogen Lacazia loboi inferred from rDNA and DNA coding sequences. Mycological Research 113: 851-857.
 

Thomas J. Sharpton, Daniel E. Neafsey, James E. Galagan and John W. Taylor. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology 2008, 9:R24 (doi:10.1186/gb-2008-9-1-r24).
 

Bidartondo, M. et al.  2008. Preserving Accuracy in GenBank. Science (letters) 319:1616.
 

Carrero, L.L., Nino-Vega, G., Teixeira, M.M., Carvalho, M.J.A., Soares, C.M.A., Pereira, M., Jesuino, R.S.A., McEwen, J.G., Mendoza, L., Taylor, J.W., Felipe, M.S., and San-Blas, G. 2008. New Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogen. Fungal Genetics and Biology 45(5): 605-612.
 

Heitman, J., Kronstad, J.W., Taylor, J.W., and Casselton, L.A. 2007. Sex in fungi: molecular determination and evolutionary implications. In Sex in fungi: molecular determination and evolutionary implications. ASM Press, Washington USA. p. xxv + 542 pp. Table of contents.
 

Morgan, J.A.T., Vredenburg,V.T., Rachowicz, L.J., Knapp, R.A., Stice, M.J., Tunstall, T., Bingham, R.E., Parker, J.M., Longcore, J.E., Moritz, C., Briggs, C.J., Taylor, J.W. 2007. Enigmatic amphibian declines and emerging infectious disease: population genetics of the frog killing fungus Batrachochytrium dendrobatidis. PNAS 104:13845-13850.
 

Mary L. Berbee, John W. Taylor. 2007. Rhynie chert: a window into a lost world of complex plant-fungus interactions. New Phytologist 174(3): 475–479. doi:10.1111/j.1469-8137.2007.02080.x
 

Taylor, J.W., Turner, E., Pringle, A., Dettman, J., Johannesson, H. 2007. Fungal species: thoughts on their recognition, maintenance and selection. Pp. 313-339, In 'Fungi in the Environment'. (British Mycological Society Symposia No. 25) eds. G.M. Gadd, S.C. Watkinson and P.S. Dyer. Cambridge: Cambridge University Press.
 

John W. Taylor & Mary L. Berbee. 2006. Dating divergences in the Fungal Tree of Life: review and new analyses. Mycologia 2006 98: 838-849.
 

Meredith Blackwell, David S. Hibbett, John W. Taylor & Joseph W. Spatafora. 2006. Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 2006 98: 829-837.
 

Taylor, John W.; Turner, Elizabeth; Townsend, Jeffrey P.; Dettman, Jeremy R.; Jacobson, David. 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the Royal Society of London B Biological Sciences 361(1475): 1947-1963.
 

James TY, Kauff F, Schoch C, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan D, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JH, 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, and Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. doi: 10.1038/nature05110
 

David J. Jacobson, Jeremy R. Dettman, Rachel I. Adams, Cornelia Boesl, Shahana Sultana, Till Roenneberg, Martha Merrow, Margarida Duarte, Isabel Marques, Alexandra Ushakova, Patrícia Carneiro, Arnaldo Videira, Laura Navarro-Sampedro, María Olmedo, Luis M. Corrochano and John W. Taylor. 2006. New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales. Mycologia 98(4): 550-559.
 

Jeremey R. Dettman, David J. Jacobson and John W. Taylor. 2006. Multilocus sequence data reveal extensive phylogenetic species diversity within theNeurospora discreta complex. Mycologia 98(3): 436–446.
 

Matute, D.R., Sepulveda, V.E., Quesada, L.M., Goldman, G.H., Taylor, J.W., Restrepo, A., McEwen, J.G. 2006. Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis. J. Clinical Microbiology 44: 2153-2157.
 

H. Johannesson, T. Kasuga, R.A. Schaller, B. Good, M.J. Gardner, J.P. Townsend, G.T. Cole and J.W. Taylor. 2006. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology 43(8): 545-559.
 

Taylor, J.W. 2006. Evolution of human-pathogenic fungi: Phylogenies and species. Pp. 113-132 and Color Plate 5. In: Molecular Principles of Fungal Pathogenesis, J. Heitman et al. (eds). ASM Press, Washington, D.C.
 

