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2024
Schutz, K., Melie, T., Smith, S.D. & Quandt, C.A. 2024. Patterns recovered in phylogenetic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts. Microbial Genomics 10(4): https://doi.org/10.1099/mgen.0.001233
Haelewaters, D., Quandt, C.A., Bartrop, L., Cazabonne, J., Crockatt, M.E., Cunha, S.P., De Lange, R., Dominici, L., Douglas, B., Drechsler-Santos, E.S., Heilmann-Clausen, J.B., Irga, P.J., Jakob, S., Lofgren, L., Martin, T.E., Muchane, M.N., Stallman, J.K., Verbeken, A., Walker, A.K. & Gonçalves, S.C. (2024). The power of citizen science to advance fungal conservation. Conservation Letters https://doi.org/10.1111/conl.13013
Haelewaters, D., Matthews, T. J., Wayman, J. P., Cazabonne, J., Heyman, F., Quandt, C. A., & Martin, T. E. (2024). Biological knowledge shortfalls impede conservation efforts in poorly studied taxa—A case study of Laboulbeniomycetes. Journal of Biogeography, 00, 1–11. https://doi.org/10.1111/jbi.14725
Pogoda, C.S., Keepers, K.G., Reinart, S., Talukder, Z.I., Smart, B.C., Attia, Z., Corwin, J.A., Money, K.L., Collier-sanz, E.C.E., Underwood, W., Gulya, T.J., Quandt, C.A., Kane, N.C. & Hulke, B.S. (2024). Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance. Molecular Ecology. https://doi.org/10.1111/mec.17218
Rahimlou, S., Quandt, C.A., James, T.Y. (2024). Metabolic Constraints and Dependencies Between “Uncultivable” Fungi and Their Hosts. In: Hsueh, YP., Blackwell, M. (eds) Fungal Associations. The Mycota, vol 9. Springer, Cham. https://doi.org/10.1007/978-3-031-41648-4_2
2023
Hyde, K.D., Abdel-Wahab, M.A., Abdollahzadeh, J., Abeywickrama, P.D., ... , Quandt, C.A., ... Zucconi, L. et al. (2023). Global consortium for the classification of fungi and fungus-like taxa. Mycosphere, 14(1): 1960-2012. DOI: 10.5943/mycosphere/14/1/23
Alexiev, A., Melie, T., Martindale, R., Delacey, C., Quandt, C.A. & McKenzie, V. (2023). Mr. Toad's wild fungi: Fungal isolate diversity on Colorado boreal toads and their capacity for pathogen inhibition. Fungal Ecology, 66:101297. DOI: 10.1016/j.funeco.2023.101297
Danz, A. & Quandt, C. A. (2023). A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms. Frontiers in Microbiology, 14, 1281648. https://doi.org/10.3389/fmicb.2023.1281648
Warre Van Caenegem, Aimée Blondelle, Iris Dumolein, Brianna Santamaria, Carl W. Dick, Thomas Hiller, Jingyu Liu, C. Alisha Quandt, Rosa V. Villarreal Saucedo, Annemieke Verbeken & Danny Haelewaters (2023) Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction, Mycologia, DOI: 10.1080/00275514.2023.2230114
Seto, K., Simmons, D.R., Quandt, C.A., Frenken, T., Dirks, A.C., Clemons, R.A., McKindles, K.M., McKay, R.M.L. & James, T.Y. 2023.
A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. Mbio, e01313-23. https://doi.org/10.1128/mbio.01313-23
Quandt, C. A., Marino, J. A., Simmons, D. R., Davis, W. J., Hassett, B. T., Picard, K. T., & James, T. Y. 2023. Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding. Fungal Ecology, 64, 101248.
Tina Melie, Stacy Pirro, Andrew N. Miller, Stacey D. Smith, Kyle S. Schutz, and C. Alisha Quandt. 2023. Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina. Mycologia. https://doi.org/10.1080/00275514.2023.2186743© 2023 The Mycological Society of America.