Aa, E., Townsend, J. P., Adams, R. I., Nielsen, K. M., Taylor, J. W. 2006. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 6(5): 702-715.
 

Matute, D.R., McEwen, J.G., Montes, B.A., San-Blas, G., Bagagli, E., Rauscher, J.T., Restrepo, A., Morais, F., Nino-Vega, G., Taylor, J.W. 2006. Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Molecular Biology and Evolution 23: 65-73.
 

Takao Kasuga, Jeffrey P. Townsend, Chaoguang Tian, Luz B. Gilbert, Gertrud Mannhaupt, John W. Taylor and N. Louise Glass. 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469–6485.
 

Rachowicz, L. J., Hero, J.-M., Alford, R. A., Taylor, J. W., Morgan, J. A. T., Vredenberg, V. T., Collins, J. P. and C. J. Briggs. 2005. The novel and endemic pathogen hypotheses: Competing explanations for the origin of emerging infectious diseases of wildlife. Conservation Biology 19:1441-1447.
 

Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. 2005. Recombination shapes the natural population structure of the hyperthermophilic archaeonSulfolobus ‘islandicus’. Molecular Biology and Evolution 22(12): 2354-2361; doi:10.1093/molbev/msi233
 

Johannesson, H., J.P. Townsend, C.-Y. Hung, G.T. Cole, J.W. Taylor. 2005. Concerted evolution of the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii.  Genetics 171:109-117.
 

Pringle, A., D.M. Baker, J.L. Platt, J.P. Wares, J.P. Latge and J.W. Taylor. 2005. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59(9): 1886-1899.
 

Pawlowska, T.E. and J.W. Taylor. 2005. Arbuscular mycorrhizal fungi: Hyphal fusion and multigenomic structure (reply). Nature 433(7022): E4 (doi: 10.1038/nature03295).
 

Jeffrey P. Townsend and John W. Taylor. 2005. Designing experiments using spotted microarrays to detect gene regulation differences within and among Species. Methods in Enzymology 395: 597-617.
 

Nascimento, T., Martinez, R., Lopes, A. R., Bernardes, L. A. D., Barco, C. P., Goldman, M. H. S., Taylor, J. W., McEwen, J. G., Nobrega, M. P., Nobrega, F. G. and Goldman, G. H. 2004. Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studies. Journal of Clinical Microbiology 42: 5007-5014.
 

Dettman, J.R. and Taylor, J.W. 2004. Mutation and evolution of microsatellite loci in Neurospora. Genetics 168: 1231-1248.
 

John W. Taylor, Joseph Spatafora, Kerry O'Donnell, Francois Lutzoni, Timothy James, David S. Hibbett, David Geiser, Thomas D. Bruns and Meredith Blackwell. 2004. The Fungi. In: Assembling the tree of life. Edited by Joel Cracraft and Michael J. Donoghue. Oxford University Press, pp. 171 - 194.
 

Johannesson, H., Vidal, P., Guarro, J., Herr, R. A., Cole, G. T., John W. Taylor. 2004. Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives. Molecular Biology and Evolution 21(6):1134-1145.
 

Pawlowska, T. E. and Taylor, J. W. 2004. Organization of genetic variation in individuals of arbuscular mycorrhizal fungi. Nature 427(6976): 733-737.
 

David J. Jacobson, Amy J. Powell, Jeremy R. Dettman, Gregory S. Saenz, Magdalen M. Barton, Megan D. Hiltz, William H. Dvorachek, Jr., N. Louise Glass, John W. Taylor and Donald O. Natvig. 2004. Neurospora in temperate forests of western North America. Mycologia 96(1): 66-74.
 

Medina, M., Collins, A.G., Taylor, J.W., Valentine, J.W., Lipps, J.H., Amaral-Zettler, L., and M. L. Sogin. 2003. Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa. International Journal of Astrobiology 2 (3) : 203–211.
 

Birgitte Andersen, Kristian F. Nielsen, Ulf Thrane, Tim Szaro, John Taylor and Bruce B. Jarvis. 2003. Molecular and phenotypic descriptions of Stachybotrys chlorohalonata sp. nov. and two chemotypes of Stachybotrys chartarum found in water-damaged buildings. Mycologia 95: 1227-1238.
 

S. Kroken, N. L. Glass, J. W. Taylor, O. C. Yoder, B. G. Turgeon. 2003. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proceedings of the National Academy of Sciences of the United States of America 100(26): 15670-15675.
 

Takao Kasuga, Thomas J. White, Gina Koenig, Juan McEwen, Angela Restrepo, Elizabetha Castañeda, Carlos da Silva Lacaz, Elisabeth M. Heins-Vaccari, Roseli S. de Freitas, Rosely M. Zancopé-Oliveira, Zhenyu Qin, Ricardo Negroni, Deidre A. Carter, Yuzuru Mikami, Miki Tamura, María Lucía Taylor, Georgina F. Miller, Natteewan Poonwan and John W Taylor. 2003. Phylogeography of the fungal pathogen Histoplasma capsulatum. Molecular Ecology 12: 3383-3401.
 

Dettman, J. R., D. J. Jacobson, Taylor, J. W. 2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryoteNeurospora. Evolution 57(12): 2703-2720.
 

Dettman, J. R., Jacobson, D. J., Turner, E., Pringle, A., Taylor, J. W. 2003. Reproductive isolation and phylogenetic divergence in Neurospora: Comparing methods of species recognition in a model eukaryote. Evolution 57(12): 2721-2741.
 

Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science Aug 15 2003: 976-978, published online July 24, 2003. (10.1126/science.1086909)
 

Taylor, J. W. and M. C. Fisher. 2003. Fungal multilocus sequence typing - it's not just for bacteria [Review]. Current Opinion in Microbiology 6(4): 351-356.
 

Pringle, A., D. Chen and J. W. Taylor. 2003. Sexual fecundity is correlated to size in the lichenized fungus Xanthoparmelia cumberlandia. Bryologist 106(2): 221-225.
 

T. Kasuga, T. J. White and J. W. Taylor 2002. Estimation of nucleotide substitution rates in eurotiomycete fungi. Molecular Biology and Evolution 19(12): 2318-24.
 

Högberg, Nils, Kroken, Scott, Thor, Göran & Taylor, John W. 2002. Reproductive mode and genetic variation suggest a North American origin of EuropeanLetharia vulpina. Molecular Ecology 11 (7): 1191-1196.
 

Katherine F. LoBuglio and John W. Taylor. 2002. Recombination and genetic differentiation in the mycorrhizal fungus Cenococcum geophilum Fr. Mycologia 94(5): 772-780.
 

Michael Cruse, Robin Telerant, Thomas Gallagher, Thomas Lee & John W. Taylor. 2002. Cryptic species in Stachybotrys chartarum. Mycologia 94(5): 814-822.
 

Anne Pringle and John W. Taylor. 2002. The fitness of filamentous fungi. Trends in Microbiology. 10(10): 474-481.
 

Leonel Mendoza, John W. Taylor and Libero Ajello. 2002. The class mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Annual Review of Microbiology 56: 315-344.
 

Matthew C. Fisher, Bruce Rannala, Vishnu Chaturvedi, and John W. Taylor. 2002. Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human Coccidioides infections Proc. Natl. Acad. Sci. USA. 99: 9067-9071.
 

Matthew C. Fisher, Gina L. Koenig, Thomas J. White and John W. Taylor. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94(1): 73-84.
 

Scott Kroken and John W. Taylor. 2001. Outcrossing and recombination in the lichenized fungus Letharia. Fungal Genetics and Biology 34(2): 83-92.
 

Scott Kroken and John W. Taylor. 2001. A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia.Mycologia 93: 38–53.
 

Jeremy R. Dettman, Fred M. Harbinski, John W. Taylor. 2001. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora andGelasinospora. Fungal Genetics and Biology 34(1): 44-61.
 

D. A. Carter, J. W. Taylor, B. Dechairo, A. Burt, G. L. Koenig, T. J. White. 2001. Amplified Single-Nucleotide Polymorphisms and a (GA)_n Microsatellite Marker Reveal Genetic Differentiation between Populations of Histoplasma capsulatum from the Americas. Fungal Genetics and Biology 34(1): 37-48.
 