João F. Moreira Salgado, C. Alisha Quandt, and Jason E. Stajich. Phylogenetics and phylogenomics to understand fungal diversity. Authorea. March 10, 2023. DOI: 10.22541/au.167845826.61933731/v1
2022
Grupe II AC, Smith ME, Weier A, Healy R, Caiafa MV, Pfister DH, Haelewaters D, Quandt CA (2022). Two new species of Phaeohelotium (Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Systematics and Evolution 10: 231–249. doi: 10.3114/ fuse.2022.10.1
Pogoda, CS, Reinert, S, Talukder, ZI, Corwin, J, Money, KL, Collier-zans, ECE, Underwood, W, Gulya, TJ, Quandt, CA, Kane, NC, and BC Hulke. “Heritable associations with microbial communities contribute to host-pathogen interactions.” In revision. Biorxiv: https://doi.org/10.1101/2020.07.16.207597
Amses, KR, Simmons, DR, Longcore, JE, Mondo, SJ, Seto, K, Jeronimo Alves, GH, Bonds, AE, Quandt, CA, Davis, WJ, Chang, Y, Federici, BA, Kuo, A, LaButti, K, Pangilinan, J, Andreopoulos, W, Tritt, A, Riley, R, Hundley, H, Johnson, J, Lipzen, A, Barry, K, Lang, BF, Cuomo CA, Buchler, NE, Grigoriev, IG, Spatafora, JW, Stajich, JE, and TY James. "Diploid-dominant life cycles characterize the early evolution of Fungi." 2022. Proceedings of the National Academy of Sciences 119(3). https://doi.org/10.1073/pnas.2116841119
Ciobanu, D, Chan, S, Ahrendt, SA, Quandt, CA, Benny, GL, Smith, ME, James, TY, and J-F Cheng. "Single-cell genomics wet-bench protocol collection for environmental microbial Eukaryotes." 2022. STAR Protocols 3: 100968.
2021
Rämä, T, and CA Quandt. “Fungal cultivability and ways to increase it for natural products discovery.” 2021. Frontiers in Microbiology 12: 706044
Quandt, CA and D Haelewaters. "Phylogenetic advances in Leotiomycetes, an understudied clade of taxonomically and ecologically diverse fungi." 2021. In: Zaragoza, O. (ed) Encyclopedia of Mycology 1: 284-294 Oxford: Elsevier. https://www.sciencedirect.com/science/article/pii/B9780128199909000524#s0130
Ciobanu, D, Clum, A, Ahrendt, SA, Andreoupoulos, W, Salamov, A, Chan, S, Quandt, CA, Foster, B, Meier-Kolthoff, JP, Tang, Y-T, Schwientek, P, Benny, GL, Smith, ME, Bauer, D, Deshpande, S, Barry, K, Copeland, A, Singer, S, Woyke, T, Grigoriev, I, James, TY, and J-F Cheng. “A Single-Cell Genomics Pipeline for Environmental Microbial Eukaryotes.” 2021 iScience 24(4): 102290.
2020
Grupe, AC and CA Quandt. “A growing pandemic: a review of Nosema parasites in globally distributed domesticated and native bees.” 2020 PLOS Pathogens 16(6): e1008580. https://doi.org/10.1371/journal.ppat.1008580
2019
Davis, WJ, Jeronimo, GH, Simmons, DR, Quandt, CA, and TY James. “Revisiting the aquatic phycomycete flora of the Douglas Lake region since the time of Dogma and Sparrow.” 2019 Philippine Journal of Systematic Biology 13 (2): 1-14.
Amend, A, Burgaud, G, Cunliff, M, Edgcomb, VP, Ettinger, CL, Gutiérrez, MH, Heitman, J,Hom, EFY, Ianiri, G, Jones, AC, Kagami, M, Picard, KT, Quandt, CA, Raghukumar, S, Riquellme, M, Stajich, J, Vargas-Muñiz, J, Walker, A, Yarden, O, and AS Gladfelter. “Fungi in the marine environment: open questions and unsolved problems.” 2019 mBio 10: e01189-18.
Olarte, RA, Menke, J, Zhang Y, Sullivan, S, Slot, J, Huang, YJ, Badalamenti, JP, Quandt, CA, Spatafora, JW, and KE Bushley. “Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum.” 2019 BMC Genomics 20: 120.
2018
Ahrendt, SR, Quandt, CA, Ciobanu, D, Clum, A, Salamov, A, Andreopoulos, W, Cheng, J-F, Woyke, T, Pelin, A, Henrissat, B, Reynolds, NK, Benny, GL, Smith, ME, James, TY, and IV Grigoriev. “Leveraging single-cell genomics to expand the Fungal Tree of Life.” 2018 Nature Microbiology 3: 1417-1428.
Quandt, CA, Patterson, W, and JW Spatafora. “Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host-jumping in the fungal genus Tolypocladium.” 2018 Mycologia 110: 104-117.
2024
Schutz, K., Melie, T., Smith, S.D. & Quandt, C.A. 2024. Patterns recovered in phylogenetic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts. Microbial Genomics 10(4): https://doi.org/10.1099/mgen.0.001233
Haelewaters, D., Quandt, C.A., Bartrop, L., Cazabonne, J., Crockatt, M.E., Cunha, S.P., De Lange, R., Dominici, L., Douglas, B., Drechsler-Santos, E.S., Heilmann-Clausen, J.B., Irga, P.J., Jakob, S., Lofgren, L., Martin, T.E., Muchane, M.N., Stallman, J.K., Verbeken, A., Walker, A.K. & Gonçalves, S.C. (2024). The power of citizen science to advance fungal conservation. Conservation Letters https://doi.org/10.1111/conl.13013
Haelewaters, D., Matthews, T. J., Wayman, J. P., Cazabonne, J., Heyman, F., Quandt, C. A., & Martin, T. E. (2024). Biological knowledge shortfalls impede conservation efforts in poorly studied taxa—A case study of Laboulbeniomycetes. Journal of Biogeography, 00, 1–11. https://doi.org/10.1111/jbi.14725
Pogoda, C.S., Keepers, K.G., Reinart, S., Talukder, Z.I., Smart, B.C., Attia, Z., Corwin, J.A., Money, K.L., Collier-sanz, E.C.E., Underwood, W., Gulya, T.J., Quandt, C.A., Kane, N.C. & Hulke, B.S. (2024). Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance. Molecular Ecology. https://doi.org/10.1111/mec.17218
Rahimlou, S., Quandt, C.A., James, T.Y. (2024). Metabolic Constraints and Dependencies Between “Uncultivable” Fungi and Their Hosts. In: Hsueh, YP., Blackwell, M. (eds) Fungal Associations. The Mycota, vol 9. Springer, Cham. https://doi.org/10.1007/978-3-031-41648-4_2
2023
Hyde, K.D., Abdel-Wahab, M.A., Abdollahzadeh, J., Abeywickrama, P.D., ... , Quandt, C.A., ... Zucconi, L. et al. (2023). Global consortium for the classification of fungi and fungus-like taxa. Mycosphere, 14(1): 1960-2012. DOI: 10.5943/mycosphere/14/1/23
Alexiev, A., Melie, T., Martindale, R., Delacey, C., Quandt, C.A. & McKenzie, V. (2023). Mr. Toad's wild fungi: Fungal isolate diversity on Colorado boreal toads and their capacity for pathogen inhibition. Fungal Ecology, 66:101297. DOI: 10.1016/j.funeco.2023.101297
Danz, A. & Quandt, C. A. (2023). A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms. Frontiers in Microbiology, 14, 1281648. https://doi.org/10.3389/fmicb.2023.1281648
Warre Van Caenegem, Aimée Blondelle, Iris Dumolein, Brianna Santamaria, Carl W. Dick, Thomas Hiller, Jingyu Liu, C. Alisha Quandt, Rosa V. Villarreal Saucedo, Annemieke Verbeken & Danny Haelewaters (2023) Five new species of Gloeandromyces (Fungi, Laboulbeniales) from tropical American bat flies (Diptera, Streblidae), revealed by morphology and phylogenetic reconstruction, Mycologia, DOI: 10.1080/00275514.2023.2230114
Seto, K., Simmons, D.R., Quandt, C.A., Frenken, T., Dirks, A.C., Clemons, R.A., McKindles, K.M., McKay, R.M.L. & James, T.Y. 2023.
A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. Mbio, e01313-23. https://doi.org/10.1128/mbio.01313-23
Quandt, C. A., Marino, J. A., Simmons, D. R., Davis, W. J., Hassett, B. T., Picard, K. T., & James, T. Y. 2023. Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding. Fungal Ecology, 64, 101248.
Tina Melie, Stacy Pirro, Andrew N. Miller, Stacey D. Smith, Kyle S. Schutz, and C. Alisha Quandt. 2023. Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina. Mycologia. https://doi.org/10.1080/00275514.2023.2186743© 2023 The Mycological Society of America.