Vassiliki Koufopanou, Austin Burt, Timothy Szaro and John W. Taylor. 2001. Gene Genealogies, Cryptic Species, and Molecular Evolution in the Human Pathogen Coccidioides immitis and Relatives (Ascomycota, Onygenales). Molecular Biology and Evolution 18: 1246-1258.
 

Matthew C. Fisher, Gina L. Koenig, Thomas J. White, Gioconda San-Blas, Ricardo Negroni, Bodo Wanke, Gutierrez Alvarez and John W. Taylor. 2001. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of Human migration. Proc. Natl. Acad. Sci. USA. 98(8): 4558–4562.
 

Mendoza, L., L. Ajello, J.W. Taylor. 2001. The taxonomic status of Lacazia loboi and Rhinosporidium seeberi has been finally resolved with the use of molecular tools. Revista Iberoamericana de Micologia 18(3): 95-98.
 

Roger A. Herr, Eric J. Tarcha, Paulo R. Taborda, John W. Taylor, Libero Ajello and Leonel Mendoza. 2001. Phylogenetic analysis of Lacazia loboi places this previously uncharacterized pathogen within the dimorphic Onygenales. Journal of Clinical Microbiology 39(1): 309-314.
 

Mary L. Berbee and John W. Taylor. 2001. Fungal Molecular Evolution: Gene Trees and Geologic Time. The Mycota: a comprehensive treatise on fungi as experimental systems for basic and applied research. Volume VII: Systematics and Evolution, Part B, pp.229-245. (published in 2000, labeled 2001 by Springer)
 

David M. Geiser, Joe W. Dorner, Bruce W. Horn and John W. Taylor. 2000. The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavusand Aspergillus oryzae. Fungal Genetics and Biology 31(1): 169-179.
 

J. G. McEwen, J. W. Taylor, D. Carter, J. Xu, M. S. Felipe, R. Vilgalys, T. G. Mitchell, T. Kasuga, T. White, T. Bui and C. M. Soares. 2000. Molecular typing of pathogenic fungi. Medical Mycology 38: 189-197.
 

Geiser, D. M., F. M. Harbinski and J. W. Taylor. 2000. Molecular and analytical tools for characterizing Aspergillus and Penicillium species at the intra- and interspecific levels. Pp 179-188. In: Integration of modern taxonomic methods for Penicillium and Aspergillus classification (R. A. Samson and J. I. Pitt, eds.). Harwood Academic Publishers, Gordon and Breach Publishing Group, Amsterdam. ISBN 90-5823-159-3.
 

Skouboe, P, Taylor, J.W., Frisvad, J.C., Lauritsen, D, Larsen, L., Albaek, Cl, Boysen, M, and L. Rossen. 2000. Molecular methods for differentiation of closely related Penicillium species. Pp 381-394. In: Integration of modern taxonomic methods for Penicillium and Aspergillus classification (R. A. Samson and J. I. Pitt, eds.). Harwood Academic Publishers, Gordon and Breach Publishing Group, Amsterdam. ISBN 90-5823-159-3.
 

Kroken, S. and Taylor, J. W. 2000. Phylogenetic species, reproductive mode, and specificity of the green alga Trebouxia forming lichens with the fungal genus Letharia. Bryologist V103, 645-660.
 

John W. Taylor, David J. Jacobson, Scott Kroken, Takao Kasuga, David M. Geiser, David S. Hibbett and Matthew C. Fisher. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, Vol. 31(1): pp. 21-32.
 

Burt, A., Koufopanou, V., Taylor, J.W. 2000. Population genetics of human-pathogenic fungi.  Pp. 229-244 In: Molecular Epidemiology of Infectious Diseases, R.C.A. Thompson (ed.). Arnold, London.
 

M. C. Fisher, G. Koenig, T. J. White J. W. Taylor. 2000. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis. Molecular Biology and Evolution 17: 1164-1174.
 

Fisher MC, Koenig GL, White TJ, Taylor JW. 2000. Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis. Journal of Clinical Microbiology 38(2):807-13.
 

Deborah R. Greene, Gina Koenig, Matthew C. Fisher, John W. Taylor. 2000. Soil isolation and molecular identification of Coccidioides immitis. Mycologia: Vol. 92, No. 3, pages 406-410.