João F. Moreira Salgado, C. Alisha Quandt, and Jason E. Stajich. Phylogenetics and phylogenomics to understand fungal diversity. Authorea. March 10, 2023. DOI: 10.22541/au.167845826.61933731/v1
2022
Grupe II AC, Smith ME, Weier A, Healy R, Caiafa MV, Pfister DH, Haelewaters D, Quandt CA (2022). Two new species of Phaeohelotium (Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Systematics and Evolution 10: 231–249. doi: 10.3114/ fuse.2022.10.1
Pogoda, CS, Reinert, S, Talukder, ZI, Corwin, J, Money, KL, Collier-zans, ECE, Underwood, W, Gulya, TJ, Quandt, CA, Kane, NC, and BC Hulke. “Heritable associations with microbial communities contribute to host-pathogen interactions.” In revision. Biorxiv: https://doi.org/10.1101/2020.07.16.207597
Amses, KR, Simmons, DR, Longcore, JE, Mondo, SJ, Seto, K, Jeronimo Alves, GH, Bonds, AE, Quandt, CA, Davis, WJ, Chang, Y, Federici, BA, Kuo, A, LaButti, K, Pangilinan, J, Andreopoulos, W, Tritt, A, Riley, R, Hundley, H, Johnson, J, Lipzen, A, Barry, K, Lang, BF, Cuomo CA, Buchler, NE, Grigoriev, IG, Spatafora, JW, Stajich, JE, and TY James. "Diploid-dominant life cycles characterize the early evolution of Fungi." 2022. Proceedings of the National Academy of Sciences 119(3). https://doi.org/10.1073/pnas.2116841119
Ciobanu, D, Chan, S, Ahrendt, SA, Quandt, CA, Benny, GL, Smith, ME, James, TY, and J-F Cheng. "Single-cell genomics wet-bench protocol collection for environmental microbial Eukaryotes." 2022. STAR Protocols 3: 100968.
2021
Rämä, T, and CA Quandt. “Fungal cultivability and ways to increase it for natural products discovery.” 2021. Frontiers in Microbiology 12: 706044
Quandt, CA and D Haelewaters. "Phylogenetic advances in Leotiomycetes, an understudied clade of taxonomically and ecologically diverse fungi." 2021. In: Zaragoza, O. (ed) Encyclopedia of Mycology 1: 284-294 Oxford: Elsevier. https://www.sciencedirect.com/science/article/pii/B9780128199909000524#s0130
Ciobanu, D, Clum, A, Ahrendt, SA, Andreoupoulos, W, Salamov, A, Chan, S, Quandt, CA, Foster, B, Meier-Kolthoff, JP, Tang, Y-T, Schwientek, P, Benny, GL, Smith, ME, Bauer, D, Deshpande, S, Barry, K, Copeland, A, Singer, S, Woyke, T, Grigoriev, I, James, TY, and J-F Cheng. “A Single-Cell Genomics Pipeline for Environmental Microbial Eukaryotes.” 2021 iScience 24(4): 102290.
2020
Grupe, AC and CA Quandt. “A growing pandemic: a review of Nosema parasites in globally distributed domesticated and native bees.” 2020 PLOS Pathogens 16(6): e1008580. https://doi.org/10.1371/journal.ppat.1008580
2019
Davis, WJ, Jeronimo, GH, Simmons, DR, Quandt, CA, and TY James. “Revisiting the aquatic phycomycete flora of the Douglas Lake region since the time of Dogma and Sparrow.” 2019 Philippine Journal of Systematic Biology 13 (2): 1-14.
Amend, A, Burgaud, G, Cunliff, M, Edgcomb, VP, Ettinger, CL, Gutiérrez, MH, Heitman, J,Hom, EFY, Ianiri, G, Jones, AC, Kagami, M, Picard, KT, Quandt, CA, Raghukumar, S, Riquellme, M, Stajich, J, Vargas-Muñiz, J, Walker, A, Yarden, O, and AS Gladfelter. “Fungi in the marine environment: open questions and unsolved problems.” 2019 mBio 10: e01189-18.
Olarte, RA, Menke, J, Zhang Y, Sullivan, S, Slot, J, Huang, YJ, Badalamenti, JP, Quandt, CA, Spatafora, JW, and KE Bushley. “Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum.” 2019 BMC Genomics 20: 120.
2018
Ahrendt, SR, Quandt, CA, Ciobanu, D, Clum, A, Salamov, A, Andreopoulos, W, Cheng, J-F, Woyke, T, Pelin, A, Henrissat, B, Reynolds, NK, Benny, GL, Smith, ME, James, TY, and IV Grigoriev. “Leveraging single-cell genomics to expand the Fungal Tree of Life.” 2018 Nature Microbiology 3: 1417-1428.
Quandt, CA, Patterson, W, and JW Spatafora. “Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host-jumping in the fungal genus Tolypocladium.” 2018 Mycologia 110: 104-117.